[ { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/25eyv-y8h36", "eprint_status": "archive", "datestamp": "2023-12-08 20:26:45", "lastmod": "2024-01-09 22:23:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Godneeva", "given": "Baira" } }, { "id": "Fejes-T\u00f3th-K", "name": { "family": "Fejes Toth", "given": "Katalin" }, "orcid": "0000-0001-6558-2636" }, { "id": "Quan-Baiyi", "name": { "family": "Quan", "given": "Baiyi" }, "orcid": "0000-0001-6313-4274" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Aravin-A-A", "name": { "family": "Aravin", "given": "Alexei A." }, "orcid": "0000-0002-6956-8257" } ] }, "title": "Impact of Germline Depletion of Bonus on Chromatin State in Drosophila Ovaries", "ispublished": "pub", "full_text_status": "public", "keywords": "General Medicine", "note": "
\u00a9 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
\n\nWe thank members of the Aravin and Kulbachinskiy labs for discussion. We thank Andrey Kulbachinskiy, Maria Ninova, and Peiwei Chen for comments on the manuscript. We are grateful to the Bloomington Stock Center for providing fly stocks, and Hugo Bellen for providing the antibodies. We thank Igor Antoshechkin (Millard and Muriel Jacobs Genetics and Genomics Laboratory, Caltech) for help with sequencing, and Giada Spigolon (Biological Imaging Facility, Caltech) for help with microscopy.
\n\nThis work was supported by grants from the National Institutes of Health (R01 GM097363 to A.A.A. and R01 GM110217 to K.F.T.) and by the HHMI Faculty Scholar Award to A.A.A.
\n\nB.G. and A.A.A. conceptualized the study. B.G. designed and performed experiments, data curation, and formal analysis, except LC-MS runs and raw data processing, which were performed at the Caltech PEL facility by B.G., B.Q., T.-F.C. and B.G. prepared figures and drafted the manuscript. B.G., K.F.T. and A.A.A. edited the manuscript. All authors have read and agreed to the published version of the manuscript.
\n\nThe data presented in this study are available from the corresponding author on reasonable request.
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/cells12222629/s1, Figure S1: Average plot profiles of H3K27me3 (A), H3K27ac (B), and H3K9ac (C) over the gene body in control and Bon germline knockdown ovaries (BonusKD).
\n\nThe authors declare no conflict of interest.
", "abstract": "Gene expression is controlled via complex regulatory mechanisms involving transcription factors, chromatin modifications, and chromatin regulatory factors. Histone modifications, such as H3K27me3, H3K9ac, and H3K27ac, play an important role in controlling chromatin accessibility and transcriptional output. In vertebrates, the Transcriptional Intermediary Factor 1 (TIF1) family of proteins play essential roles in transcription, cell differentiation, DNA repair, and mitosis. Our study focused on Bonus, the sole member of the TIF1 family in Drosophila, to investigate its role in organizing epigenetic modifications. Our findings demonstrated that depleting Bonus in ovaries leads to a mild reduction in the H3K27me3 level over transposon regions and alters the distribution of active H3K9ac marks on specific protein-coding genes. Additionally, through mass spectrometry analysis, we identified novel interacting partners of Bonus in ovaries, such as PolQ, providing a comprehensive understanding of the associated molecular pathways. Furthermore, our research revealed Bonus's interactions with the Polycomb Repressive Complex 2 and its co-purification with select histone acetyltransferases, shedding light on the underlying mechanisms behind these changes in chromatin modifications.", "date": "2023-11", "date_type": "published", "publication": "Cells", "volume": "12", "number": "22", "publisher": "MDPI AG", "pagerange": "2629", "issn": "2073-4409", "official_url": "https://authors.library.caltech.edu/records/25eyv-y8h36", "funders": { "items": [ { "grant_number": "R01 GM097363" }, { "grant_number": "R01 GM110217" }, {} ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.3390/cells12222629", "pmcid": "PMC10670193", "primary_object": { "basename": "cells-12-02629.pdf", "url": "https://authors.library.caltech.edu/records/25eyv-y8h36/files/cells-12-02629.pdf" }, "related_objects": [ { "basename": "cells-12-02629-s001.zip", "url": "https://authors.library.caltech.edu/records/25eyv-y8h36/files/cells-12-02629-s001.zip" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Godneeva, Baira; Fejes Toth, Katalin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ffcec-zw111", "eprint_status": "archive", "datestamp": "2023-10-30 19:18:39", "lastmod": "2024-01-09 22:18:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mah-Som-Annelise-Y", "name": { "family": "Mah-Som", "given": "Annelise Y." }, "orcid": "0000-0003-4139-8206" }, { "name": { "family": "Daw", "given": "Jil" } }, { "id": "Huynh-Diana", "name": { "family": "Huynh", "given": "Diana" } }, { "name": { "family": "Wu", "given": "Mengcheng" } }, { "name": { "family": "Creekmore", "given": "Benjamin C." } }, { "name": { "family": "Burns", "given": "William" } }, { "name": { "family": "Skinner", "given": "Steven A." } }, { "name": { "family": "Holla", "given": "\u00d8ystein L." } }, { "name": { "family": "Smeland", "given": "Marie F." } }, { "name": { "family": "Planes", "given": "Marc" } }, { "name": { "family": "Uguen", "given": "Kevin" } }, { "name": { "family": "Redon", "given": "Sylvia" } }, { "name": { "family": "Bierhals", "given": "Tatjana" } }, { "name": { "family": "Scholz", "given": "Tasja" } }, { "name": { "family": "Denecke", "given": "Jonas" } }, { "name": { "family": "Mensah", "given": "Martin A." } }, { "name": { "family": "Sczakiel", "given": "Henrike L." } }, { "name": { "family": "Tichy", "given": "Heidelis" } }, { "name": { "family": "Verheyen", "given": "Sarah" } }, { "name": { "family": "Blatterer", "given": "Jasmin" } }, { "name": { "family": "Schreiner", "given": "Elisabeth" } }, { "name": { "family": "Thies", "given": "Jenny" } }, { "name": { "family": "Lam", "given": "Christina" } }, { "name": { "family": "Spaeth", "given": "Christine G." } }, { "name": { "family": "Pena", "given": "Loren" } }, { "name": { "family": "Ramsey", "given": "Keri" } }, { "name": { "family": "Narayanan", "given": "Vinodh" } }, { "name": { "family": "Seaver", "given": "Laurie H." } }, { "name": { "family": "Rodriguez", "given": "Diana" } }, { "name": { "family": "Afenjar", "given": "Alexandra" } }, { "name": { "family": "Burglen", "given": "Lydie" } }, { "name": { "family": "Lee", "given": "Edward B." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "name": { "family": "Weihl", "given": "Conrad C." } }, { "name": { "family": "Shinawi", "given": "Marwan S." } } ] }, "title": "An autosomal-dominant childhood-onset disorder associated with pathogenic variants in VCP", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics (clinical); Genetics", "note": "\u00a9 2023 American Society of Human Genetics.
\n\nThis research would be impossible without the generosity of our probands and their families, and we thank them from the bottom of our hearts. We were not able to recognize as authors all clinical and research team members who helped care for these individuals, but their contributions were invaluable. We would also like to thank Kathryn Russell and Moriel Singer-Berk of the Broad Institute for their assistance with variant classification. E.B.L. is supported by National Institutes of Health grant RF1AG065341. T.-F.C. is supported by National Institute of Neurological Disorders and Stroke grant R01NS102279. C.C.W. is supported by National Institute on Aging grant R01AG031867 and National Institute of Arthritis and Musculoskeletal and Skin Diseases grant K24AR073317.
\n\nConceptualization, M.S.S.; writing \u2013 original draft, A.Y.M. with proband supplements contributed by W.B., M.F.S., K.U., T.S., H.L.S., H.T., S.V., J.T., C.G.S., K.R., L.H.S., and A.A.; writing \u2013 review & editing, A.Y.M.-S., B.C.C., L.P., E.B.L., C.C.W., and M.S.S.; investigation \u2013 clinical & variant analysis, W.B., S.A.S., \u00d8.L.H., M.F.S., M.P., K.U., S.R., T.B., T.S., M.A.M, H.L.S., H.T., S.V., J.B., E.S., J.T., C.L., C.G.S, L.P., K.R., V.N., L.H.S, D.R., A.A., L.B., and M.S.S.; supervision \u2013 clinical, C.L., J.D., and M.S.S.; investigation \u2013 in vitro, J.D., D.H., and M.W. with supervision by T.-F.C. and C.C.W.; visualization, A.Y.M.-S. and B.C.C.
\n\nWe, or the sequencing laboratory, have submitted these variants and associated phenotypes to ClinVar under accession numbers 1331681, 2582677, 1303410, 2582678, 2582679, 1913089, 2429745, 2582680, 2582681, 2582682, 2444456, 1303647, and 2575609. Anonymized data will be shared by request from any qualified investigator.
\n\nThe authors declare no competing interests.
", "abstract": "Valosin-containing protein (VCP) is an AAA\u207a ATPase that plays critical roles in multiple ubiquitin-dependent cellular processes. Dominant pathogenic variants in VCP are associated with adult-onset multisystem proteinopathy (MSP), which manifests as myopathy, bone disease, dementia, and/or motor neuron disease. Through GeneMatcher, we identified 13 unrelated individuals who harbor heterozygous VCP variants (12 de novo and 1 inherited) associated with a childhood-onset disorder characterized by developmental delay, intellectual disability, hypotonia, and macrocephaly. Trio exome sequencing or a multigene panel identified nine missense variants, two in-frame deletions, one frameshift, and one splicing variant. We performed in vitro functional studies and in silico modeling to investigate the impact of these variants on protein function. In contrast to MSP variants, most missense variants had decreased ATPase activity, and one caused hyperactivation. Other variants were predicted to cause haploinsufficiency, suggesting a loss-of-function mechanism. This cohort expands the spectrum of VCP-related disease to include neurodevelopmental disease presenting in childhood.
", "date": "2023-10-25", "date_type": "published", "publication": "American Journal of Human Genetics", "publisher": "Cell Press", "issn": "0002-9297", "official_url": "https://authors.library.caltech.edu/records/ffcec-zw111", "funders": { "items": [ { "grant_number": "RF1AG065341" }, { "grant_number": "R01NS102279" }, { "grant_number": "R01AG031867" }, { "grant_number": "K24AR073317" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.ajhg.2023.10.007", "primary_object": { "basename": "1-s2.0-S0002929723003609-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/ffcec-zw111/files/1-s2.0-S0002929723003609-mmc1.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Mah-Som, Annelise Y.; Daw, Jil; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ryb4b-15p31", "eprint_status": "archive", "datestamp": "2023-10-16 16:31:36", "lastmod": "2024-01-09 22:19:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mohanty-Atish", "name": { "family": "Mohanty", "given": "Atish" }, "orcid": "0000-0003-1464-3165" }, { "name": { "family": "Nam", "given": "Arin" } }, { "name": { "family": "Srivastava", "given": "Saumya" } }, { "id": "Jones-Jeff", "name": { "family": "Jones", "given": "Jeff" }, "orcid": "0000-0002-7142-2222" }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "name": { "family": "Singhal", "given": "Sharad S." }, "orcid": "0000-0002-6415-8160" }, { "name": { "family": "Guo", "given": "Linlin" } }, { "name": { "family": "Cho", "given": "Hyejin" }, "orcid": "0000-0002-9954-8118" }, { "name": { "family": "Li", "given": "Aimin" } }, { "name": { "family": "Behal", "given": "Amita" } }, { "name": { "family": "Mirzapoiazova", "given": "Tamara" }, "orcid": "0000-0001-9353-229X" }, { "name": { "family": "Massarelli", "given": "Erminia" }, "orcid": "0000-0001-7798-7286" }, { "name": { "family": "Koczywas", "given": "Marianna" }, "orcid": "0000-0002-1588-6292" }, { "name": { "family": "Arvanitis", "given": "Leonidas D." }, "orcid": "0000-0002-4744-8350" }, { "name": { "family": "Walser", "given": "Tonya" }, "orcid": "0000-0002-3319-4361" }, { "name": { "family": "Villaflor", "given": "Victoria" }, "orcid": "0000-0002-9111-1034" }, { "name": { "family": "Hamilton", "given": "Stanley" }, "orcid": "0000-0002-8331-1052" }, { "name": { "family": "Mambetsariev", "given": "Isa" }, "orcid": "0000-0003-2882-0249" }, { "name": { "family": "Sattler", "given": "Martin" }, "orcid": "0000-0001-5053-4199" }, { "name": { "family": "Nasser", "given": "Mohd W." }, "orcid": "0000-0003-2070-4972" }, { "name": { "family": "Jain", "given": "Maneesh" }, "orcid": "0000-0002-2020-3687" }, { "name": { "family": "Batra", "given": "Surinder K." }, "orcid": "0000-0001-9470-9317" }, { "name": { "family": "Soldi", "given": "Raffaella" }, "orcid": "0000-0002-2176-3694" }, { "name": { "family": "Sharma", "given": "Sunil" } }, { "name": { "family": "Fakih", "given": "Marwan" }, "orcid": "0000-0002-6554-5488" }, { "name": { "family": "Mohanty", "given": "Saswat Kumar" }, "orcid": "0000-0002-1813-589X" }, { "name": { "family": "Mainan", "given": "Avijit" }, "orcid": "0000-0002-1264-3674" }, { "name": { "family": "Wu", "given": "Xiwei" }, "orcid": "0000-0002-7071-1671" }, { "name": { "family": "Chen", "given": "Yihong" } }, { "name": { "family": "He", "given": "Yanan" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "name": { "family": "Roy", "given": "Susmita" }, "orcid": "0000-0001-6411-4347" }, { "name": { "family": "Orban", "given": "John" }, "orcid": "0000-0002-3895-1800" }, { "name": { "family": "Kulkarni", "given": "Prakash" } }, { "name": { "family": "Salgia", "given": "Ravi" }, "orcid": "0000-0001-9643-7626" } ] }, "title": "Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2023 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).
\n\nThis work was supported, in part, by NIH grants R01CA218545 (to R.Sa.), R01CA247471 (to R.Sa.), and R01GM141290 (to J.O.). S.R. acknowledges support from the Department of Biotechnology (DBT) (grant no. BT/12/IYBA/2019/12) and Science and Engineering Research Board (SERB), Department of Science and Technology (DST), and the Government of India (grant no. SRG/2020/001295). The cartoons were made using BioRender.com. S.Si. acknowledges support from Department of Defense (W81XWH-22-1-0331). E.M. acknowledges support from Department of Defense (W81XWH-22-1-0450).
\n\nConceptualization: A.M., P.K., and R.Sa. Methodology: A.M., A.N., S.Sr., L.G., S.S.S., H.C., X.W., A.L., J.J., B.L., R.So., S.K.M., A.M., Y.C., and Y.H. Investigation: A.M., A.N., S.Sr., S.S.S., and L.G. Visualization: A.M., P.K., R.S., T.-F.C., J.O., and S.R. Supervision: R.Sa., E.M., J.O., T.-F.C., S.R., and X.W. Writing\u2014original draft: A.M., A.N., and P.K. Writing\u2014review and editing: A.M. A.N., S.Sr., J.J., B.L., S.S.S., L.G., H.C., A.L., A.B., T.M., E.M., M.K., L.D.A., T.W., V.V., S.H., I.M., M.S., M.W.N., M.J., S.K.B., R.So., S.Sh., M.F., S.K.M., A.M., X.W., Y.C., Y.H., T.-F.C., S.R., J.O., P.K., and R.Sa.
\n\nAll data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The RNA sequencing data discussed in this publication have been deposited in NCBI's GEO and are accessible via GEO series accession number GSE192619. The DNA sequencing data have been submitted to the SRA database with the accession number PRJNA792406 (www.ncbi.nlm.nih.gov/sra/PRJNA792406).
\n\nEC 20-029 is pending as U.S. Patent Application no. 18/017,982 and lists R.Sa., A.M., and P.K. as co-inventors. It was filed on 25 January 2023, is the national stage application corresponding to PCT/US2021/044711, and claims priority to U.S. Provisional Application no. 63/062,628, filed on 7 August 2020. The application is owned by City of Hope, and City of Hope is the applicant. S.Sh. and R.So. have equity in Iterion Therpaeutics that is developing BC 2059. The other authors declare that they have no competing interests.
", "abstract": "Inherent or acquired resistance to sotorasib poses a substantialt challenge for NSCLC treatment. Here, we demonstrate that acquired resistance to sotorasib in isogenic cells correlated with increased expression of integrin \u03b24 (ITGB4), a component of the focal adhesion complex. Silencing ITGB4 in tolerant cells improved sotorasib sensitivity, while overexpressing ITGB4 enhanced tolerance to sotorasib by supporting AKT-mTOR bypass signaling. Chronic treatment with sotorasib induced WNT expression and activated the WNT/\u03b2-catenin signaling pathway. Thus, silencing both ITGB4 and \u03b2-catenin significantly improved sotorasib sensitivity in tolerant, acquired, and inherently resistant cells. In addition, the proteasome inhibitor carfilzomib (CFZ) exhibited synergism with sotorasib by down-regulating ITGB4 and \u03b2-catenin expression. Furthermore, adagrasib phenocopies the combination effect of sotorasib and CFZ by suppressing KRAS activity and inhibiting cell cycle progression in inherently resistant cells. Overall, our findings unveil previously unrecognized nongenetic mechanisms underlying resistance to sotorasib and propose a promising treatment strategy to overcome resistance.", "date": "2023-10-13", "date_type": "published", "publication": "Science Advances", "volume": "9", "number": "41", "publisher": "American Association for the Advancement of Science", "pagerange": "eade3816", "issn": "2375-2548", "official_url": "https://authors.library.caltech.edu/records/ryb4b-15p31", "funders": { "items": [ { "grant_number": "R01CA218545" }, { "grant_number": "R01CA247471" }, { "grant_number": "R01GM141290" }, { "grant_number": "BT/12/IYBA/2019/12" }, { "grant_number": "SRG/2020/001295" }, { "grant_number": "W81XWH-22-1-0331" }, { "grant_number": "W81XWH-22-1-0450" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/sciadv.ade3816", "pmcid": "PMC10575592", "primary_object": { "basename": "sciadv.ade3816.pdf", "url": "https://authors.library.caltech.edu/records/ryb4b-15p31/files/sciadv.ade3816.pdf" }, "related_objects": [ { "basename": "sciadv.ade3816_data_files_s1_to_s3.zip", "url": "https://authors.library.caltech.edu/records/ryb4b-15p31/files/sciadv.ade3816_data_files_s1_to_s3.zip" }, { "basename": "sciadv.ade3816_sm.pdf", "url": "https://authors.library.caltech.edu/records/ryb4b-15p31/files/sciadv.ade3816_sm.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Mohanty, Atish; Nam, Arin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3c47s-eeq68", "eprint_id": 122009, "eprint_status": "archive", "datestamp": "2024-01-09 20:23:37", "lastmod": "2024-01-09 20:23:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tu-Jiaobing", "name": { "family": "Tu", "given": "Jiaobing" }, "orcid": "0000-0002-7653-6640" }, { "id": "Min-Jihong", "name": { "family": "Min", "given": "Jihong" }, "orcid": "0000-0002-5788-1473" }, { "id": "Song-Yu-Med-Eng", "name": { "family": "Song", "given": "Yu" }, "orcid": "0000-0002-4185-2256" }, { "id": "Xu-Changhao", "name": { "family": "Xu", "given": "Changhao" }, "orcid": "0000-0002-6817-3341" }, { "id": "Li-Jiahong", "name": { "family": "Li", "given": "Jiahong" }, "orcid": "0000-0001-7938-9589" }, { "id": "Moore-Jeff", "name": { "family": "Moore", "given": "Jeff" }, "orcid": "0000-0002-8867-6632" }, { "id": "Hanson-Justin", "name": { "family": "Hanson", "given": "Justin" }, "orcid": "0000-0002-5647-7954" }, { "id": "Hu-Erin", "name": { "family": "Hu", "given": "Erin" }, "orcid": "0009-0004-8806-9105" }, { "id": "Parimon-Tanyalak", "name": { "family": "Parimon", "given": "Tanyalak" }, "orcid": "0000-0002-4790-0730" }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "Ting-Yu" } }, { "id": "Davoodi-Elham", "name": { "family": "Davoodi", "given": "Elham" }, "orcid": "0000-0001-8578-9431" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Chen-Peter", "name": { "family": "Chen", "given": "Peter" }, "orcid": "0000-0002-5330-1718" }, { "id": "Hsu-Jeffrey-J", "name": { "family": "Hsu", "given": "Jeffrey J." }, "orcid": "0000-0002-9971-5916" }, { "id": "Rossiter-Harry-B", "name": { "family": "Rossiter", "given": "Harry B." }, "orcid": "0000-0002-7884-0726" }, { "id": "Gao-Wei", "name": { "family": "Gao", "given": "Wei" }, "orcid": "0000-0002-8503-4562" } ] }, "title": "A wireless patch for the monitoring of C-reactive protein in sweat", "ispublished": "pub", "full_text_status": "public", "keywords": "Computer Science Applications; Biomedical Engineering; Medicine (miscellaneous); Bioengineering; Biotechnology", "note": "\u00a9 The Author(s), under exclusive licence to Springer Nature Limited 2023. \n\nThis project was supported by the American Heart Association grant 19TPA34850157, National Institutes of Health (NIH) grants R01HL155815 and R21DK13266, National Science Foundation grant 2145802, Office of Naval Research grants N00014-21-1-2483 and N00014-21-1-2845, High Impact Pilot Research Award T31IP1666 from the Tobacco-Related Disease Research Program, Sloan Research Fellowship and the Technology Ventures Internal Project Fund at Cedars-Sinai. J.T. was supported by the National Science Scholarship from the Agency of Science Technology and Research (A*STAR) Singapore. E.D. was supported by NIH grant T32EB027629. We gratefully acknowledge critical support and infrastructure provided for this work by the Kavli Nanoscience Institute at Caltech. We acknowledge support from the Beckman Institute of Caltech to the Molecular Materials Research Center and Jake Evans for help with XPS. The Proteome Exploration Laboratory is supported by the Beckman Institute and NIH grant 1S10OD02001301. We thank G. R. Rossman for assistance in Raman spectroscopy. We also thank E. Bayoumi, E. Pascual and P.-E. Chen at Cedars-Sinai Medical Center for their assistance in participant recruitment. We thank R. M. Torrente-Rodr\u00edguez for constructive feedback on manuscript preparation. \n\nContributions. W.G. and J.T. initiated the concept and designed the overall studies. W.G. supervised the work. J.T., J. Min and Y.S. led the experiments and collected the overall data. C.X., J.L., T.-Y.W., E.D. and T.-F.C. contributed to sensor characterization and validation. J. Moore, J.H., E.H., T.P., P.C., J.J.H. and H.B.R. contributed to the design of the human trials and to the system's evaluation in the participants. All authors contributed to data analysis and provided feedback on the paper. \n\nData availability. The main data supporting the results in this study are available within the paper and its Supplementary Information. Source data for Figs. 3 and 5 are provided with this paper. All raw and analysed datasets generated during the study are available from the corresponding author on request. \n\nThe authors declare no competing interests.\n\nSupplemental Material - 41551_2023_1059_MOESM1_ESM.pdf
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", "abstract": "The quantification of protein biomarkers in blood at picomolar-level sensitivity requires labour-intensive incubation and washing steps. Sensing proteins in sweat, which would allow for point-of-care monitoring, is hindered by the typically large interpersonal and intrapersonal variations in its composition. Here we report the design and performance of a wearable and wireless patch for the real-time electrochemical detection of the inflammatory biomarker C-reactive (CRP) protein in sweat. The device integrates iontophoretic sweat extraction, microfluidic channels for sweat sampling and for reagent routing and replacement, and a graphene-based sensor array for quantifying CRP (via an electrode functionalized with anti-CRP capture antibodies-conjugated gold nanoparticles), ionic strength, pH and temperature for the real-time calibration of the CRP sensor. In patients with chronic obstructive pulmonary disease, with active or past infections or who had heart failure, the elevated concentrations of CRP measured via the patch correlated well with the protein's levels in serum. Wearable biosensors for the real-time sensitive analysis of inflammatory proteins in sweat may facilitate the management of chronic diseases.", "date": "2023-10", "date_type": "published", "publication": "Nature Biomedical Engineering", "volume": "7", "number": "10", "publisher": "Nature Publishing Group", "pagerange": "1293-1306", "id_number": "CaltechAUTHORS:20230628-295410000.8", "issn": "2157-846X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-295410000.8", "funders": { "items": [ { "agency": "American Heart Association", "grant_number": "19TPA34850157" }, { "agency": "NIH", "grant_number": "R01HL155815" }, { "agency": "NIH", "grant_number": "R21DK13266" }, { "agency": "NSF", "grant_number": "ECCS-2145802" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-21-1-2483" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-21-1-2845" }, { "agency": "California Tobacco-Related Disease Research Program", "grant_number": "T31IP1666" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Cedars-Sinai Medical Center" }, { "agency": "Agency for Science, Technology and Research (A*STAR)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "T32EB027629" }, { "agency": "NIH", "grant_number": "1S10OD02001301" } ] }, "local_group": { "items": [ { "id": "Kavli-Nanoscience-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41551-023-01059-5", "pmcid": "PMC10592261", "primary_object": { "basename": "nihms-1921920.pdf", "url": "https://authors.library.caltech.edu/records/3c47s-eeq68/files/nihms-1921920.pdf" }, "related_objects": [ { "basename": "41551_2023_1059_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/3c47s-eeq68/files/41551_2023_1059_MOESM1_ESM.pdf" }, { "basename": "41551_2023_1059_MOESM3_ESM.mp4", "url": "https://authors.library.caltech.edu/records/3c47s-eeq68/files/41551_2023_1059_MOESM3_ESM.mp4" }, { "basename": "41551_2023_1059_MOESM4_ESM.mp4", "url": "https://authors.library.caltech.edu/records/3c47s-eeq68/files/41551_2023_1059_MOESM4_ESM.mp4" }, { "basename": "41551_2023_1059_MOESM5_ESM.mp4", "url": "https://authors.library.caltech.edu/records/3c47s-eeq68/files/41551_2023_1059_MOESM5_ESM.mp4" }, { "basename": "41551_2023_1059_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/3c47s-eeq68/files/41551_2023_1059_MOESM6_ESM.xlsx" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Tu, Jiaobing; Min, Jihong; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ed76t-rjk79", "eprint_status": "archive", "datestamp": "2023-11-09 22:31:44", "lastmod": "2024-01-09 22:19:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schiava-Marianela", "name": { "family": "Schiava", "given": "Marianela" }, "orcid": "0000-0002-2709-265X" }, { "name": { "family": "Ikenaga", "given": "Chiseko" }, "orcid": "0000-0003-2264-1696" }, { "name": { "family": "Topf", "given": "Ana" }, "orcid": "0000-0002-9227-2526" }, { "name": { "family": "Caballero-\u00c1vila", "given": "Marta" }, "orcid": "0000-0001-9850-8504" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" } }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "name": { "family": "Daw", "given": "Jil" }, "orcid": "0000-0002-8002-076X" }, { "name": { "family": "Stojkovic", "given": "Tanya" }, "orcid": "0000-0002-4054-2838" }, { "name": { "family": "Villar-Quiles", "given": "Rocio" }, "orcid": "0000-0001-6706-3506" }, { "name": { "family": "Nishino", "given": "Ichizo" }, "orcid": "0000-0001-9452-112X" }, { "name": { "family": "Inoue", "given": "Michio" }, "orcid": "0000-0003-2757-3266" }, { "name": { "family": "Nishimori", "given": "Yukako" } }, { "name": { "family": "Saito", "given": "Yoshihiko" }, "orcid": "0000-0003-1643-4797" }, { "name": { "family": "Katsuno", "given": "Masahisa" }, "orcid": "0000-0001-9453-9311" }, { "name": { "family": "Noda", "given": "Seiya" } }, { "name": { "family": "Ito", "given": "Chihiro" } }, { "name": { "family": "Otsuka", "given": "Mieko" } }, { "name": { "family": "Nahir", "given": "Sruthi" } }, { "name": { "family": "Manousakis", "given": "Georgios" }, "orcid": "0000-0002-8309-9426" }, { "name": { "family": "Walk", "given": "David" }, "orcid": "0000-0001-7941-1993" }, { "name": { "family": "Quinn", "given": "Colin" }, "orcid": "0000-0003-0618-5854" }, { "name": { "family": "Alfano", "given": "Lindsay" }, "orcid": "0000-0002-2263-7569" }, { "name": { "family": "Sahenk", "given": "Zarife" }, "orcid": "0000-0003-2974-3943" }, { "name": { "family": "Tasca", "given": "Giorgio" }, "orcid": "0000-0003-0849-9144" }, { "name": { "family": "Monforte", "given": "Mauro" }, "orcid": "0000-0002-4327-6969" }, { "name": { "family": "Sabatelli", "given": "Mario" }, "orcid": "0000-0001-6635-4985" }, { "name": { "family": "Bisogni", "given": "Giulia" }, "orcid": "0000-0001-7314-3393" }, { "name": { "family": "Oldfors", "given": "Anders" }, "orcid": "0000-0003-2523-1414" }, { "name": { "family": "Rydeliu", "given": "Anna" }, "orcid": "0000-0002-6742-1825" }, { "name": { "family": "Pal", "given": "Endre" }, "orcid": "0000-0001-6525-0754" }, { "name": { "family": "Paradas", "given": "Carmen" }, "orcid": "0000-0002-6917-2236" }, { "name": { "family": "Velez", "given": "Beatriz" }, "orcid": "0000-0001-5796-5872" }, { "name": { "family": "De Bleecker", "given": "Jan L." }, "orcid": "0000-0002-1328-1812" }, { "name": { "family": "Farugia", "given": "Maria Elena" } }, { "name": { "family": "Longman", "given": "Cheryl" } }, { "name": { "family": "Harms", "given": "Matthew B." }, "orcid": "0000-0002-3395-1633" }, { "name": { "family": "Ralston", "given": "Stuart" }, "orcid": "0000-0002-2804-7586" }, { "name": { "family": "Zanoteli", "given": "Edmar" }, "orcid": "0000-0002-4991-6760" }, { "name": { "family": "Silva", "given": "Andre Macedo Serafim da" } }, { "name": { "family": "Sotoca", "given": "Javier" }, "orcid": "0000-0003-3400-1434" }, { "name": { "family": "Juntas-Morales", "given": "Raul" }, "orcid": "0000-0003-2205-1741" }, { "name": { "family": "Bevilacqua", "given": "Jorge" }, "orcid": "0000-0002-0525-9308" }, { "name": { "family": "Balart", "given": "Mireya" } }, { "name": { "family": "Talbot", "given": "Stuart" } }, { "name": { "family": "Straub", "given": "Volker" }, "orcid": "0000-0001-9046-3540" }, { "name": { "family": "Guglieri", "given": "Michela" }, "orcid": "0000-0002-8455-0637" }, { "name": { "family": "Marini-Bettolo", "given": "Chiara" } }, { "name": { "family": "Diaz-Manera", "given": "Jordi" }, "orcid": "0000-0003-2941-7988" }, { "name": { "family": "Weihl", "given": "Conrad Chris" }, "orcid": "0000-0002-3816-6124" } ] }, "title": "Clinical Classification of Variants in the Valosin-Containing Protein Gene Associated With Multisystem Proteinopathy", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics (clinical); Neurology (clinical)", "note": "\u00a9 2023 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND), which permits downloading and sharing the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.
\n\nThe authors are grateful to all families, site investigators, clinical evaluators, research nurses, geneticist, pathologists, and physiotherapists who actively collaborated in the collecting data process. All the authors of this manuscript comply with the ethical guidelines for authorship and publishing of the Neurology journal.
\n\nTwo grants from the National Institute of Health (R01AG031867 and K24R073317 to C.W.) and a grant from Academy of Medical Sciences (APR04/007 to J.D.-M.).
\n\nThe authors report no relevant disclosures. Go to Neurology.org/NG for full disclosure.
", "abstract": "Background and Objectives: Pathogenic variants in the valosin-containing protein (VCP) gene cause a phenotypically heterogeneous disorder that includes myopathy, motor neuron disease, Paget disease of the bone, frontotemporal dementia, and parkinsonism termed multisystem proteinopathy. This hallmark pleiotropy makes the classification of novel VCP variants challenging. This retrospective study describes and assesses the effect of 19 novel or nonpreviously clinically characterized VCP variants identified in 28 patients (26 unrelated families) in the retrospective VCP International Multicenter Study.
Methods: A 6-item clinical score was developed to evaluate the phenotypic level of evidence to support the pathogenicity of the novel variants. Each item is allocated a value, a score ranging from 0.5 to 5.5 points. A receiver-operating characteristic curve was used to identify a cutoff value of 3 to consider a variant as high likelihood disease associated. The scoring system results were confronted with results of in vitro ATPase activity assays and with in silico analysis.
Results: All variants were missense, except for one small deletion-insertion, 18 led to amino acid changes within the N and D1 domains, and 13 increased the enzymatic activity. The clinical score coincided with the functional studies in 17 of 19 variants and with the in silico analysis in 12 of 19. For 12 variants, the 3 predictive tools agreed, and for 7 variants, the predictive tools disagreed. The pooled data supported the pathogenicity of 13 of 19 novel VCP variants identified in the study.
Discussion: This study provides data to support pathogenicity of 14 of 19 novel VCP variants and provides guidance for clinicians in the evaluation of novel variants in the VCP gene.
", "date": "2023-10", "date_type": "published", "publication": "Neurology Genetics", "volume": "9", "number": "5", "publisher": "Wolters Kluwer", "pagerange": "e200093", "issn": "2376-7839", "official_url": "https://authors.library.caltech.edu/records/ed76t-rjk79", "funders": { "items": [ { "grant_number": "R01AG031867" }, { "grant_number": "K24R073317" }, { "grant_number": "APR04/007" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1212/nxg.0000000000200093", "primary_object": { "basename": "NXG-2023-000033.pdf", "url": "https://authors.library.caltech.edu/records/ed76t-rjk79/files/NXG-2023-000033.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Schiava, Marianela; Ikenaga, Chiseko; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d9008-tnp79", "eprint_status": "archive", "datestamp": "2023-11-10 19:26:31", "lastmod": "2024-01-09 22:22:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Luzzi-Anna", "name": { "family": "Luzzi", "given": "Anna" }, "orcid": "0000-0003-0899-9704" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Iacovino-Michelina", "name": { "family": "Iacovino", "given": "Michelina" }, "orcid": "0000-0002-1076-3146" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Skeletal muscle cell protein dysregulation highlights the pathogenesis mechanism of myopathy-associated p97/VCP R155H mutations", "ispublished": "pub", "full_text_status": "public", "keywords": "Neurology (clinical); Neurology", "note": "\u00a9 2023 Luzzi, Wang, Li, Iacovino and Chou. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
\n\nThe acknowledgments are for Michael Kyba Ph.D., and Rita Perlingeiro Ph.D., of Minneapolis University, MN, for providing the plasmids to transfect the iPSCs for skeletal muscle differentiation.
\n\nThis work was supported by funds from the National Institute of Neurological Disorders and Stroke (NINDS), R01NS102279.
\n\nAL, MI, and T-FC wrote the main manuscript. AL prepared Figures 1\u20134, Supplementary Figures S1\u2013S5, and Table 1. FW and SL analyzed Figures 3, ,44 and the Supplementary Figures S3, S4. All authors contributed to the article and approved the submitted version.
\n\nThe original contributions presented in the study are publicly available. This data can be found in PRIDE under the accession number PXD044004: https://www.ebi.ac.uk/pride/archive/projects/PXD044004.
\n\nThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
", "abstract": "p97/VCP, a hexametric member of the AAA-ATPase superfamily, has been associated with a wide range of cellular protein pathways, such as proteasomal degradation, the unfolding of polyubiquitinated proteins, and autophagosome maturation. Autosomal dominant p97/VCP mutations cause a rare hereditary multisystem disorder called IBMPFD/ALS (Inclusion Body Myopathy with Paget's Disease and Frontotemporal Dementia/Amyotrophic Lateral Sclerosis), characterized by progressive weakness and subsequent atrophy of skeletal muscles, and impacting bones and brains, such as Parkinson's disease, Lewy body disease, Huntington's disease, and amyotrophic lateral ALS. Among all disease-causing mutations, Arginine 155 to Histidine (R155H/+) was reported to be the most common one, affecting over 50% of IBMPFD patients, resulting in disabling muscle weakness, which might eventually be life-threatening due to cardiac and respiratory muscle involvement. Induced pluripotent stem cells (iPSCs) offer an unlimited resource of cells to study pathology's underlying molecular mechanism, perform drug screening, and investigate regeneration. Using R155H/+ patients' fibroblasts, we generated IPS cells and corrected the mutation (Histidine to Arginine, H155R) to generate isogenic control cells before differentiating them into myotubes. The further proteomic analysis allowed us to identify differentially expressed proteins associated with the R155H mutation. Our results showed that R155H/+ cells were associated with dysregulated expression of several proteins involved in skeletal muscle function, cytoskeleton organization, cell signaling, intracellular organelles organization and function, cell junction, and cell adhesion. Our findings provide molecular evidence of dysfunctional protein expression in R155H/+ myotubes and offer new therapeutic targets for treating IBMPFD/ALS.", "date": "2023-08-03", "date_type": "published", "publication": "Frontiers in Neurology", "volume": "14", "publisher": "Frontiers Media", "pagerange": "1211635", "issn": "1664-2295", "official_url": "https://authors.library.caltech.edu/records/d9008-tnp79", "funders": { "items": [ { "grant_number": "R01NS102279" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "pmcid": "PMC10435852", "primary_object": { "basename": "fneur-14-1211635.pdf", "url": "https://authors.library.caltech.edu/records/d9008-tnp79/files/fneur-14-1211635.pdf" }, "related_objects": [ { "basename": "Image_1.JPEG", "url": "https://authors.library.caltech.edu/records/d9008-tnp79/files/Image_1.JPEG" }, { "basename": "Image_2.JPEG", "url": "https://authors.library.caltech.edu/records/d9008-tnp79/files/Image_2.JPEG" }, { "basename": "Image_3.JPEG", "url": "https://authors.library.caltech.edu/records/d9008-tnp79/files/Image_3.JPEG" }, { "basename": "Image_4.JPEG", "url": "https://authors.library.caltech.edu/records/d9008-tnp79/files/Image_4.JPEG" }, { "basename": "Image_5.JPEG", "url": "https://authors.library.caltech.edu/records/d9008-tnp79/files/Image_5.JPEG" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Luzzi, Anna; Wang, Feng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/mxsw3-j4b85", "eprint_id": 122241, "eprint_status": "archive", "datestamp": "2023-08-22 21:23:20", "lastmod": "2023-12-22 23:14:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "LaPorte-Matthew-G", "name": { "family": "LaPorte", "given": "Matthew G." } }, { "id": "Alverez-Celeste", "name": { "family": "Alverez", "given": "Celeste" } }, { "id": "Chatterley-Alexander", "name": { "family": "Chatterley", "given": "Alexander" } }, { "id": "Kovaliov-Marina", "name": { "family": "Kovaliov", "given": "Marina" }, "orcid": "0000-0002-4837-7654" }, { "id": "Carder-Evan-J", "name": { "family": "Carder", "given": "Evan J." }, "orcid": "0000-0001-5727-0632" }, { "id": "Houghton-Michael-J", "name": { "family": "Houghton", "given": "Michael J." } }, { "id": "Lim-Chaemin", "name": { "family": "Lim", "given": "Chaemin" } }, { "id": "Miller-Eric-R", "name": { "family": "Miller", "given": "Eric R." }, "orcid": "0009-0003-3584-4254" }, { "id": "Samankumara-Lalith-P", "name": { "family": "Samankumara", "given": "Lalith P." } }, { "id": "Liang-Mary", "name": { "family": "Liang", "given": "Mary" } }, { "id": "Kerrigan-Kaylan", "name": { "family": "Kerrigan", "given": "Kaylan" } }, { "id": "Yue-Zhizhou", "name": { "family": "Yue", "given": "Zhizhou" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Tomaino-Francesca", "name": { "family": "Tomaino", "given": "Francesca" }, "orcid": "0000-0001-8991-5415" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" }, "orcid": "0000-0003-4742-2668" }, { "id": "Green-Neal", "name": { "family": "Green", "given": "Neal" }, "orcid": "0000-0001-5851-5152" }, { "id": "Stott-Gordon-M", "name": { "family": "Stott", "given": "Gordon M." }, "orcid": "0000-0002-9148-6100" }, { "id": "Srivastava-Apurva-K", "name": { "family": "Srivastava", "given": "Apurva" }, "orcid": "0000-0002-6390-7553" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Wipf-Peter", "name": { "family": "Wipf", "given": "Peter" }, "orcid": "0000-0001-7693-5863" }, { "id": "Huryn-Donna-M", "name": { "family": "Huryn", "given": "Donna M." }, "orcid": "0000-0001-5542-4968" } ] }, "title": "Optimization of 1,2,4-Triazole-Based p97 Inhibitors for the Treatment of Cancer", "ispublished": "pub", "full_text_status": "public", "keywords": "Organic Chemistry; Drug Discovery; Biochemistry", "note": "\u00a9 2023 American Chemical Society. \n\nThe authors gratefully acknowledge James Burnett, Desirae Crocker, Alyssa Thornton, and Taber Maskrey (Pitt) for experimental contributions, William Moore and John Giraldes (Leidos), Barbara Mroczkowski (NCI), Mark Wolf and Bill Paquette (AMRI, Curia), Raymond Deshaies (CalTech), and Michelle Arkin (UCSF) for helpful discussions, Andrew Flint (Leidos) for helpful discussions and review of the manuscript, AMRI/Curia for chiral separation and scale-up of intermediates, and Robert Suto and XtalBiostructures for preliminary SPR data. \n\nThe project was funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health, under Chemical Biology Consortium Contract No. HHSN261200800001E, Agreement No. 29XS127TO15. \n\nAuthor Contributions: The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript. \n\nThe authors declare no competing financial interest.\n\nSupplemental Material - ml3c00163_si_001.pdf
", "abstract": "The AAA+ ATPase p97 (valosin-containing protein, VCP) is a master regulator of protein homeostasis and therefore represents a novel target for cancer therapy. Starting from a known allosteric inhibitor, NMS-873, we systematically optimized this scaffold, in particular, by applying a benzene-to-acetylene isosteric replacement strategy, specific incorporation of F, and eutomer/distomer identification, which led to compounds that exhibited nanomolar biochemical and cell-based potency. In cellular pharmacodynamic assays, robust effects on biomarkers of p97 inhibition and apoptosis, including increased levels of ubiquitinated proteins, CHOP and cleaved caspase 3, were observed. Compound (R)-29 (UPCDC-30766) represents the most potent allosteric inhibitor of p97 reported to date.", "date": "2023-07-13", "date_type": "published", "publication": "ACS Medicinal Chemistry Letters", "volume": "14", "number": "7", "publisher": "American Chemical Society", "pagerange": "977-985", "id_number": "CaltechAUTHORS:20230711-988768900.15", "issn": "1948-5875", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230711-988768900.15", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HHSN261200800001E" }, { "agency": "NIH", "grant_number": "29XS127TO15" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1021/acsmedchemlett.3c00163", "pmcid": "PMC10351062", "primary_object": { "basename": "ml3c00163_si_001.pdf", "url": "https://authors.library.caltech.edu/records/mxsw3-j4b85/files/ml3c00163_si_001.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "LaPorte, Matthew G.; Alverez, Celeste; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wv2m3-0f603", "eprint_id": 122009, "eprint_status": "archive", "datestamp": "2023-08-22 21:13:31", "lastmod": "2023-12-22 23:33:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tu-Jiaobing", "name": { "family": "Tu", "given": "Jiaobing" }, "orcid": "0000-0002-7653-6640" }, { "id": "Min-Jihong", "name": { "family": "Min", "given": "Jihong" }, "orcid": "0000-0002-5788-1473" }, { "id": "Song-Yu-Med-Eng", "name": { "family": "Song", "given": "Yu" }, "orcid": "0000-0002-4185-2256" }, { "id": "Xu-Changhao", "name": { "family": "Xu", "given": "Changhao" }, "orcid": "0000-0002-6817-3341" }, { "id": "Li-Jiahong", "name": { "family": "Li", "given": "Jiahong" }, "orcid": "0000-0001-7938-9589" }, { "id": "Moore-Jeff", "name": { "family": "Moore", "given": "Jeff" }, "orcid": "0000-0002-8867-6632" }, { "id": "Hanson-Justin", "name": { "family": "Hanson", "given": "Justin" }, "orcid": "0000-0002-5647-7954" }, { "id": "Hu-Erin", "name": { "family": "Hu", "given": "Erin" }, "orcid": "0009-0004-8806-9105" }, { "id": "Parimon-Tanyalak", "name": { "family": "Parimon", "given": "Tanyalak" }, "orcid": "0000-0002-4790-0730" }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "Ting-Yu" } }, { "id": "Davoodi-Elham", "name": { "family": "Davoodi", "given": "Elham" }, "orcid": "0000-0001-8578-9431" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Chen-Peter", "name": { "family": "Chen", "given": "Peter" }, "orcid": "0000-0002-5330-1718" }, { "id": "Hsu-Jeffrey-J", "name": { "family": "Hsu", "given": "Jeffrey J." }, "orcid": "0000-0002-9971-5916" }, { "id": "Rossiter-Harry-B", "name": { "family": "Rossiter", "given": "Harry B." }, "orcid": "0000-0002-7884-0726" }, { "id": "Gao-Wei", "name": { "family": "Gao", "given": "Wei" }, "orcid": "0000-0002-8503-4562" } ] }, "title": "A wireless patch for the monitoring of C-reactive protein in sweat", "ispublished": "pub", "full_text_status": "public", "keywords": "Computer Science Applications; Biomedical Engineering; Medicine (miscellaneous); Bioengineering; Biotechnology", "note": "\u00a9 The Author(s), under exclusive licence to Springer Nature Limited 2023. \n\nThis project was supported by the American Heart Association grant 19TPA34850157, National Institutes of Health (NIH) grants R01HL155815 and R21DK13266, National Science Foundation grant 2145802, Office of Naval Research grants N00014-21-1-2483 and N00014-21-1-2845, High Impact Pilot Research Award T31IP1666 from the Tobacco-Related Disease Research Program, Sloan Research Fellowship and the Technology Ventures Internal Project Fund at Cedars-Sinai. J.T. was supported by the National Science Scholarship from the Agency of Science Technology and Research (A*STAR) Singapore. E.D. was supported by NIH grant T32EB027629. We gratefully acknowledge critical support and infrastructure provided for this work by the Kavli Nanoscience Institute at Caltech. We acknowledge support from the Beckman Institute of Caltech to the Molecular Materials Research Center and Jake Evans for help with XPS. The Proteome Exploration Laboratory is supported by the Beckman Institute and NIH grant 1S10OD02001301. We thank G. R. Rossman for assistance in Raman spectroscopy. We also thank E. Bayoumi, E. Pascual and P.-E. Chen at Cedars-Sinai Medical Center for their assistance in participant recruitment. We thank R. M. Torrente-Rodr\u00edguez for constructive feedback on manuscript preparation. \n\nContributions. W.G. and J.T. initiated the concept and designed the overall studies. W.G. supervised the work. J.T., J. Min and Y.S. led the experiments and collected the overall data. C.X., J.L., T.-Y.W., E.D. and T.-F.C. contributed to sensor characterization and validation. J. Moore, J.H., E.H., T.P., P.C., J.J.H. and H.B.R. contributed to the design of the human trials and to the system's evaluation in the participants. All authors contributed to data analysis and provided feedback on the paper. \n\nData availability. The main data supporting the results in this study are available within the paper and its Supplementary Information. Source data for Figs. 3 and 5 are provided with this paper. All raw and analysed datasets generated during the study are available from the corresponding author on request. \n\nThe authors declare no competing interests.\n\nSupplemental Material - 41551_2023_1059_MOESM1_ESM.pdf
Supplemental Material - 41551_2023_1059_MOESM3_ESM.mp4
Supplemental Material - 41551_2023_1059_MOESM4_ESM.mp4
Supplemental Material - 41551_2023_1059_MOESM5_ESM.mp4
Supplemental Material - 41551_2023_1059_MOESM6_ESM.xlsx
", "abstract": "The quantification of protein biomarkers in blood at picomolar-level sensitivity requires labour-intensive incubation and washing steps. Sensing proteins in sweat, which would allow for point-of-care monitoring, is hindered by the typically large interpersonal and intrapersonal variations in its composition. Here we report the design and performance of a wearable and wireless patch for the real-time electrochemical detection of the inflammatory biomarker C-reactive (CRP) protein in sweat. The device integrates iontophoretic sweat extraction, microfluidic channels for sweat sampling and for reagent routing and replacement, and a graphene-based sensor array for quantifying CRP (via an electrode functionalized with anti-CRP capture antibodies-conjugated gold nanoparticles), ionic strength, pH and temperature for the real-time calibration of the CRP sensor. In patients with chronic obstructive pulmonary disease, with active or past infections or who had heart failure, the elevated concentrations of CRP measured via the patch correlated well with the protein's levels in serum. Wearable biosensors for the real-time sensitive analysis of inflammatory proteins in sweat may facilitate the management of chronic diseases.", "date": "2023-06-28", "date_type": "published", "publication": "Nature Biomedical Engineering", "publisher": "Nature Publishing Group", "id_number": "CaltechAUTHORS:20230628-295410000.8", "issn": "2157-846X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-295410000.8", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "American Heart Association", "grant_number": "19TPA34850157" }, { "agency": "NIH", "grant_number": "R01HL155815" }, { "agency": "NIH", "grant_number": "R21DK13266" }, { "agency": "NSF", "grant_number": "ECCS-2145802" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-21-1-2483" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-21-1-2845" }, { "agency": "California Tobacco-Related Disease Research Program", "grant_number": "T31IP1666" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Cedars-Sinai Medical Center" }, { "agency": "Agency for Science, Technology and Research (A*STAR)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "T32EB027629" }, { "agency": "NIH", "grant_number": "1S10OD02001301" } ] }, "local_group": { "items": [ { "id": "Kavli-Nanoscience-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41551-023-01059-5", "primary_object": { "basename": "41551_2023_1059_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/wv2m3-0f603/files/41551_2023_1059_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "41551_2023_1059_MOESM3_ESM.mp4", "url": "https://authors.library.caltech.edu/records/wv2m3-0f603/files/41551_2023_1059_MOESM3_ESM.mp4" }, { "basename": "41551_2023_1059_MOESM4_ESM.mp4", "url": "https://authors.library.caltech.edu/records/wv2m3-0f603/files/41551_2023_1059_MOESM4_ESM.mp4" }, { "basename": "41551_2023_1059_MOESM5_ESM.mp4", "url": "https://authors.library.caltech.edu/records/wv2m3-0f603/files/41551_2023_1059_MOESM5_ESM.mp4" }, { "basename": "41551_2023_1059_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/wv2m3-0f603/files/41551_2023_1059_MOESM6_ESM.xlsx" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Tu, Jiaobing; Min, Jihong; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qyt6a-qje60", "eprint_id": 122025, "eprint_status": "archive", "datestamp": "2023-08-22 21:09:22", "lastmod": "2023-12-22 23:14:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Findlay-Andrew-R", "name": { "family": "Findlay", "given": "Andrew R." }, "orcid": "0000-0002-8728-9833" }, { "id": "Paing-May-M", "name": { "family": "Paing", "given": "May M." } }, { "id": "Daw-Jil-A", "name": { "family": "Daw", "given": "Jil A." }, "orcid": "0000-0002-8002-076X" }, { "id": "Haller-Meade", "name": { "family": "Haller", "given": "Meade" }, "orcid": "0000-0001-6083-7660" }, { "id": "Bengoechea-Ibaceta-Rocio", "name": { "family": "Bengoechea", "given": "Rocio" }, "orcid": "0000-0002-9029-019X" }, { "id": "Pittman-Sara-K", "name": { "family": "Pittman", "given": "Sara K." } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" }, "orcid": "0000-0003-4742-2668" }, { "id": "Miller-Timothy-M", "name": { "family": "Miller", "given": "Timothy M." }, "orcid": "0000-0002-3424-5511" }, { "id": "True-Heather-L", "name": { "family": "True", "given": "Heather L." }, "orcid": "0000-0003-4824-9529" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Weihl-Conrad-C", "name": { "family": "Weihl", "given": "Conrad C." }, "orcid": "0000-0002-3816-6124" } ] }, "title": "DNAJB6 isoform specific knockdown: Therapeutic potential for limb girdle muscular dystrophy D1", "ispublished": "pub", "full_text_status": "public", "keywords": "Drug Discovery; Molecular Medicine", "note": "\u00a9 2023 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). \n\nThis work was supported by grants from the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS): ARF (K08AR075894, R03AR081395), CCW (R01AR068797, K24AR073317); the American Society of Gene and Cell therapy (ASGCT): ARF (Career Development Award); the Children's Discovery Institute of Saint Louis Children's Hospital: ARF (Faculty Scholar Award- MIFR20221004); and the LGMD-1D DNAJB6 Foundation and International Registry (ARF). The graphical abstract was created with BioRender. \n\nAuthor contributions. A.R.F.: conceptualization, formal analysis, funding acquisition, investigation, methodology, resources, supervision, validation, visualization, writing original draft, writing \u2013 review and editing. M.M.P., J.A.D., M.E.H., R.B., S.K.P., S.L., F.W., and T.C.: investigation, methodology. H.L.T. and T.M.M.: conceptualization, writing \u2013 review and editing. C.C.W.: conceptualization, funding acquisition, resources, supervision, validation, writing \u2013 review and editing. \n\nData availability. Qualified researchers may request access to the data that support the findings of this study from the corresponding author. \n\nDeclaration of interests. A.R.F. and C.C.W. are co-inventors on a pending patent application related to this publication (USPTO serial no. 17/932,996).\n\nPublished - main.pdf
Supplemental Material - 1-s2.0-S216225312300135X-mmc1.xlsx
", "abstract": "Dominant missense mutations in DNAJB6, a co-chaperone of HSP70, cause limb girdle muscular dystrophy (LGMD) D1. No treatments are currently available. Two isoforms exist, DNAJB6a and DNAJB6b, each with distinct localizations in muscle. Mutations reside in both isoforms, yet evidence suggests that DNAJB6b is primarily responsible for disease pathogenesis. Knockdown treatment strategies involving both isoforms carry risk, as DNAJB6 knockout is embryonic lethal. We therefore developed an isoform-specific knockdown approach using morpholinos. Selective reduction of each isoform was achieved in vitro in primary mouse myotubes and human LGMDD1 myoblasts, as well as in vivo in mouse skeletal muscle. To assess isoform specific knockdown in LGMDD1, we created primary myotube cultures from a knockin LGMDD1 mouse model. Using mass spectrometry, we identified an LGMDD1 protein signature related to protein homeostasis and myofibril structure. Selective reduction of DNAJB6b levels in LGMDD1 myotubes corrected much of the proteomic disease signature toward wild type levels. Additional in vivo functional data is required to determine if selective reduction of DNAJB6b is a viable therapeutic target for LGMDD1.", "date": "2023-06-13", "date_type": "published", "publication": "Molecular Therapy - Nucleic Acids", "volume": "32", "publisher": "Cell Press", "pagerange": "937-948", "id_number": "CaltechAUTHORS:20230628-257129000.25", "issn": "2162-2531", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-257129000.25", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K08AR075894" }, { "agency": "NIH", "grant_number": "R03AR081395" }, { "agency": "NIH", "grant_number": "R01AR068797" }, { "agency": "NIH", "grant_number": "K24AR073317" }, { "agency": "American Society of Gene and Cell Therapy" }, { "agency": "Saint Louis Children's Hospital", "grant_number": "MIFR20221004" }, { "agency": "LGMD-1D DNAJB6 Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.omtn.2023.05.017", "pmcid": "PMC10280091", "primary_object": { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/qyt6a-qje60/files/main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S216225312300135X-mmc1.xlsx", "url": "https://authors.library.caltech.edu/records/qyt6a-qje60/files/1-s2.0-S216225312300135X-mmc1.xlsx" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Findlay, Andrew R.; Paing, May M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fgyyk-pb390", "eprint_id": 121953, "eprint_status": "archive", "datestamp": "2023-08-22 21:06:40", "lastmod": "2023-12-22 23:08:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jones-Jeffrey-J", "name": { "family": "Jones", "given": "Jeff" }, "orcid": "0000-0002-7142-2222" }, { "id": "MacKrell-Elliot-J", "name": { "family": "MacKrell", "given": "Elliot J." } }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "Ting-Yu" } }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Roukes-M-L", "name": { "family": "Roukes", "given": "Michael L." }, "orcid": "0000-0002-2916-6026" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization", "ispublished": "pub", "full_text_status": "public", "keywords": "Applied Mathematics; Computer Science Applications; Molecular Biology; Biochemistry; Structural Biology", "note": "\u00a9 The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. \n\nThe authors would like to thank numerous Caltech graduate students for their feedback and discussions that are an invaluable resource for understanding how to convey concise information about biological systems from complex analyses. A manual covering all the available functions along with explanation of each function and tutorials can be found at https://jefsocal.github.io/tidyproteomics. An R Shiny application is available at http://bioinformatics.pel.caltech.edu/tidyproteomics/.\n\nThe Proteome Exploration Laboratory was supported by NIH OD010788, NIH OD020013, the Betty and Gordon Moore\nFoundation through grant GBMF775 and the Beckman Institute at Caltech. The Shiny app is hosted by The Proteome\nExploration Laboratory at the Caltech Beckman Institute. This work was supported by the Institute for Collaborative\nBiotechnologies through cooperative agreement W911NF-19-2-0026 from the U.S. Army Research Office. The content of\nthe information does not necessarily reflect the position or the policy of the Government, and no official endorsement\nshould be inferred. In addition, partial support was provided by the Wellcome Leap Delta Tissue Program. \n\nContributions. JJ developed the tidyproteomics code base. EM developed the shiny application. TYW, BL, TFC and MLR provided insight to workflow processes and analysis. All authors read and approved the final manuscript. \n\nAvailability and requirements. Project name: tidyproteomics. Project homepage: https://github.com/jeffsocal/tidyproteomics. Operating system: platform independent. Programming language: R. Other requirements: none. License: MIT. Any restrictions to use by non-academics: none. \n\nAvailability of data and materials. The datasets analyzed within the current study are available in the Tidyproteomics code repository, https://github.com/jeffsocal/tidyproteomics and Shiny app https://github.com/ejmackrell/tidyproteomics-interactive. Access to both the protein and peptide data sets are immediately available upon loading the package. Additionally, the data set is available from the Caltech data repository, https://data.caltech.edu/records/aevwq-2ps50, taken from Wang et al. [38]. \n\nContributions. JJ developed the tidyproteomics code base. EM developed the shiny application. TYW, BL, TFC and MLR provided insight to workflow processes and analysis. All authors read and approved the final manuscript. \n\nThe authors declare that they have no competing interests.\n\nPublished - 12859_2023_Article_5360.pdf
Supplemental Material - 12859_2023_5360_MOESM1_ESM.docx
", "abstract": "Background. The analysis of mass spectrometry-based quantitative proteomics data can be challenging given the variety of established analysis platforms, the differences in reporting formats, and a general lack of approachable standardized post-processing analyses such as sample group statistics, quantitative variation and even data filtering. We developed tidyproteomics to facilitate basic analysis, improve data interoperability and potentially ease the integration of new processing algorithms, mainly through the use of a simplified data-object. \n\nResults: The R package tidyproteomics was developed as both a framework for standardizing quantitative proteomics data and a platform for analysis workflows, containing discrete functions that can be connected end-to-end, thus making it easier to define complex analyses by breaking them into small stepwise units. Additionally, as with any analysis workflow, choices made during analysis can have large impacts on the results and as such, tidyproteomics allows researchers to string each function together in any order, select from a variety of options and in some cases develop and incorporate custom algorithms. \n\nConclusions: Tidyproteomics aims to simplify data exploration from multiple platforms, provide control over individual functions and analysis order, and serve as a tool to assemble complex repeatable processing workflows in a logical flow. Datasets in tidyproteomics are easy to work with, have a structure that allows for biological annotations to be added, and come with a framework for developing additional analysis tools. The consistent data structure and accessible analysis and plotting tools also offers a way for researchers to save time on mundane data manipulation tasks.", "date": "2023-06-06", "date_type": "published", "publication": "BMC Bioinformatics", "volume": "24", "publisher": "BioMed Central", "pagerange": "Art. No. 239", "id_number": "CaltechAUTHORS:20230615-129123000.8", "issn": "1471-2105", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230615-129123000.8", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "OD010788" }, { "agency": "NIH", "grant_number": "OD020013" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF775" }, { "agency": "Wellcome Leap" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-19-2-0026" }, { "agency": "Caltech Beckman Institute" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1186/s12859-023-05360-7", "pmcid": "PMC10246047", "primary_object": { "basename": "12859_2023_Article_5360.pdf", "url": "https://authors.library.caltech.edu/records/fgyyk-pb390/files/12859_2023_Article_5360.pdf" }, "related_objects": [ { "basename": "12859_2023_5360_MOESM1_ESM.docx", "url": "https://authors.library.caltech.edu/records/fgyyk-pb390/files/12859_2023_5360_MOESM1_ESM.docx" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Jones, Jeff; MacKrell, Elliot J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/me61v-mhy57", "eprint_id": 122033, "eprint_status": "archive", "datestamp": "2023-08-22 20:53:20", "lastmod": "2023-12-22 23:34:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dutka-Przemys\u0142aw", "name": { "family": "Dutka", "given": "Przemys\u0142aw" }, "orcid": "0000-0003-3819-1618" }, { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Hurt-Robert-C", "name": { "family": "Hurt", "given": "Robert C." }, "orcid": "0000-0002-4347-6901" }, { "id": "Salahshoor-Hossein", "name": { "family": "Salahshoor", "given": "Hossein" }, "orcid": "0000-0002-7264-7650" }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "Ting-Yu" } }, { "id": "Malounda-Dina", "name": { "family": "Malounda", "given": "Dina" }, "orcid": "0000-0001-7086-9877" }, { "id": "Lu-George-Jiaozhi", "name": { "family": "Lu", "given": "George J." }, "orcid": "0000-0002-4689-9686" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Shapiro-M-G", "name": { "family": "Shapiro", "given": "Mikhail G." }, "orcid": "0000-0002-0291-4215" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET", "ispublished": "pub", "full_text_status": "public", "keywords": "Molecular Biology; Structural Biology", "note": "\u00a9 2023 The Author(s). Published by Elsevier. Under a Creative Commons license. Attribution 4.0 International (CC BY 4.0).\n\nThe authors are grateful to Catherine Oikonomou for helpful editorial comments. We thank Songye Chen for assistance with tomography data collection. Electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. The Proteome Exploration Laboratory (PEL) is supported by the Beckman Institute and National Institutes of Health 1S10OD02001301. This work was supported by the National Institutes of Health (R01-AI127401 to G.J.J. and R01-EB018975 to M.G.S.) and the Caltech Center for Environmental Microbial Interactions (CEMI). Related research in the Shapiro Laboratory is supported by the Packard Foundation, the Chan Zuckerberg Initiative, and the Heritage Medical Research Institute. M.G.S. is a Howard Hughes Medical Institute Investigator. \n\nAuthor contributions. P.D. conceived experiments, prepared samples, acquired and analyzed data, performed data exploration, drafted the manuscript, and prepared the figures. L.A.M. initiated the project and collected data for Mega GVs. R.C.H. performed mutation screening for GvpA and participated in initial sample preparation and optimization for Mega GVs. H.S. performed finite element simulation and analyzed data. T.-Y.W. performed XLMS experiments and analyzed the data. D.M. expressed and purified GV samples. G.L. participated in initial sample preparation and optimization for Mega GVs. T.-F.C. supervised XLMS experiments. All authors participated in correction of the manuscript. M.G.S. participated in guidance, experimental design, funding, and correction/advising on writing the manuscript. G.J.J. participated in guidance, experimental design, funding, and correction/advising on writing the manuscript. \n\nData and code availability:\nThe unprocessed tilt series used for the data analysis are available upon request. Representative tomograms for Ana, Mega, and Halo GVs have been deposited in the Electron Microscopy Data Bank under accession codes EMDB: EMD-29922, EMD-29925, EMD-29924, EMD-29923. Subtomogram averages for native Ana and AnaS GV shell have been deposited in EMDB under accession codes EMD-29921 and EMD-29916, respectively. The integrative model of Ana GvpA/GvpC has been deposited in the Protein Data Bank (PDB): 8GBS. The XLMS data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD038631. The code for ultrasound data collection and processing is available upon request. \n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S0969212623000941-main.pdf
Supplemental Material - 1-s2.0-S0969212623000941-mmc1.pdf
", "abstract": "Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a \u03b2 sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.", "date": "2023-05-04", "date_type": "published", "publication": "Structure", "volume": "31", "number": "5", "publisher": "Cell Press", "pagerange": "518-528", "id_number": "CaltechAUTHORS:20230628-257245000.39", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-257245000.39", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1S10OD02001301" }, { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "NIH", "grant_number": "R01 EB018975" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Chan Zuckerberg Initiative" }, { "agency": "Heritage Medical Research Institute" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Heritage-Medical-Research-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.str.2023.03.011", "pmcid": "PMC10185304", "primary_object": { "basename": "1-s2.0-S0969212623000941-main.pdf", "url": "https://authors.library.caltech.edu/records/me61v-mhy57/files/1-s2.0-S0969212623000941-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0969212623000941-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/me61v-mhy57/files/1-s2.0-S0969212623000941-mmc1.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Dutka, Przemys\u0142aw; Metskas, Lauren Ann; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t3k1f-dtw80", "eprint_id": 120139, "eprint_status": "archive", "datestamp": "2023-08-20 09:07:12", "lastmod": "2023-12-13 17:18:00", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tan-Chieh-Hsiang", "name": { "family": "Tan", "given": "Chieh-Hsiang" }, "orcid": "0000-0002-5432-0160" }, { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Park-Heenam", "name": { "family": "Park", "given": "Heenam" }, "orcid": "0000-0001-7911-5828" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "LINKIN-associated proteins necessary for tissue integrity during collective cell migration", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nWe thank Barbara Perry, Wilber Palma and Stephanie Nava for laboratory assistance. We thank members of our laboratory for discussions. Mutant alleles- mvk-1(tm6628), trd-1(tm2764), vha-19(tm2225), prx-3(tm6469), and rod-1(tm6186) were provided by the MITANI Lab through the National Bio-Resource Project of the MEXT, Japan. Some strains were obtained from the Caenorhabditis Genetics Center (CGC), which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was also facilitated by WormBase, a knowledgebase for nematode research; and by the Alliance of Genome Resources, a research platform that facilitates cross species research, This research was supported by NIH R01HD086596 (PWS and TFC), R01HD091327 (PWS), and R24 0D023041 (PWS). \n\nThe authors have declared no competing interest.\n\nSubmitted - 2023.02.08.527750v1.full.pdf
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", "abstract": "Cell adhesion plays essential roles in almost every aspect of metazoan biology. Previously, using the developmental migration of the nematode male gonad as a platform, LINKIN (Human: ITFG1,C. elegans: lnkn-1), a relatively understudied transmembrane protein conserved across the metazoa, was found to be necessary for tissue integrity during migration. InC. elegans, loss of lnkn-1 results in the detachment of the lead migratory cell from the rest of the developing male gonad. Three interactors of ITFG1/lnkn-1-RUVBL1/ruvb-1, RUVBL2/ruvb-2, and alpha-tubulin were identified by proteomic analysis using the human HEK293T cells and validated in the nematode male gonad. The ITFG1-RUVBL1 interaction has since been independently validated in a breast cancer cell line model that also implicates the involvement of the pair in metastasis. In this study, we showed that epitope-tagged ITFG1 localized to the cell surface of MDA-MB-231 breast cancer cells. Using unbiased mass spectrometry-based proteomics, we identified a new list of potential interactors of ITFG1. Loss-of-function analysis of their C. elegans orthologs found that three of the interactors - ATP9A/tat-5, NME1/ndk-1, and ANAPC2/apc-2 displayed migratory detachment phenotypes similar to that of lnkn-1. Taken together with the other genes whose reduction of function phenotype is the same as LINKIN (notably cohesion and condensin) suggests the involvement of membrane remodeling and chromosome biology in the tight adhesion dependent on LINKIN, and support the hypothesis for a structure role of chromosomes in post-mitotic cells.", "date": "2023-03-21", "date_type": "published", "id_number": "CaltechAUTHORS:20230316-182235000.22", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182235000.22", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)" }, { "agency": "NIH", "grant_number": "P40 OD010440" }, { "agency": "NIH", "grant_number": "R01HD086596" }, { "agency": "NIH", "grant_number": "R01HD091327" }, { "agency": "NIH", "grant_number": "R24 0D023041" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2023.02.08.527750", "primary_object": { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-3.xlsx" }, "related_objects": [ { "basename": "media-4.xlsx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-4.xlsx" }, { "basename": "media-5.docx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-5.docx" }, { "basename": "media-6.docx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-6.docx" }, { "basename": "2023.02.08.527750v1.full.pdf", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/2023.02.08.527750v1.full.pdf" }, { "basename": "media-1.xlsx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-1.xlsx" }, { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/t3k1f-dtw80/files/media-2.xlsx" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Tan, Chieh-Hsiang; Cheng, Kai-Wen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vv73j-vph14", "eprint_id": 120144, "eprint_status": "archive", "datestamp": "2023-08-20 09:04:21", "lastmod": "2023-12-22 23:45:05", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Grace-Z", "name": { "family": "Wang", "given": "Grace Z." }, "orcid": "0000-0002-0938-304X" }, { "id": "Warren-Elizabeth-A", "name": { "family": "Warren", "given": "Elizabeth A." } }, { "id": "Haas-Allison-L", "name": { "family": "Haas", "given": "Allison L." }, "orcid": "0000-0002-2154-4328" }, { "id": "S\u00e1nchez-Pe\u00f1a-Andrea", "name": { "family": "S\u00e1nchez Pe\u00f1a", "given": "Andrea" }, "orcid": "0000-0002-4843-3652" }, { "id": "Kiedrowski-Megan-R", "name": { "family": "Kiedrowski", "given": "Megan R." }, "orcid": "0000-0003-4610-182X" }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Bomberger-Jennifer-M", "name": { "family": "Bomberger", "given": "Jennifer M." }, "orcid": "0000-0003-4767-6238" }, { "id": "Tirrell-D-A", "name": { "family": "Tirrell", "given": "David A." }, "orcid": "0000-0003-3175-4596" }, { "id": "Limoli-Dominique-H", "name": { "family": "Limoli", "given": "Dominique H." }, "orcid": "0000-0002-4130-337X" } ] }, "title": "Staphylococcal secreted cytotoxins are competition sensing signals for Pseudomonas aeruginosa", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nThis work was supported by the Jacobs Institute for Molecular Engineering for Medicine and the Center for Environmental Microbial Interactions at Caltech, and by the Institute for Collaborative Biotechnologies through cooperative agreement W911NF-19-2-0026 from the U.S. Army Research Office, the Cystic Fibrosis Foundation (LIMOLI19R3 to DHL and BOMBER18G0 to JMB), and the National Institutes of Health (1R35GM142760-01 to DHL and 1R01HL142587 to JMB). We thank Drs. Megan Bergkessel (University of Dundee), Melanie Spero (University of Oregon), Alex Horswill (University of Colorado Denver), Mike Schurr (University of Colorado Denver), and Li Wu (University of Iowa) for helpful discussions and valuable insight. We also thank members of the Limoli and Tirrell Labs for careful editing of the manuscript and helpful discussions. We thank Dr. Jeff Jones (Caltech) for an in-house pipeline for proteomics data processing, Dr. J. Muse Davis for the use of the stereoscope, and Drs. Joseph Mougous and Anupama Khare for the generous gifts of the ClpV1-GFPmut3 and P'pvdA-mScarlet reporters, respectively. \n\nThe authors have declared no competing interest.\n\nSubmitted - 2023.01.29.526047v1.full.pdf
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", "abstract": "Coinfection with two notorious opportunistic pathogens, the Gram-negative Pseudomonas aeruginosa and Gram-positiveStaphylococcus aureus, dominates chronic pulmonary infections. While coinfection is associated with poor patient outcomes, the interspecies interactions responsible for such decline remain unknown. Here, we dissected molecular mechanisms of interspecies sensing between P. aeruginosa and S. aureus. We discovered that P. aeruginosa senses S. aureus secreted peptides and, counterintuitively, moves towards these toxins. P. aeruginosa tolerates such a strategy through \"competition sensing\", whereby it preempts imminent danger/competition by arming cells with type six secretion (T6S) and iron acquisition systems. Intriguingly, while T6S is predominantly described as weaponry targeting Gram-negative and eukaryotic cells, we find that T6S is essential for full P. aeruginosa competition with S. aureus, a previously undescribed role for T6S. Importantly, competition sensing was activated during coinfection of bronchial epithelia, including T6S islands targeting human cells. This study reveals critical insight into both interspecies competition and how antagonism may cause collateral damage to the host environment.", "date": "2023-03-21", "date_type": "published", "id_number": "CaltechAUTHORS:20230316-182348000.27", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182348000.27", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Jacobs Institute for Molecular Engineering for Medicine" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-19-2-0026" }, { "agency": "Cystic Fibrosis Foundation", "grant_number": "LIMOLI19R3" }, { "agency": "Cystic Fibrosis Foundation", "grant_number": "BOMBER18G0" }, { "agency": "NIH", "grant_number": "1R35GM142760-01" }, { "agency": "NIH", "grant_number": "1R01HL142587" } ] }, "local_group": { "items": [ { "id": "Jacobs-Institute-for-Molecular-Engineering-for-Medicine" }, { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2023.01.29.526047", "primary_object": { "basename": "2023.01.29.526047v1.full.pdf", "url": "https://authors.library.caltech.edu/records/vv73j-vph14/files/2023.01.29.526047v1.full.pdf" }, "related_objects": [ { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/vv73j-vph14/files/media-1.pdf" }, { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/vv73j-vph14/files/media-2.xlsx" }, { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/vv73j-vph14/files/media-3.xlsx" }, { "basename": "media-4.xlsx", "url": "https://authors.library.caltech.edu/records/vv73j-vph14/files/media-4.xlsx" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Wang, Grace Z.; Warren, Elizabeth A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cdpes-fvh20", "eprint_id": 120177, "eprint_status": "archive", "datestamp": "2023-08-20 08:47:42", "lastmod": "2023-12-13 16:47:53", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Findlay-Andrew-R", "name": { "family": "Findlay", "given": "Andrew R." }, "orcid": "0000-0002-8728-9833" }, { "id": "Paing-May-M", "name": { "family": "Paing", "given": "May M." } }, { "id": "Daw-Jil-A", "name": { "family": "Daw", "given": "Jil A." }, "orcid": "0000-0002-8002-076X" }, { "id": "Bengoechea-Ibaceta-Rocio", "name": { "family": "Bengoechea", "given": "Rocio" }, "orcid": "0000-0002-9029-019X" }, { "id": "Pittman-Sara-K", "name": { "family": "Pittman", "given": "Sara K." } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" }, "orcid": "0000-0003-4742-2668" }, { "id": "Miller-Timothy-M", "name": { "family": "Miller", "given": "Timothy M." }, "orcid": "0000-0002-3424-5511" }, { "id": "True-Heather-L", "name": { "family": "True", "given": "Heather L." }, "orcid": "0000-0003-4824-9529" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Weihl-Conrad-C", "name": { "family": "Weihl", "given": "Conrad C." }, "orcid": "0000-0002-3816-6124" } ] }, "title": "DNAJB6 Isoform Specific Knockdown: Therapeutic Potential for LGMDD1", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nThis work was supported by grants from: The National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS): ARF (K08AR075894, R03AR081395), CCW (R01AR068797, K24AR073317); The American Society of Gene and Cell therapy (ASGCT): ARF (Career Development Award); The Children's Discovery Institute of Saint Louis Children's Hospital: ARF (Faculty Scholar Award- MIFR20221004); and the LGMD-1D DNAJB6 Foundation and International Registry (ARF). \n\nAuthor Contributions: \nARF: Conceptualization, formal analysis, funding acquisition, investigation, methodology, resources, supervision, validation, visualization, writing original draft, writing \u2013 review and editing. \nMMP, JAD, RB, SKP, SL, FW, TC: Investigation, methodology. \nHLT, TMM: Conceptualization, writing \u2013 review and editing. \nCCW: Conceptualization, funding acquisition, resources, supervision, validation, writing \u2013 review and editing. \n\nCompeting Interest Statement. ARF and CCW are co-inventors on a pending patent application related to this publication (USPTO serial no. 17/932,996).\n\nSubmitted - 2022.11.17.516920v1.full.pdf
Supplemental Material - media-1.xlsx
", "abstract": "Dominant missense mutations in DNAJB6, an HSP40 co-chaperone, cause limb girdle muscular dystrophy (LGMD) D1. No treatments are currently available. Two isoforms exist, DNAJB6a and DNAJB6b, each with distinct localizations in muscle. Mutations reside in both isoforms, yet evidence suggests only DNAJB6b is responsible for disease pathogenesis. Mechanistic data supports either a toxic gain of function, a dominant negative mechanism, or a combination of both. Knockdown treatment strategies involving both isoforms carry risk as DNAJB6 knockout is embryonic lethal. We therefore developed an isoform specific knockdown approach using morpholinos. Selective reduction of each isoform was achievedin-vitroin primary mouse myotubes and human myoblasts, as well asin-vivoin mouse skeletal muscle. To assess isoform specific knockdown in LGMDD1, we created primary myotube cultures from aknock-inLGMDD1 mouse model. Using mass spectrometry, we identified an LGMDD1 protein signature related to protein homeostasis and myofibril structure. Selective reduction of DNAJB6b levels in LGMDD1 myotubes corrected much of the proteomic disease signature towards wild type levels. While additionalin-vivofunctional data is required, these findings suggest selective reduction of DNAJB6b may be a viable therapeutic target for LGMDD1.", "date": "2023-03-17", "date_type": "published", "id_number": "CaltechAUTHORS:20230316-182861000.70", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182861000.70", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K08AR075894" }, { "agency": "NIH", "grant_number": "R03AR081395" }, { "agency": "NIH", "grant_number": "R01AR068797" }, { "agency": "NIH", "grant_number": "K24AR073317" }, { "agency": "American Society of Gene and Cell Therapy" }, { "agency": "Saint Louis Children's Hospital", "grant_number": "MIFR20221004" }, { "agency": "LGMD-1D DNAJB6 Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.11.17.516920", "primary_object": { "basename": "2022.11.17.516920v1.full.pdf", "url": "https://authors.library.caltech.edu/records/cdpes-fvh20/files/2022.11.17.516920v1.full.pdf" }, "related_objects": [ { "basename": "media-1.xlsx", "url": "https://authors.library.caltech.edu/records/cdpes-fvh20/files/media-1.xlsx" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Findlay, Andrew R.; Paing, May M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/82fne-ypv78", "eprint_id": 119571, "eprint_status": "archive", "datestamp": "2023-08-20 08:34:01", "lastmod": "2023-12-22 23:35:10", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Guna-Alina", "name": { "family": "Guna", "given": "Alina" }, "orcid": "0000-0003-0757-1255" }, { "id": "Stevens-Taylor-A", "name": { "family": "Stevens", "given": "Taylor A." }, "orcid": "0000-0002-6232-5316" }, { "id": "Inglis-Alison-J", "name": { "family": "Inglis", "given": "Alison J." }, "orcid": "0000-0002-9008-8565" }, { "id": "Replogle-Joseph-M", "name": { "family": "Replogle", "given": "Joseph M." }, "orcid": "0000-0003-1832-919X" }, { "id": "Esantsi-Theodore-K", "name": { "family": "Esantsi", "given": "Theodore K." } }, { "id": "Muthukumar-Gayathri", "name": { "family": "Muthukumar", "given": "Gayathri" } }, { "id": "Shaffer-Kelly-C-L", "name": { "family": "Shaffer", "given": "Kelly C.L." }, "orcid": "0000-0002-6212-1428" }, { "id": "Wang-Maxine-L", "name": { "family": "Wang", "given": "Maxine L." }, "orcid": "0000-0002-5285-1857" }, { "id": "Pogson-Angela-N", "name": { "family": "Pogson", "given": "Angela N." }, "orcid": "0000-0002-6927-2456" }, { "id": "Jones-Jeffrey-J", "name": { "family": "Jones", "given": "Jeff J." }, "orcid": "0000-0002-7142-2222" }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Weissman-Jonathan-S", "name": { "family": "Weissman", "given": "Jonathan S." }, "orcid": "0000-0003-2445-670X" }, { "id": "Voorhees-R-M", "name": { "family": "Voorhees", "given": "Rebecca M." }, "orcid": "0000-0003-1640-2293" } ] }, "title": "MTCH2 is a mitochondrial outer membrane protein insertase", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nWe thank T. Pleiner and Z. Levine for careful reading and input on the manuscript. We thank: the Whitehead Institute Flow Cytometry Core and Kathy Daniels for access to FACS machines; the Whitehead Institute Genome Technology Core for support with sequencing of screen libraries; the Caltech Flow cytometry facility; and the Ting-Yu Wang and the Proteome Exploration Laboratory at Caltech for support for mass spectrometry. \n\nResearch reported in this publication was supported by: Howard Hughes Medical Institute (JSW), Human Frontier Science Program 2019L/LT000858 (AG), the Heritage Medical Research Institute (RMV), and the Larry L. Hillblom Foundation (AJI). \n\nCompeting Interest Statement. JMR consults for Maze Therapeutics and is a consultant for and equity holder in Waypoint Bio. JSW declares outside interest in 5 AM Venture, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, Tessera Therapeutics and Third Rock Ventures. RMV is a consultant and equity holder in Gate Bioscience.\n\nSubmitted - 2022.09.15.508165v1.full.pdf
Supplemental Material - media-1.pdf
Supplemental Material - media-2.xlsx
Supplemental Material - media-3.xlsx
Supplemental Material - media-4.xlsx
", "abstract": "In the mitochondrial outer membrane, tail-anchored (TA) proteins play critical roles in cytoplasmic-mitochondrial communication. Using genome-wide CRISPRi screens, we identify factors involved in mitochondrial TA biogenesis in human cells. We show that MTCH2, and its paralog MTCH1, are required for insertion of biophysically diverse mitochondrial TAs, but not outer membrane \u03b2-barrel proteins. In a reconstituted system, purified MTCH2 is sufficient to mediate insertion into proteoliposomes. Functional and mutational studies reveal that MTCH2 uses membrane-embedded hydrophilic residues to function as a gatekeeper for outer membrane protein biogenesis, controlling mislocalization of TAs into the endoplasmic reticulum and the sensitivity of leukemia cells to apoptosis. Our identification of MTCH2 as an insertase provides a mechanistic explanation for the diverse phenotypes and disease states associated with MTCH2 dysfunction.One-Sentence SummaryMTCH2 is both necessary and sufficient for insertion of diverse \u03b1-helical proteins into the mitochondrial outer membrane, and is the defining member of a family of insertases that have co-opted the SLC25 transporter fold.", "date": "2023-02-28", "date_type": "published", "id_number": "CaltechAUTHORS:20230228-37943000.2", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230228-37943000.2", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Human Frontier Science Program", "grant_number": "2019L/LT000858" }, { "agency": "Heritage Medical Research Institute" }, { "agency": "Larry L. Hillblom Foundation" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.09.15.508165", "primary_object": { "basename": "2022.09.15.508165v1.full.pdf", "url": "https://authors.library.caltech.edu/records/82fne-ypv78/files/2022.09.15.508165v1.full.pdf" }, "related_objects": [ { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/82fne-ypv78/files/media-1.pdf" }, { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/82fne-ypv78/files/media-2.xlsx" }, { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/82fne-ypv78/files/media-3.xlsx" }, { "basename": "media-4.xlsx", "url": "https://authors.library.caltech.edu/records/82fne-ypv78/files/media-4.xlsx" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Guna, Alina; Stevens, Taylor A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/30bf9-66677", "eprint_id": 119570, "eprint_status": "archive", "datestamp": "2023-08-22 17:58:55", "lastmod": "2023-12-22 23:35:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Guna-Alina", "name": { "family": "Guna", "given": "Alina" }, "orcid": "0000-0003-0757-1255" }, { "id": "Stevens-Taylor-A", "name": { "family": "Stevens", "given": "Taylor A." }, "orcid": "0000-0002-6232-5316" }, { "id": "Inglis-Alison-J", "name": { "family": "Inglis", "given": "Alison J." }, "orcid": "0000-0002-9008-8565" }, { "id": "Replogle-Joseph-M", "name": { "family": "Replogle", "given": "Joseph M." }, "orcid": "0000-0003-1832-919X" }, { "id": "Esantsi-Theodore-K", "name": { "family": "Esantsi", "given": "Theodore K." } }, { "id": "Muthukumar-Gayathri", "name": { "family": "Muthukumar", "given": "Gayathri" } }, { "id": "Shaffer-Kelly-C-L", "name": { "family": "Shaffer", "given": "Kelly C. L." }, "orcid": "0000-0002-6212-1428" }, { "id": "Wang-Maxine-L", "name": { "family": "Wang", "given": "Maxine L." }, "orcid": "0000-0002-5285-1857" }, { "id": "Pogson-Angela-N", "name": { "family": "Pogson", "given": "Angela N." }, "orcid": "0000-0002-6927-2456" }, { "id": "Jones-Jeffrey-J", "name": { "family": "Jones", "given": "Jeff J." }, "orcid": "0000-0002-7142-2222" }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Weissman-Jonathan-S", "name": { "family": "Weissman", "given": "Jonathan S." }, "orcid": "0000-0003-2445-670X" }, { "id": "Voorhees-R-M", "name": { "family": "Voorhees", "given": "Rebecca M." }, "orcid": "0000-0003-1640-2293" } ] }, "title": "MTCH2 is a mitochondrial outer membrane protein insertase", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. \n\nWe thank J. Nunnari and M. Le Vasseur for sharing the mitochondrial split GFP system. We thank T. Pleiner for technical assistance and Z. Levine for careful reading and input on the manuscript. We thank the Whitehead Institute Flow Cytometry Core and K. Daniels for access to FACS machines; the Whitehead Institute Genome Technology Core for support with sequencing of screen libraries; the Caltech Flow cytometry facility; and T. Y. Wang and for support for mass spectrometry. \n\nResearch reported in this publication was supported by Howard Hughes Medical Institute (J.S.W.), Human Frontier Science Program 2019L/LT000858 (A.G.), the Heritage Medical Research Institute (R.M.V.), the Larry L. Hillblom Foundation (A.J.I.), and NIH F31-NS115380 (J.M.R.). \n\nAuthor contributions: A.G., J.S.W., and R.M.V. conceived the study. A.G., T.A.S., A.J.I., J.M.R., J.S.W., and R.M.V. were responsible for the design, analysis, and interpretation of experiments. A.G., T.A.S., and A.J.I. performed most of the experiments in the study with help from J.M.R., T.K.E., G.M., B.L., K.C.S., M.L.W., and A.N.P. T.C., B.L., and J.J.J. advised the design, sample processing, and analysis for all mass spectrometry experiments. A.G. and R.M.V. drafted the manuscript with input from all authors. \n\nCompeting interests: J.M.R. consults for Maze Therapeutics and is a consultant for and equity holder in Waypoint Bio. J.S.W. declares outside interest in 5 AM Venture, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, Tessera Therapeutics, and Third Rock Ventures. R.M.V. is a consultant and equity holder in Gate Bioscience.\n\nAccepted Version - nihms-1847457.pdf
Supplemental Material - science.add1856_mdar_reproducibility_checklist.pdf
Supplemental Material - science.add1856_sm.pdf
Supplemental Material - science.add1856_tables_s1_to_s4.zip
", "abstract": "In the mitochondrial outer membrane, \u03b1-helical transmembrane proteins play critical roles in cytoplasmic-mitochondrial communication. Using genome-wide CRISPR screens, we identified mitochondrial carrier homolog 2 (MTCH2), and its paralog MTCH1, and showed that it is required for insertion of biophysically diverse tail-anchored (TA), signal-anchored, and multipass proteins, but not outer membrane \u03b2-barrel proteins. Purified MTCH2 was sufficient to mediate insertion into reconstituted proteoliposomes. Functional and mutational studies suggested that MTCH2 has evolved from a solute carrier transporter. MTCH2 uses membrane-embedded hydrophilic residues to function as a gatekeeper for the outer membrane, controlling mislocalization of TAs into the endoplasmic reticulum and modulating the sensitivity of leukemia cells to apoptosis. Our identification of MTCH2 as an insertase provides a mechanistic explanation for the diverse phenotypes and disease states associated with MTCH2 dysfunction.", "date": "2022-10-21", "date_type": "published", "publication": "Science", "volume": "378", "number": "6617", "publisher": "American Association for the Advancement of Science", "pagerange": "317-322", "id_number": "CaltechAUTHORS:20230228-36558000.1", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230228-36558000.1", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Human Frontier Science Program", "grant_number": "2019L/LT000858" }, { "agency": "Heritage Medical Research Institute" }, { "agency": "Larry L. Hillblom Foundation" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F31-NS115380" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/science.add1856", "pmcid": "PMC9674023", "primary_object": { "basename": "science.add1856_mdar_reproducibility_checklist.pdf", "url": "https://authors.library.caltech.edu/records/30bf9-66677/files/science.add1856_mdar_reproducibility_checklist.pdf" }, "related_objects": [ { "basename": "science.add1856_sm.pdf", "url": "https://authors.library.caltech.edu/records/30bf9-66677/files/science.add1856_sm.pdf" }, { "basename": "science.add1856_tables_s1_to_s4.zip", "url": "https://authors.library.caltech.edu/records/30bf9-66677/files/science.add1856_tables_s1_to_s4.zip" }, { "basename": "nihms-1847457.pdf", "url": "https://authors.library.caltech.edu/records/30bf9-66677/files/nihms-1847457.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Guna, Alina; Stevens, Taylor A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xkjb1-6t811", "eprint_id": 117493, "eprint_status": "archive", "datestamp": "2023-08-22 17:54:06", "lastmod": "2023-12-22 23:19:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Puskar-Ryan", "name": { "family": "Puskar", "given": "Ryan" } }, { "id": "Du-Truong-Chloe", "name": { "family": "Du Truong", "given": "Chloe" } }, { "id": "Swain-Kyle", "name": { "family": "Swain", "given": "Kyle" } }, { "id": "Chowdhury-Saborni", "name": { "family": "Chowdhury", "given": "Saborni" } }, { "id": "Chan-Ka-Yi", "name": { "family": "Chan", "given": "Ka-Yi" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "Ting Yu" } }, { "id": "Poh-Yu-Ping", "name": { "family": "Poh", "given": "Yu-Ping" }, "orcid": "0000-0001-6709-2147" }, { "id": "Mazor-Yuval", "name": { "family": "Mazor", "given": "Yuval" }, "orcid": "0000-0001-5072-0928" }, { "id": "Liu-Haijun", "name": { "family": "Liu", "given": "Haijun" }, "orcid": "0000-0003-0537-0302" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Nannenga-Brent-L", "name": { "family": "Nannenga", "given": "Brent L." }, "orcid": "0000-0001-6859-3429" }, { "id": "Chiu-Po-Lin", "name": { "family": "Chiu", "given": "Po-Lin" }, "orcid": "0000-0001-8608-7650" } ] }, "title": "Molecular asymmetry of a\u00a0photosynthetic supercomplex from green sulfur bacteria", "ispublished": "pub", "full_text_status": "public", "keywords": "General Physics and Astronomy; General Biochemistry, Genetics and Molecular Biology; General Chemistry; Multidisciplinary", "note": "\u00a9 The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nWe thank Chihiro Azai, Patricia Baker, and Hila Toporik for advising us on the procedure for culture growth. We very much appreciate Robert Blankenship and Kevin Redding for fruitful scientific discussion. We thank Dewight Williams and David Lowry for the EM assistance in the Eyring Materials Center (EMC) at Arizona State University (ASU). We acknowledge using the Titan Krios TEM at the EMC and the funding for the instrumentation by NSF MRI 1531991. A portion of this research was supported by NIH grant U24GM129547 and performed at the Pacific Northwest Center for Cryo-EM (PNCC) at Oregon Health & Science University (OHSU), Portland, OR, and accessed through EMSL (grid.436923.9), a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research (PNCC proposal number: 160074). We thank Omar Davulcu for the EM assistance at the PNCC site. We acknowledge the funding support by Army Research Office (ARO) (W911NF2010321) to P.-L.C., the support by the DOE, Office of Basic Energy Sciences, Photosynthetic Systems Program (DE-FG02-07ER15902) to H.L., and the GPU device support by the NVIDIA GPU Grant Program to P.-L.C. We especially thank John C.H. Spence for initiating the idea for the quantum biology project, and we missed the days discussing sciences and making discoveries together. \n\nAuthor contributions. R.P., C.D.T., K.S., and Y.-P.P. performed cell culture and protein purification. R.P. and C.D.T. prepared frozen specimens for cryo-EM data collection. S.C. and K.-Y.C. performed the characterization of purified protein complexes. S.L., K.-W.C., T.-Y.W., H.L., and T.-F.C. performed mass spectrometric experiments and analyses. P.-L.C. processed cryo-EM image data and performed structural modeling, analyses, and interpretations. Y.M. performed the calculations to analyze possible excitation energy transfer pathways. R.P., Y.-P.P., and P.-L.C. prepared figures. B.N. and P.-L.C. initiated and supervised the project. R.P., Y.M., B.N., and P.-L.C. wrote the manuscript with input from all the authors. \n\nData availability. Cryo-EM density maps (MRC format) of the RC-FMO2 and RC-FMO1 protein complexes determined in this study were deposited in the Electron Microscopy Data Bank (EMDB) under accession numbers EMD-26471 (RC-FMO\u2082) and EMD-26469 (RC-FMO\u2081). Model coordinates were deposited in the Protein Data Bank (PDB) under accession numbers 7UEB (RC-FMO2; 10.2210/pdb7ueb/pdb) and 7UEA (RC-FMO1; 10.2210/pdb7uea/pdb). All the data are available in the EMDB and wwPDB databases or from the corresponding author upon request. \n\nThe authors declare no competing interests.", "abstract": "The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex mediates the transfer of\u00a0light energy from the chlorosome antenna complex to the RC. Here we determine the structure of the photosynthetic supercomplex from the GSB Chlorobaculum tepidum using single-particle cryogenic electron microscopy (cryo-EM) and identify the cytochrome c subunit (PscC), two accessory protein subunits (PscE and PscF), a second FMO trimeric complex, and a linker pigment between FMO and the RC core. The protein subunits that are assembled with the symmetric RC core generate an asymmetric photosynthetic supercomplex. One linker bacteriochlorophyll (BChl) is located in one of the two FMO-PscA interfaces, leading to differential efficiencies of the two energy transfer branches. The two FMO trimeric complexes establish two different binding interfaces with the RC cytoplasmic surface, driven by the associated accessory subunits. This structure of the GSB photosynthetic supercomplex provides mechanistic insight into the light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex from the primitive homodimeric RC.", "date": "2022-10-03", "date_type": "published", "publication": "Nature Communications", "volume": "13", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 5824", "id_number": "CaltechAUTHORS:20221019-343672700.6", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221019-343672700.6", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "MRI-1531991" }, { "agency": "NIH", "grant_number": "U24GM129547" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF2010321" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-07ER15902" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-022-33505-4", "pmcid": "PMC9529944", "resource_type": "article", "pub_year": "2022", "author_list": "Puskar, Ryan; Du Truong, Chloe; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n862v-p0803", "eprint_id": 117750, "eprint_status": "archive", "datestamp": "2023-08-22 17:53:54", "lastmod": "2023-12-22 23:19:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "LeBlanc-Amy-K", "name": { "family": "LeBlanc", "given": "Amy K." }, "orcid": "0000-0001-7656-9859" }, { "id": "Mazcko-Christina-N", "name": { "family": "Mazcko", "given": "Christina N." }, "orcid": "0000-0002-2543-7781" }, { "id": "Fan-Timothy-M", "name": { "family": "Fan", "given": "Timothy M." }, "orcid": "0000-0003-2510-7050" }, { "id": "Vail-David-M", "name": { "family": "Vail", "given": "David M." }, "orcid": "0000-0002-1964-3693" }, { "id": "Flesner-Brian-K", "name": { "family": "Flesner", "given": "Brian K." }, "orcid": "0000-0002-2459-7054" }, { "id": "Bryan-Jeffrey-N", "name": { "family": "Bryan", "given": "Jeffrey N." }, "orcid": "0000-0002-6820-9850" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" }, "orcid": "0000-0003-4742-2668" }, { "id": "Harris-Scott", "name": { "family": "Harris", "given": "Scott" }, "orcid": "0000-0002-0400-9905" }, { "id": "Vargas-Jesse-D", "name": { "family": "Vargas", "given": "Jesse D." }, "orcid": "0000-0002-3671-6778" }, { "id": "Govindharajulu-Jeevan-P", "name": { "family": "Govindharajulu", "given": "Jeevan P." }, "orcid": "0000-0002-3705-4120" }, { "id": "Jaganathan-Soumya", "name": { "family": "Jaganathan", "given": "Soumya" }, "orcid": "0000-0001-8763-0109" }, { "id": "Tomaino-Francesca", "name": { "family": "Tomaino", "given": "Francesca" }, "orcid": "0000-0001-8991-5415" }, { "id": "Srivastava-Apurva-K", "name": { "family": "Srivastava", "given": "Apurva K." }, "orcid": "0000-0002-6390-7553" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Stott-Gordon-M", "name": { "family": "Stott", "given": "Gordon M." }, "orcid": "0000-0002-9148-6100" }, { "id": "Covey-Joseph-M", "name": { "family": "Covey", "given": "Joseph M." }, "orcid": "0000-0002-5696-8999" }, { "id": "Mroczkowski-Barbara", "name": { "family": "Mroczkowski", "given": "Barbara" }, "orcid": "0000-0002-6107-2580" }, { "id": "Doroshow-James-H", "name": { "family": "Doroshow", "given": "James H." }, "orcid": "0000-0002-4463-1790" } ] }, "title": "Comparative Oncology Assessment of a Novel Inhibitor of Valosin-Containing Protein in Tumor-Bearing Dogs", "ispublished": "pub", "full_text_status": "public", "keywords": "Cancer Research; Oncology", "note": "Canine SPE and IF assays were conducted at the Colorado State University Veterinary Clinical Pathology Laboratory, with special thanks to Dr. Russell Moore. NCI-Frederick is accredited by AAALAC International and follows the Public Health Service Policy for the Care and Use of Laboratory Animals. Animal care was provided in accordance with the procedures outlined in the \"Guide for Care and Use of Laboratory Animals (National Research Council; 1996; National Academy Press; Washington, DC).\" This project has been funded in whole or in part with federal funds from the NCI, NIH, under Contract Nos. HHSN261201500003 and 75N91019D00024 and Task Order No. 75N091019F00129. This work was supported by the Intramural Program of the NCI, NIH (Z01-BC006161). The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.\n\nThe costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.", "abstract": "Pet dogs with naturally occurring cancers play an important role in studies of cancer biology and drug development. We assessed tolerability, efficacy, and pharmacokinetic/pharmacodynamic relationships with a first-in-class small molecule inhibitor of valosin-containing protein (VCP/p97), CB-5339, administered to 24 tumor-bearing pet dogs. Tumor types assessed included solid malignancies, lymphomas, and multiple myeloma. Through a stepwise dose and schedule escalation schema, we determined the maximum tolerated dose to be 7.5 mg/kg when administered orally on a 4 days on, 3 days off schedule per week for 3 consecutive weeks. Adverse events were minimal and mainly related to the gastrointestinal system. Pharmacokinetic/pharmacodynamic data suggest a relationship between exposure and modulation of targets related to induction of the unfolded protein response, but not to tolerability of the agent. An efficacy signal was detected in 33% (2/6) of dogs with multiple myeloma, consistent with a mechanism of action relating to induction of proteotoxic stress in a tumor type with abundant protein production. Clinical trials of CB-5339 in humans with acute myelogenous leukemia and multiple myeloma are ongoing.", "date": "2022-10-01", "date_type": "published", "publication": "Molecular Cancer Therapeutics", "volume": "21", "number": "10", "publisher": "American Association for Cancer Research", "pagerange": "1510-1523", "id_number": "CaltechAUTHORS:20221107-998820100.20", "issn": "1535-7163", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221107-998820100.20", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HHSN261201500003" }, { "agency": "NIH", "grant_number": "75N91019D00024" }, { "agency": "NIH", "grant_number": "75N091019F00129" }, { "agency": "NIH", "grant_number": "Z01-BC006161" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1158/1535-7163.mct-22-0167", "pmcid": "PMC9538592", "resource_type": "article", "pub_year": "2022", "author_list": "LeBlanc, Amy K.; Mazcko, Christina N.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/55c4m-41492", "eprint_id": 116160, "eprint_status": "archive", "datestamp": "2023-08-22 17:48:29", "lastmod": "2023-12-22 23:34:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Spero-Melanie-A", "name": { "family": "Spero", "given": "Melanie A." }, "orcid": "0000-0003-3291-2138" }, { "id": "Jones-Jeffrey-J", "name": { "family": "Jones", "given": "Jeff" }, "orcid": "0000-0002-7142-2222" }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "Dianne K." }, "orcid": "0000-0003-1647-1918" } ] }, "title": "Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa", "ispublished": "pub", "full_text_status": "public", "keywords": "Molecular Biology; Microbiology", "note": "\u00a9 2022 John Wiley & Sons. \n\nAccepted manuscript online: 08 August 2022. Manuscript accepted: 04 August 2022. Manuscript revised: 31 July 2022. Manuscript received: 25 April 2022. \n\nGrants to D.K.N. from the NIH (1R21AI146987-02) and the Doren Family Foundation supported this research. M.A.S. was supported by a postdoctoral fellowship from the Cystic Fibrosis Foundation (SPERO19F0). We thank Megan Bergkessel (University of Dundee) for help with Tn-seq analyses, including providing custom scripts, and Nathan Dalleska and the Resnick Water and Environment Laboratory (Caltech) for help with metabolite analyses. We also thank John Bettinger for providing the python code used to analyze methionine oxidation levels via the \u00b9\u2078O-H\u2082O\u2082 labeling method that he and colleagues developed (Bettinger et al.) The Proteome Exploration Laboratory was supported by NIH OD010788, NIH OD020013, the Betty and Gordon Moore Foundation through grant GBMF775 and the Beckman Institute at Caltech. \n\nData Availability Statement: The proteomic data that supports the findings of this study are openly available in PRIDE at http://www.ebi.ac.uk/pride, accession number PXD033396.\n\nAccepted Version - Molecular_Microbiology_-_2022_-_Spero_-_Mechanisms_of_chlorate_toxicity_and_resistance_in_Pseudomonas_aeruginosa.pdf
Supplemental Material - mmi14972-sup-0001-figs1-s3.docx
Supplemental Material - mmi14972-sup-0002-tables1.xlsx
Supplemental Material - mmi14972-sup-0003-tables2.xlsx
Supplemental Material - mmi14972-sup-0004-tables3.xlsx
Supplemental Material - mmi14972-sup-0005-tables4.xlsx
Supplemental Material - mmi14972-sup-0006-tables5.xlsx
", "abstract": "Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Towards identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically-induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a \u2206msrA\u2206msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.", "date": "2022-10", "date_type": "published", "publication": "Molecular Microbiology", "volume": "118", "number": "4", "publisher": "Wiley", "pagerange": "321-335", "id_number": "CaltechAUTHORS:20220808-223822000", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220808-223822000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1R21AI146987-02" }, { "agency": "Doren Family Foundation" }, { "agency": "Cystic Fibrosis Foundation", "grant_number": "SPERO19F0" }, { "agency": "NIH", "grant_number": "OD010788" }, { "agency": "NIH", "grant_number": "OD020013" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF775" }, { "agency": "Caltech Beckman Institute" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" }, { "id": "Resnick-Sustainability-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1111/mmi.14972", "pmcid": "PMC9589919", "primary_object": { "basename": "mmi14972-sup-0005-tables4.xlsx", "url": "https://authors.library.caltech.edu/records/55c4m-41492/files/mmi14972-sup-0005-tables4.xlsx" }, "related_objects": [ { "basename": "mmi14972-sup-0006-tables5.xlsx", "url": "https://authors.library.caltech.edu/records/55c4m-41492/files/mmi14972-sup-0006-tables5.xlsx" }, { "basename": "Molecular_Microbiology_-_2022_-_Spero_-_Mechanisms_of_chlorate_toxicity_and_resistance_in_Pseudomonas_aeruginosa.pdf", "url": "https://authors.library.caltech.edu/records/55c4m-41492/files/Molecular_Microbiology_-_2022_-_Spero_-_Mechanisms_of_chlorate_toxicity_and_resistance_in_Pseudomonas_aeruginosa.pdf" }, { "basename": "mmi14972-sup-0001-figs1-s3.docx", "url": "https://authors.library.caltech.edu/records/55c4m-41492/files/mmi14972-sup-0001-figs1-s3.docx" }, { "basename": "mmi14972-sup-0002-tables1.xlsx", "url": "https://authors.library.caltech.edu/records/55c4m-41492/files/mmi14972-sup-0002-tables1.xlsx" }, { "basename": "mmi14972-sup-0003-tables2.xlsx", "url": "https://authors.library.caltech.edu/records/55c4m-41492/files/mmi14972-sup-0003-tables2.xlsx" }, { "basename": "mmi14972-sup-0004-tables3.xlsx", "url": "https://authors.library.caltech.edu/records/55c4m-41492/files/mmi14972-sup-0004-tables3.xlsx" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Spero, Melanie A.; Jones, Jeff; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w8tyx-7qq38", "eprint_id": 115017, "eprint_status": "archive", "datestamp": "2023-08-22 17:28:39", "lastmod": "2023-12-22 23:31:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ravanfar-Raheleh", "name": { "family": "Ravanfar", "given": "Raheleh" }, "orcid": "0000-0003-2992-0575" }, { "id": "Sheng-Yuling", "name": { "family": "Sheng", "given": "Yuling" } }, { "id": "Shahgholi-Mona", "name": { "family": "Shahgholi", "given": "Mona" }, "orcid": "0000-0002-8879-4305" }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Jones-Jeff", "name": { "family": "Jones", "given": "Jeff" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Gray-H-B", "name": { "family": "Gray", "given": "Harry B." }, "orcid": "0000-0002-7937-7876" }, { "id": "Winkler-Jay-R", "name": { "family": "Winkler", "given": "Jay R." }, "orcid": "0000-0002-4453-9716" } ] }, "title": "Surface cysteines could protect the SARS-CoV-2 main protease from oxidative damage", "ispublished": "pub", "full_text_status": "public", "keywords": "SARS-CoV-2 main protease; Reactive oxygen species; Cysteine; Inorganic Chemistry; Biochemistry", "note": "\u00a9 2022 Elsevier Inc. \n\nReceived 2 March 2022, Revised 28 April 2022, Accepted 29 May 2022, Available online 2 June 2022. \n\nWe thank Dr. Jennifer Keeffe for assistance with SEC-MALS. Experimental work was performed in the Caltech Mass Spectrometry Laboratory in the Division of Chemistry and Chemical Engineering; and the Beckman Institute Laser Resource Center and Proteome Exploration Laboratory supported by the Arnold and Mabel Beckman Foundation. The work was supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under award number R01DK019038. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.\n\nCRediT authorship contribution statement:\nRaheleh Ravanfar: Investigation, Methodology, Writing \u2013 original draft, Writing \u2013 review & editing. Yuling Sheng: Investigation. Mona Shahgholi: Investigation, Methodology, Writing \u2013 review & editing. Brett Lomenick: Investigation, Methodology, Formal analysis, Writing \u2013 review & editing. Jeff Jones: Investigation, Methodology, Formal analysis, Writing \u2013 review & editing. Tsui-Fen Chou: Writing \u2013 review & editing, Methodology. Harry B. Gray: Funding acquisition, Project administration, Writing \u2013 review & editing. Jay R. Winkler: Conceptualization, Funding acquisition, Project administration, Writing \u2013 review & editing.\n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nPublished - 1-s2.0-S0162013422001751-main.pdf
Supplemental Material - 1-s2.0-S0162013422001751-mmc1.docx
", "abstract": "The SARS-CoV-2 main protease (M\u1d56\u02b3\u1d52) is responsible for cleaving twelve nonstructural proteins from the viral polyprotein. M\u1d56\u02b3\u1d52, a cysteine protease, is characterized by a large number of noncatalytic cysteine (Cys) residues, none involved in disulfide bonds. In the absence of a tertiary-structure stabilizing role for these residues, a possible alternative is that they are involved in redox processes. We report experimental work in support of a proposal that surface cysteines on M^(pro) can protect the active-site Cys145 from oxidation by reactive oxygen species (ROS). In investigations of enzyme kinetics, we found that mutating three surface cysteines to serines did not greatly affect activity, which in turn indicates that these cysteines could protect Cys145 from oxidative damage.", "date": "2022-09", "date_type": "published", "publication": "Journal of Inorganic Biochemistry", "volume": "234", "publisher": "Elsevier", "pagerange": "Art. No. 111886", "id_number": "CaltechAUTHORS:20220603-698843600", "issn": "0162-0134", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220603-698843600", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "NIH", "grant_number": "R01DK019038" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.jinorgbio.2022.111886", "pmcid": "PMC9161685", "primary_object": { "basename": "1-s2.0-S0162013422001751-mmc1.docx", "url": "https://authors.library.caltech.edu/records/w8tyx-7qq38/files/1-s2.0-S0162013422001751-mmc1.docx" }, "related_objects": [ { "basename": "1-s2.0-S0162013422001751-main.pdf", "url": "https://authors.library.caltech.edu/records/w8tyx-7qq38/files/1-s2.0-S0162013422001751-main.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Ravanfar, Raheleh; Sheng, Yuling; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p1mbn-5f986", "eprint_id": 116303, "eprint_status": "archive", "datestamp": "2023-08-22 17:25:06", "lastmod": "2023-12-22 23:41:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yang-Chien-I", "name": { "family": "Yang", "given": "Chien-I" }, "orcid": "0000-0001-8606-5013" }, { "id": "Zhu-Zikun", "name": { "family": "Zhu", "given": "Zikun" }, "orcid": "0000-0001-5934-8368" }, { "id": "Jones-Jeffrey-J", "name": { "family": "Jones", "given": "Jeffrey J." } }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Shan-S-O", "name": { "family": "Shan", "given": "Shu-ou" }, "orcid": "0000-0002-6526-1733" } ] }, "title": "System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity", "ispublished": "pub", "full_text_status": "public", "keywords": "Molecular biology; Bacteriology; Omics; Multidisciplinary", "note": "\u00a9 2022 The Authors. Under a Creative Commons license - Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).\n\nReceived 7 April 2022, Revised 20 June 2022, Accepted 7 July 2022, Available online 15 July 2022, Version of Record 31 July 2022. \n\nWe thank D. Newman for critical discussions and members of the Shan lab for comments on the manuscript. The E. coli strains CAG12184 and KPS73 (\u0394fmt) are generous gifts from A. Varshavsky. We thank L. Shan, F. Wang, and C. Sanfiorenzo for the assistance in MS sample preparation, data analysis, and microscopy. Sequencing was performed at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at California Institute of Technology. This work was supported by NIH grant R35 GM136321 to S.S. and Think Global Education Trust Fellowship to C.-I.Y. \n\nAuthor contributions. Conceptualization: C.-I.Y. and S.S.; Investigation: C.-I.Y., Z.Z., and B.L.; Formal analysis: C.-I.Y, Z.Z., and J.J.; Software: Z.Z. and J.J.; Writing \u2013 original draft: C.-I.Y; Writing \u2013 review & editing: C. -I.Y, Z.Z., J.J., B.L., T.-F.C, and S.S.; Supervision: T.-F.C, and S.S. \n\nData and code availability: \nThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner, and the ribosome profiling data is available at GEO. The data are publicly available as of the date of publication. Accession numbers are listed in the key resources table. \n\nAll original code has been deposited to the ProteomeXchange Consortium and is publicly available as of the date of publication. The accession number is listed in the key resources table. \n\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. \n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S2589004222010288-main.pdf
Supplemental Material - 1-s2.0-S2589004222010288-mmc1.pdf
Supplemental Material - 1-s2.0-S2589004222010288-mmc2.xlsx
Supplemental Material - 1-s2.0-S2589004222010288-mmc3.xlsx
Supplemental Material - 1-s2.0-S2589004222010288-mmc4.xlsx
Supplemental Material - 1-s2.0-S2589004222010288-mmc5.xlsx
", "abstract": "The removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria. PDF is a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. This work used the time-resolved analyses of the Escherichia coli translatome and proteome to investigate the consequences of PDF inhibition. Loss of PDF activity rapidly induces cellular stress responses, especially those associated with protein misfolding and membrane defects, followed by a global down-regulation of metabolic pathways. Rapid membrane hyperpolarization and impaired membrane integrity were observed shortly after PDF inhibition, suggesting that the plasma membrane disruption is the most immediate and primary consequence of formyl group retention on nascent proteins. This work resolves the physiological function of a ubiquitous protein modification and uncovers its crucial role in maintaining the structure and function of the bacterial membrane.", "date": "2022-08-19", "date_type": "published", "publication": "iScience", "volume": "25", "number": "8", "publisher": "Cell Press", "pagerange": "Art. No. 104756", "id_number": "CaltechAUTHORS:20220816-373597000", "issn": "2589-0042", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220816-373597000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 GM136321" }, { "agency": "Think Global Education Trust" } ] }, "local_group": { "items": [ { "id": "Millard-and-Muriel-Jacobs-Genetics-and-Genomics-Laboratory" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.isci.2022.104756", "pmcid": "PMC9356101", "primary_object": { "basename": "1-s2.0-S2589004222010288-main.pdf", "url": "https://authors.library.caltech.edu/records/p1mbn-5f986/files/1-s2.0-S2589004222010288-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2589004222010288-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/p1mbn-5f986/files/1-s2.0-S2589004222010288-mmc1.pdf" }, { "basename": "1-s2.0-S2589004222010288-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/p1mbn-5f986/files/1-s2.0-S2589004222010288-mmc2.xlsx" }, { "basename": "1-s2.0-S2589004222010288-mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/p1mbn-5f986/files/1-s2.0-S2589004222010288-mmc3.xlsx" }, { "basename": "1-s2.0-S2589004222010288-mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/p1mbn-5f986/files/1-s2.0-S2589004222010288-mmc4.xlsx" }, { "basename": "1-s2.0-S2589004222010288-mmc5.xlsx", "url": "https://authors.library.caltech.edu/records/p1mbn-5f986/files/1-s2.0-S2589004222010288-mmc5.xlsx" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Yang, Chien-I; Zhu, Zikun; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yvx4e-r7d09", "eprint_id": 115351, "eprint_status": "archive", "datestamp": "2023-08-20 08:02:20", "lastmod": "2023-12-22 23:34:59", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dutka-Przemys\u0142aw", "name": { "family": "Dutka", "given": "Przemys\u0142aw" }, "orcid": "0000-0003-3819-1618" }, { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Hurt-Robert-C", "name": { "family": "Hurt", "given": "Robert C." }, "orcid": "0000-0002-4347-6901" }, { "id": "Salahshoor-Hossein", "name": { "family": "Salahshoor", "given": "Hossein" }, "orcid": "0000-0002-7264-7650" }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "Ting-Yu" } }, { "id": "Malounda-Dina", "name": { "family": "Malounda", "given": "Dina" }, "orcid": "0000-0001-7086-9877" }, { "id": "Lu-George-Jiaozhi", "name": { "family": "Lu", "given": "George" }, "orcid": "0000-0002-4689-9686" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Shapiro-M-G", "name": { "family": "Shapiro", "given": "Mikhail G." }, "orcid": "0000-0002-0291-4215" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nVersion 1 June 21, 2022; Version 2 - July 12, 2022. \n\nThe authors are grateful to Catherine Oikonomou for helpful editorial comments. We thank Songye Chen for assistance with tomography data collection. Electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. The Proteome Exploration Laboratory (PEL) is supported by the Beckman Institute and NIH 1S10OD02001301. This work was supported by the National Institutes of Health (grant R01-AI127401 to G.J.J. and R01-EB018975 to M.G.S.) and the Caltech Center for Environmental Microbial Interactions (CEMI). Related research in the Shapiro Laboratory is supported by the Packard Foundation, the Chan Zuckerberg Initiative and the Heritage Medical Research Institute. \n\nAuthor Contributions: P.D. conceived experiments, prepared samples, acquired and analyzed data, performed data exploration, drafted the manuscript, and prepared the figures. L.A.M initiated the project and collected data for Mega GVs. R.C.H performed mutation screening for GvpA and participated in initial sample preparation and optimization for Mega GVs. H.S. performed finite element simulation and analyzed data. T-Y.W performed XLMS experiments and analyzed the data. D.M expressed and purified GV samples. G.L. participated in initial sample preparation and optimization for Mega GVs. T-F.C. supervised XLMS experiments. All authors participated in correction of the manuscript. M.G.S. participated in guidance, experimental design, funding, and correction/advising on writing the manuscript. G.J.J participated in guidance, experimental design, funding, and correction/advising on writing the manuscript. \n\nThe authors declare no competing interests. \n\nData Availability: Cryo-ET density maps and GvpA/GvpC integrative model are available on Zenodo zenodo.org/record/6820642#.Ys0aROzMKw1\n\nSubmitted - 2022.06.21.496981v2.full.pdf
Supplemental Material - media-1.avi
", "abstract": "Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically-encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryo-electron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder\u2014a site that may act as an elongation center. High-resolution subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a \u03b2-sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.", "date": "2022-07-08", "date_type": "published", "id_number": "CaltechAUTHORS:20220706-965078000", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220706-965078000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Beckman Institute" }, { "agency": "NIH", "grant_number": "1S10OD02001301" }, { "agency": "NIH", "grant_number": "R01-AI127401" }, { "agency": "NIH", "grant_number": "R01-EB018975" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Chan Zuckerberg Initiative" }, { "agency": "Heritage Medical Research Institute" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Heritage-Medical-Research-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.06.21.496981", "primary_object": { "basename": "2022.06.21.496981v2.full.pdf", "url": "https://authors.library.caltech.edu/records/yvx4e-r7d09/files/2022.06.21.496981v2.full.pdf" }, "related_objects": [ { "basename": "media-1.avi", "url": "https://authors.library.caltech.edu/records/yvx4e-r7d09/files/media-1.avi" } ], "resource_type": "monograph", "pub_year": "2022", "author_list": "Dutka, Przemys\u0142aw; Metskas, Lauren Ann; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3f3pt-2av22", "eprint_id": 115757, "eprint_status": "archive", "datestamp": "2023-08-22 16:46:56", "lastmod": "2023-12-22 23:19:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Feng", "name": { "family": "Wang", "given": "F." } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "S." }, "orcid": "0000-0002-0829-1821" }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "T. Y." } }, { "id": "Lopez-George-A", "name": { "family": "Lopez", "given": "G. A." } }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "I." }, "orcid": "0000-0002-9934-3040" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "T. F." }, "orcid": "0000-0003-2410-2186" } ] }, "title": "P97/VCP ATPase inhibitors can rescue p97 mutation-linked motor neuron degeneration", "ispublished": "pub", "full_text_status": "public", "keywords": "amyotrophic lateral sclerosis; motor neuron disease; inclusion body myopathy associated with paget disease of bone and frontotemporal dementia; p97 inhibitor; cell cycle; General Medicine", "note": "\u00a9 The Author(s) 2022. Published by Oxford University Press on behalf of the Guarantors of Brain. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived August 27, 2021. Revised May 11, 2022. Accepted July 06, 2022. Advance access publication July 6, 2022. \n\nThe authors would like to thank the anonymous reviewers\nfor constructive criticism.\n\nThis work was supported with fund from the National Institute of Neurological Disorders and Stroke, R01NS102279. \n\nThe authors report no competing interests. \n\nF Wang, S Li and T Y Wang contributed equally to this work.\n\nPublished - fcac176.pdf
Supplemental Material - fcac176_supplementary_data.zip
", "abstract": "Mutations in p97/VCP cause two motor neuron diseases: inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia and familial amyotrophic lateral sclerosis. How p97 mutations lead to motor neuron degeneration is, however, unknown. Here we used patient-derived induced pluripotent stem cells to generate p97 mutant motor neurons. We reduced the genetic background variation by comparing mutant motor neurons to its isogenic wild type lines. Proteomic analysis reveals that p97R155H/+ motor neurons upregulate several cell cycle proteins at Day 14, but this effect diminishes by Day 20. Molecular changes linked to delayed cell cycle exit are observed in p97 mutant motor neurons. We also find that two p97 inhibitors, CB-5083 and NMS-873, restore some dysregulated protein levels. In addition, two p97 inhibitors and a food and drug administration-approved cyclin-dependent kinase 4/6 inhibitor, Abemaciclib, can rescue motor neuron death. Overall, we successfully used iPSC-derived motor neurons, identified dysregulated proteome and transcriptome and showed that p97 inhibitors rescue phenotypes in this disease model.", "date": "2022-07-04", "date_type": "published", "publication": "Brain Communications", "volume": "4", "number": "4", "publisher": "Oxford University Press", "pagerange": "Art. No. fcac176", "id_number": "CaltechAUTHORS:20220722-768560000", "issn": "2632-1297", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220722-768560000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01NS102279" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/braincomms/fcac176", "pmcid": "PMC9294923", "primary_object": { "basename": "fcac176.pdf", "url": "https://authors.library.caltech.edu/records/3f3pt-2av22/files/fcac176.pdf" }, "related_objects": [ { "basename": "fcac176_supplementary_data.zip", "url": "https://authors.library.caltech.edu/records/3f3pt-2av22/files/fcac176_supplementary_data.zip" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Wang, F.; Li, S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/srr9h-szg36", "eprint_id": 115440, "eprint_status": "archive", "datestamp": "2023-08-22 16:13:06", "lastmod": "2023-12-22 23:23:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Rosencrans-William-M", "name": { "family": "Rosencrans", "given": "William M." }, "orcid": "0000-0003-1461-8891" }, { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Stott-Gordon-M", "name": { "family": "Stott", "given": "Gordon M." }, "orcid": "0000-0002-9148-6100" }, { "id": "Mroczkowski-Barbara", "name": { "family": "Mroczkowski", "given": "Barbara" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Sulforaphane is Synergistic with CB\u20105083\u2009and Inhibits Colony Formation of CB\u20105083\u2010Resistant HCT116 Cells", "ispublished": "pub", "full_text_status": "public", "keywords": "p97; VCP; CB-5083; Sulforaphane; CHOP; Organic Chemistry; General Pharmacology, Toxicology and Pharmaceutics; Molecular Medicine; Drug Discovery; Biochemistry; Pharmacology", "note": "\u00a9 2022 Wiley-VCH GmbH. \n\nIssue Online: 07 June 2022; Version of Record online: 22 April 2022; Manuscript revised: 04 April 2022; Manuscript received: 17 January 2022. \n\nResearch Funding: National Institute of Neurological Disorders and Stroke. Grant Number: R01NS102279; National Cancer Institute, National Institutes of Health. Grant Numbers: 75N91019D00024, 75N091019F00129. \n\nData Availability Statement: The data that support the findings of this study are available in the supplementary material of this article.\n\nSupplemental Material - cmdc202200030-sup-0001-misc_information.pdf
", "abstract": "Human p97 is a potential drug target in oncology. Mutation-driven drug resistance is an obstacle to the long-term efficacy of targeted therapy. We found that the ATPase activity for one of the CB-5083-resistant p97 mutants was reduced, which also attenuated the degradation of K48 ubiquitinated proteins in cells. To understand how p97 mutant cells with significantly reduced ATPase activity can still grow, we discovered reduced levels of CHOP and NF-\u03baB activation in the p97 mutant cells and these cellular changes can potentially protect HCT116 cells from death due to lowered p97 activity. In addition, the NF-kB inhibitor Sulforaphane reduces proliferation of CB-5083 resistant cells and acts synergistically with CB-5083 to block proliferation of the parental HCT116 cells. The combination of Sulforaphane and CB-5083 may be a useful treatment strategy to combat CB-5083 resistance.", "date": "2022-06-03", "date_type": "published", "publication": "ChemMedChem", "volume": "17", "number": "11", "publisher": "Wiley", "pagerange": "Art. No. e202200030", "id_number": "CaltechAUTHORS:20220708-104460300", "issn": "1860-7179", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220708-104460300", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01NS102279" }, { "agency": "NIH", "grant_number": "75N91019D00024" }, { "agency": "NIH", "grant_number": "75N091019F00129" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1002/cmdc.202200030", "primary_object": { "basename": "cmdc202200030-sup-0001-misc_information.pdf", "url": "https://authors.library.caltech.edu/records/srr9h-szg36/files/cmdc202200030-sup-0001-misc_information.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Wang, Feng; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pz0qs-0n264", "eprint_id": 114116, "eprint_status": "archive", "datestamp": "2023-08-22 15:37:13", "lastmod": "2023-12-22 23:23:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Gang", "name": { "family": "Zhang", "given": "Gang" }, "orcid": "0000-0003-0774-5710" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Zhu-Yingying", "name": { "family": "Zhu", "given": "Yingying" } }, { "id": "Huo-Ran", "name": { "family": "Huo", "given": "Ran" } }, { "id": "Abdukirim-Elyar", "name": { "family": "Abdukirim", "given": "Elyar" } }, { "id": "Kang-Guifeng", "name": { "family": "Kang", "given": "Guifeng" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Discovery of small-molecule inhibitors of RUVBL1/2 ATPase", "ispublished": "pub", "full_text_status": "public", "keywords": "RUVBL1; Pontin; RUVBL2, Reptin; AAA ATPase; Organic synthesis; Docking; Pyrazolo[1,5-a]pyrimidine-3-carboxamide; Proteomics; Organic Chemistry; Clinical Biochemistry; Drug Discovery; Pharmaceutical Science; Molecular Biology; Molecular Medicine; Biochemistry", "note": "\u00a9 2022 Elsevier. \n\nReceived 25 January 2022, Revised 7 March 2022, Accepted 22 March 2022, Available online 26 March 2022, Version of Record 29 March 2022. \n\nThis work was supported in part by the National Institute of Child Health and Human Development R01 HD086596 and The Cultivation Fund of School of Pharmaceutical Sciences, Capital Medical University (2021).\n\nAccepted Version - nihms-1795336.pdf
Supplemental Material - 1-s2.0-S0968089622001183-mmc1.docx
", "abstract": "RUVBL1 and RUVBL2 are highly conserved AAA ATPases (ATPases Associated with various cellular Activities) and highly relevant to the progression of cancer, which makes them attractive targets for novel therapeutic anticancer drugs. In this work, docking-based virtual screening was performed to identify compounds with activity against the RUVBL1/2 complex. Seven compounds showed inhibitory activity against the complex in both enzymatic and cellular assays. A series of pyrazolo[1,5-a]pyrimidine-3-carboxamide analogs were synthesized based on the scaffold of compound 15 with inhibitory activity and good potential for structural manipulation. Analysis of the structure\u2013activity relationship identified the benzyl group on R\u2082 and aromatic ring-substituted piperazinyl on R\u2084 as essential for inhibitory activity against the RUVBL1/2 complex. Of these, compound 18, which has IC\u2085\u2080 values of 6.0 \u00b1 0.6 \u03bcM and 7.7 \u00b1 0.9 \u03bcM against RUVBL1/2 complex and RUVBL1 respectively, showed the most potent inhibition in cell lines A549, H1795, HCT116, and MDA-MB-231 with IC\u2085\u2080 values of 15 \u00b1 1.2 \u03bcM, 15 \u00b1 1.8 \u03bcM, 11 \u00b1 1.0 \u03bcM, and 8.9 \u00b1 0.9 \u03bcM respectively. A docking study of the compound was performed to predict the binding mode of pyrazolo[1,5-a]pyrimidine-3-carboxamides. Furthermore, mass spectrometry-based proteomic analysis was employed to explore cellular proteins dysregulated by treatment with compounds 16, 18, and 19. Together, the data from these analyses suggest that that compound 18 could serve as a starting point for structural modifications in order to improve potency, selectivity, and pharmacokinetic parameters of potential therapeutic molecules.", "date": "2022-05-15", "date_type": "published", "publication": "Bioorganic and Medicinal Chemistry", "volume": "62", "publisher": "Elsevier", "pagerange": "Art. No. 116726", "id_number": "CaltechAUTHORS:20220329-753949840", "issn": "0968-0896", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220329-753949840", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 HD086596" }, { "agency": "Capital Medical University" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.bmc.2022.116726", "pmcid": "PMC9034851", "primary_object": { "basename": "1-s2.0-S0968089622001183-mmc1.docx", "url": "https://authors.library.caltech.edu/records/pz0qs-0n264/files/1-s2.0-S0968089622001183-mmc1.docx" }, "related_objects": [ { "basename": "nihms-1795336.pdf", "url": "https://authors.library.caltech.edu/records/pz0qs-0n264/files/nihms-1795336.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Zhang, Gang; Wang, Feng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3ep27-sk395", "eprint_id": 114531, "eprint_status": "archive", "datestamp": "2023-10-09 21:01:36", "lastmod": "2023-12-22 23:39:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Zhang-Gang", "name": { "family": "Zhang", "given": "Gang" }, "orcid": "0000-0003-0774-5710" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "NMS-873 Leads to Dysfunctional Glycometabolism in A p97-Independent Manner in HCT116 Colon Cancer Cells", "ispublished": "pub", "full_text_status": "public", "keywords": "p97 inhibitor; glycometabolism; resistance; protein stability; proteomics; Pharmaceutical Science", "note": "\u00a9 2022 by the authors. Licensee MDPI, Basel, Switzerland.\nThis is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived: 24 February 2022; Accepted: 26 March 2022; Published: 31 March 2022. \n\nWe thank Ariane Helou at Caltech's Beckman Institute for editing the manuscript. \n\nThis work was supported in part with funds from the National Institute of Neurological Disorders and Stroke, R01NS100815, and R01NS102279. \n\nSupplementary Materials: The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/pharmaceutics14040764/s1. Figure S1: Additional data of NMS-873 regulates glycometabolism; Figure S2: Additional data of generating NMS-873 resistant cell lines; Figure S3: More data to prove NMS-873 affects glycometabolism in a p97 independent manner, and synergistic anti-proliferative effect of 2-DG and NMS-873; Figure S4: Proteomic analysis of 4 \u03bcM NMS-873-treated HCT116 and NMS-R2 cell lines; Figure S5: Volcano plot showing DS proteins of a repeated PISA T assay; Figure S6: of Additional PISA T proteomic data and NDUFAF5-HA expression result. Table S1: DE proteins of p97 inhibitors and MG132 treatments, related to Figure 1A,B; Table S2. Proteomic data of NMS-873 treated HCT116 and NMS-R2, related to Figure 3E and Figure S4; Table S3. Proteomic data of the PISA T assay using crude cell extracts and one temperature range, related to Figure S5; Table S4. Proteomic data of the PISA T assay using cell lysate and two temperature ranges, related to Figure 4A\u2013D and Figure S6A; Table S5. Functional enrichment analysis of DS proteins from PISA T assay, related to Figure 4E and Figure S6B; Table S6. Mitochondrial complexes DS proteins from PISA T assay, related to Figure 4F; Table S7. DS proteins identified in both PISA T assays, related to Figure 4B,C and Figure S5; Table S8. PCR and sequencing primers used in the study. \n\nAuthor Contributions: S.L. wrote the manuscript. F.W. and S.L. performed all cellular assays and proteomics studies. G.Z. performed the docking study. T.-F.C. supervised the project and designed the research. All authors have read and agreed to the published version of the manuscript. \n\nInstitutional Review Board Statement: Not applicable. \n\nInformed Consent Statement: Not applicable. \n\nData Availability Statement: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [63] partner repository with the dataset identifier PXD025898 and 10.6019/PXD025898. All relevant data generated during this study are included in the article and the Supplementary Information. This paper does not report original code. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nPublished - pharmaceutics-14-00764-v3.pdf
Supplemental Material - pharmaceutics-14-00764-s001.zip
", "abstract": "Adenosine triphosphate (ATP)\u2013competitive p97 inhibitor CB-5339, the successor of CB-5083, is being evaluated in Phase 1 clinical trials for anti-cancer therapy. Different modes-of-action p97 inhibitors such as allosteric inhibitors are useful to overcome drug-induced resistance, one of the major problems of targeted therapy. We previously demonstrated that allosteric p97 inhibitor NMS-873 can overcome CB-5083-induced resistance in HCT116. Here we employed chemical proteomics and drug-induced thermal proteome changes to identify drug targets, in combination with drug-resistant cell lines to dissect on- and off-target effects. We found that NMS-873 but not CB-5083 affected glycometabolism. By establishing NMS-873-resistant HCT116 cell lines and performing both cell-based and proteomic analysis, we confirmed that NMS-873 dysregulates glycometabolism in a p97-independent manner. We then used proteome integral solubility alteration with a temperature-based method (PISA T) to identify NDUFAF5 as one of the potential targets of NMS-873 in the mitochondrial complex I. We also demonstrated that glycolysis inhibitor 2-DG enhanced the anti-proliferative effect of NMS-873. The polypharmacology of NMS-873 can be advantageous for anti-cancer therapy for colon cancer.", "date": "2022-04-01", "date_type": "published", "publication": "Pharmaceutics", "volume": "14", "number": "4", "publisher": "MDPI", "pagerange": "764", "id_number": "CaltechAUTHORS:20220429-183149900", "issn": "1999-4923", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220429-183149900", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01NS100815" }, { "agency": "NIH", "grant_number": "R01NS102279" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.3390/pharmaceutics14040764", "pmcid": "PMC9024726", "primary_object": { "basename": "pharmaceutics-14-00764-v3.pdf", "url": "https://authors.library.caltech.edu/records/3ep27-sk395/files/pharmaceutics-14-00764-v3.pdf" }, "related_objects": [ { "basename": "pharmaceutics-14-00764-s001.zip", "url": "https://authors.library.caltech.edu/records/3ep27-sk395/files/pharmaceutics-14-00764-s001.zip" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Li, Shan; Wang, Feng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fxbey-v4b88", "eprint_id": 112133, "eprint_status": "archive", "datestamp": "2023-08-22 14:37:57", "lastmod": "2023-12-22 23:30:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" }, "orcid": "0000-0003-4742-2668" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Houerbi-Nadia", "name": { "family": "Houerbi", "given": "Nadia" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Temporal proteomics reveal specific cell cycle oncoprotein downregulation by p97/VCP inhibition", "ispublished": "pub", "full_text_status": "public", "keywords": "p97 inhibitor; proteasome inhibitor; E2F1; cyclin D1; cell cycle; anticancer; proteomic; CB-5083; NMS-873; UPCDC-30245; Clinical Biochemistry; Drug Discovery; Pharmacology; Molecular Biology; Molecular Medicine; Biochemistry", "note": "\u00a9 2021 Elsevier. \n\nReceived 22 April 2021, Revised 3 August 2021, Accepted 2 November 2021, Available online 29 November 2021. \n\nThis work was supported in part with funds from the National Institute of Neurological Disorders and Stroke, R01NS100815 and R01NS102279.\n\nAuthor contributions. F.W. wrote the manuscript. F.W. and S.L. performed the cellular assays and proteomics studies. N.H. performed analysis and improved language. T.-F.C. supervised the project. \n\nData and code availability. All relevant data generated during this study are included in the article and the supplemental information. The mass spectrometry raw data related to Figures 1A\u20131D are deposited to the ProteomeXchance Consortium (https://www.ebi.ac.uk/pride/) via the PRIDE repository with the dataset identifier PXD025094 and 10.6019/PXD025094\". The mass spectrometry raw data related to Figures 1E\u20131G with dataset identifier PXD025167 and 10.6019/PXD025167\". The mass spectrometry raw data related to Figure 2 with dataset identifier PXD025225 and 10.6019/PXD025225\". This paper does not report original code. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. \n\nThe authors declare no competing interests.\n\nAccepted Version - nihms-1761463.pdf
Supplemental Material - 1-s2.0-S2451945621004827-mmc1.pdf
Supplemental Material - 1-s2.0-S2451945621004827-mmc2.xlsx
Supplemental Material - 1-s2.0-S2451945621004827-mmc3.xlsx
Supplemental Material - 1-s2.0-S2451945621004827-mmc4.xlsx
Supplemental Material - 1-s2.0-S2451945621004827-mmc5.xlsx
", "abstract": "Targeting protein quality control (PQC) pathways using proteasome or p97/VCP inhibition can effectively treat blood tumors. However, in solid tumors, only p97/VCP inhibitors are effective. To probe this difference in efficacy, we tracked HCT116 colon cancer cells using temporal proteomics to define the cellular and molecular responses to proteasome and p97 inhibition. Proteins involved in general PQC pathways were similarly upregulated by both treatments, suggesting that the proteotoxic stress caused by inhibitors does not explain the differential therapeutic effectiveness. Unexpectedly, proteins specifically dysregulated by two p97 inhibitors are involved in cell cycle control. Indeed, eleven cell cycle proteins were downregulated by p97 inhibition but not by proteasome inhibition. Western blot analysis validated the degradation of cyclin D1 and Securin, which depends on proteasome but not on p97. Differing regulation of cell cycle proteins by p97 and the proteasome may, therefore, explain the therapeutic efficacy of p97 inhibitors in colon cancer.", "date": "2022-03-17", "date_type": "published", "publication": "Cell Chemical Biology", "volume": "29", "number": "3", "publisher": "Cell Press", "pagerange": "517-529", "id_number": "CaltechAUTHORS:20211201-482793884", "issn": "2451-9456", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211201-482793884", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01NS100815" }, { "agency": "NIH", "grant_number": "R01NS102279" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.chembiol.2021.11.005", "pmcid": "PMC8934257", "primary_object": { "basename": "nihms-1761463.pdf", "url": "https://authors.library.caltech.edu/records/fxbey-v4b88/files/nihms-1761463.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2451945621004827-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/fxbey-v4b88/files/1-s2.0-S2451945621004827-mmc1.pdf" }, { "basename": "1-s2.0-S2451945621004827-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/fxbey-v4b88/files/1-s2.0-S2451945621004827-mmc2.xlsx" }, { "basename": "1-s2.0-S2451945621004827-mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/fxbey-v4b88/files/1-s2.0-S2451945621004827-mmc3.xlsx" }, { "basename": "1-s2.0-S2451945621004827-mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/fxbey-v4b88/files/1-s2.0-S2451945621004827-mmc4.xlsx" }, { "basename": "1-s2.0-S2451945621004827-mmc5.xlsx", "url": "https://authors.library.caltech.edu/records/fxbey-v4b88/files/1-s2.0-S2451945621004827-mmc5.xlsx" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Wang, Feng; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ssg88-dnx55", "eprint_id": 114444, "eprint_status": "archive", "datestamp": "2023-08-22 13:59:16", "lastmod": "2023-12-22 23:14:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nandi-Purbasha", "name": { "family": "Nandi", "given": "Purbasha" }, "orcid": "0000-0002-8047-2029" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" } }, { "id": "Columbres-Rod-Carlo-A", "name": { "family": "Columbres", "given": "Rod Carlo" } }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Williams-Dewight-R", "name": { "family": "Williams", "given": "Dewight" } }, { "id": "Poh-Yu-Ping", "name": { "family": "Poh", "given": "Yu-Ping" }, "orcid": "0000-0001-6709-2147" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Chiu-Po-Lin", "name": { "family": "Chiu", "given": "Po-Lin" }, "orcid": "0000-0001-8608-7650" } ] }, "title": "Mechanism of the alteration in domain-domain communications in human p97/VCP atpase", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Biophysics", "note": "\u00a9 2021 Biophysical Society. Published by Elsevier Inc. \n\nAvailable online 11 February 2022, Version of Record 11 February 2022.", "abstract": "Human p97/VCP, an AAA+ ATPase, regulates various cellular activities by interacting with cofactor proteins, including ubiquitin-dependent protein quality control, Golgi-biogenesis, and endoplasmic reticulum-associated degradation (ERAD). Single amino-acid mutation of R155H on the N-domain is the most prevalent, leading to a rare degenerative disease MSP1. The p97 R155H mutant exhibits abnormal ATPase activity and cofactor dysregulation. We pursued biochemical characterization in combination with single-particle cryo-electron microscopy (cryo-EM) to study the interaction of p97^(R155H) mutant with its cofactor p47 and determined the structures of the p97^(R155H)-p47 complex in full length for the first time. In contrast to the wild type, p97^(R155H) occupies approximately 40% in the dodecameric form without nucleotide binding. The p97^(R155H) dodecamer does not bind to p47 or nucleotides and bears close resemblance to the inhibitor bound CB-5083:p97 structure, implying that this may be an inactive form. In the full-length p97^(R155H)-p47 complex structure, the p47 interacts through its UBX domain in an asymmetric manner to bind the p97^(R155H) N-domain with a preference for the N-up at the highest position. The structures also established that the arginine fingers might contribute to the elevated p97^(R155H) ATPase activity. Because the N-terminal domain is spatially far away from the nucleotide-binding site, the intermediate linkers may play a key role in these functional modulations. We went further to study functions of the conserved L464 residue on the D1-D2 linker using mutagenesis and single-particle cryo-EM. The results showed the torsional constraint of the D1-D2 linker likely modulates the D2 ATPase activity, regulating the domain-domain communication in p97 ATPase.", "date": "2022-02-11", "date_type": "published", "publication": "Biophysical Journal", "volume": "121", "number": "3", "publisher": "Biophysical Society", "pagerange": "298a", "id_number": "CaltechAUTHORS:20220422-231850720", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220422-231850720", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.bpj.2021.11.1259", "resource_type": "article", "pub_year": "2022", "author_list": "Nandi, Purbasha; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g4t8n-6vc07", "eprint_id": 113337, "eprint_status": "archive", "datestamp": "2023-10-09 20:56:03", "lastmod": "2023-12-22 23:40:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" } }, { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Rosencrans-William-M", "name": { "family": "Rosencrans", "given": "William M." }, "orcid": "0000-0003-1461-8891" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "The p97 Inhibitor UPCDC-30245 Blocks Endo-Lysosomal Degradation", "ispublished": "pub", "full_text_status": "public", "keywords": "proteomics; p97 inhibitor; lysomotropic agents; endo-lysosomal degradation; coronavirus; Drug Discovery; Pharmaceutical Science; Molecular Medicine", "note": "\u00a9 2022 by the authors. Licensee MDPI, Basel, Switzerland.\nThis article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived: 2 January 2022. Accepted: 27 January 2022. Published: 7 February 2022. \n\nWe thank the Merkin Institute for Translational Research at Caltech for supporting the antiviral research. \n\nThis work was supported in part with funds from the National Institute of Neurological Disorders and Stroke, R01NS100815 and R01NS102279. \n\nAuthor Contributions: F.W. wrote the manuscript. F.W. and S.L. performed all cellular assays and proteomics studies. K.-W.C. assisted with virus experiments. W.M.R. edited the manuscript and provided experimental suggestions. T.-F.C. supervised the project and designed the research. All authors have read and agreed to the published version of the manuscript. \n\nData Availability Statement: All relevant data generated during this study are included in the article and the supplementary Information. The mass spectrometry raw data are deposited to the ProteomeXchance Consortium (https://www.ebi.ac.uk/pride/, accessed on 28, December, 2021) via the PRIDE repository with the dataset identifier PXD025822 and 10.6019/PXD025822\". Additional raw data generated during the current study and relevant information are available from the corresponding authors upon request. The data are not publicly available due to the larger size and complexity. \n\nSupplementary Materials: The following are available online at www.mdpi.com/article/10.3390/ph15020204/s1, Figure S1: (A) Functional enrichment analysis on proteins affected by UPCDC-30245. (B) The log2 fold change of LDLR, APOB and NAGLU from previous and new data set, Figure S2: UPCDC-30245 rapidly reduced the LysoTracker staining in H1299 cells. Table S1: qPCR probes used in this study. \n\nInstitutional Review Board Statement: Not applicable. \n\nInformed Consent Statement: Not applicable. \n\nThe authors declare no conflict of interest.\n\nPublished - pharmaceuticals-15-00204.pdf
Supplemental Material - pharmaceuticals-15-00204-s001.zip
", "abstract": "The diverse modes of action of small molecule inhibitors provide versatile tools to investigate basic biology and develop therapeutics. However, it remains a challenging task to evaluate their exact mechanisms of action. We identified two classes of inhibitors for the p97 ATPase: ATP competitive and allosteric. We showed that the allosteric p97 inhibitor, UPCDC-30245, does not affect two well-known cellular functions of p97, endoplasmic-reticulum-associated protein degradation and the unfolded protein response pathway; instead, it strongly increases the lipidated form of microtubule-associated proteins 1A/1B light chain 3B (LC3-II), suggesting an alteration of autophagic pathways. To evaluate the molecular mechanism, we performed proteomic analysis of UPCDC-30245 treated cells. Our results revealed that UPCDC-30245 blocks endo-lysosomal degradation by inhibiting the formation of early endosome and reducing the acidity of the lysosome, an effect not observed with the potent p97 inhibitor CB-5083. This unique effect allows us to demonstrate UPCDC-30245 exhibits antiviral effects against coronavirus by blocking viral entry.", "date": "2022-02-07", "date_type": "published", "publication": "Pharmaceuticals", "volume": "15", "number": "2", "publisher": "MDPI AG", "pagerange": "Art. No. 204", "id_number": "CaltechAUTHORS:20220208-948531000", "issn": "1424-8247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220208-948531000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "NIH", "grant_number": "R01NS100815" }, { "agency": "NIH", "grant_number": "R01NS102279" } ] }, "local_group": { "items": [ { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.3390/ph15020204", "pmcid": "PMC8880557", "primary_object": { "basename": "pharmaceuticals-15-00204.pdf", "url": "https://authors.library.caltech.edu/records/g4t8n-6vc07/files/pharmaceuticals-15-00204.pdf" }, "related_objects": [ { "basename": "pharmaceuticals-15-00204-s001.zip", "url": "https://authors.library.caltech.edu/records/g4t8n-6vc07/files/pharmaceuticals-15-00204-s001.zip" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Wang, Feng; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3g66e-qr348", "eprint_id": 109293, "eprint_status": "archive", "datestamp": "2023-08-20 05:47:07", "lastmod": "2023-12-22 23:24:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Phan-Quynh-T", "name": { "family": "Phan", "given": "Quynh T." } }, { "id": "Lin-Jianfeng", "name": { "family": "Lin", "given": "Jianfeng" }, "orcid": "0000-0002-5202-6304" }, { "id": "Solis-Norma-V", "name": { "family": "Solis", "given": "Norma V." } }, { "id": "Eng-Michael", "name": { "family": "Eng", "given": "Michael" } }, { "id": "Swidergall-Marc", "name": { "family": "Swidergall", "given": "Marc" }, "orcid": "0000-0002-5261-6267" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" }, "orcid": "0000-0003-4742-2668" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Gaffen-Sarah-L", "name": { "family": "Gaffen", "given": "Sarah L." }, "orcid": "0000-0001-8511-2041" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Filler-Scott-G", "name": { "family": "Filler", "given": "Scott G." }, "orcid": "0000-0001-7278-3700" } ] }, "title": "The Globular C1q Receptor Is Required for Epidermal Growth Factor Receptor Signaling during Candida albicans Infection", "ispublished": "pub", "full_text_status": "public", "keywords": "Candida albicans, oral epithelial cells, endocytosis, epidermal growth factor receptor, host defense", "note": "\u00a9 2021 Phan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 11 September 2021; Accepted 21 September 2021; Published 2 November 2021. \n\nWe thank Adam Diab for assistance with tissue culture. \n\nThe work was supported in part by NIH grants R01DE026600 and R01AI124566 to S.G.F., R00DE026856 to M.S., and DE022550 to S.L.G.\n\nPublished - mBio.02716-21.pdf
Submitted - 2021.05.25.445718v1.full.pdf
Supplemental Material - mbio.02716-21-sf001.pdf
Supplemental Material - mbio.02716-21-sf002.pdf
Supplemental Material - mbio.02716-21-sf003.pdf
Supplemental Material - mbio.02716-21-sf004.pdf
Supplemental Material - mbio.02716-21-sf005.pdf
Supplemental Material - mbio.02716-21-st001.xlsx
Supplemental Material - mbio.02716-21-st002.xlsx
Supplemental Material - mbio.02716-21-st003.xlsx
", "abstract": "During oropharyngeal candidiasis, Candida albicans activates the epidermal growth factor receptor (EGFR), which induces oral epithelial cells to endocytose the fungus and synthesize proinflammatory mediators. To elucidate EGFR signaling pathways that are stimulated by C. albicans, we used proteomics to identify 1,214 proteins that were associated with EGFR in C. albicans-infected cells. Seven of these proteins were selected for additional study. Among these proteins, WW domain-binding protein 2, Toll-interacting protein, interferon-induced transmembrane protein 3 (IFITM3), and the globular C1q receptor (gC1qR) were found to associate with EGFR in viable oral epithelial cells. Each of these proteins was required for maximal endocytosis of C. albicans, and all regulated fungus-induced production of interleukin-1\u03b2 (IL-1\u03b2) and/or IL-8, either positively or negatively. gC1qR was found to function as a key coreceptor with EGFR. Interacting with the C. albicans Als3 invasin, gC1qR was required for the fungus to induce autophosphorylation of both EGFR and the ephrin type A receptor 2. The combination of gC1qR and EGFR was necessary for maximal endocytosis of C. albicans and secretion of IL-1\u03b2, IL-8, and granulocyte-macrophage colony-stimulating factor (GM-CSF) by human oral epithelial cells. In mouse oral epithelial cells, inhibition of gC1qR failed to block C. albicans-induced phosphorylation, and knockdown of IFITM3 did not inhibit C. albicans endocytosis, indicating that gC1qR and IFITM3 function differently in mouse versus human oral epithelial cells. Thus, this work provides an atlas of proteins that associate with EGFR and identifies several that play a central role in the response of human oral epithelial cells to C. albicans infection.", "date": "2021-11", "date_type": "published", "publication": "mBio", "volume": "12", "number": "6", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e02716-21", "id_number": "CaltechAUTHORS:20210528-084342141", "issn": "2150-7511", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210528-084342141", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01DE026600" }, { "agency": "NIH", "grant_number": "R01AI124566" }, { "agency": "NIH", "grant_number": "R00DE026856" }, { "agency": "NIH", "grant_number": "DE022550" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/mBio.02716-21", "pmcid": "PMC8561387", "primary_object": { "basename": "mbio.02716-21-sf005.pdf", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mbio.02716-21-sf005.pdf" }, "related_objects": [ { "basename": "mBio.02716-21.pdf", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mBio.02716-21.pdf" }, { "basename": "mbio.02716-21-sf001.pdf", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mbio.02716-21-sf001.pdf" }, { "basename": "mbio.02716-21-sf002.pdf", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mbio.02716-21-sf002.pdf" }, { "basename": "mbio.02716-21-sf003.pdf", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mbio.02716-21-sf003.pdf" }, { "basename": "mbio.02716-21-st003.xlsx", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mbio.02716-21-st003.xlsx" }, { "basename": "2021.05.25.445718v1.full.pdf", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/2021.05.25.445718v1.full.pdf" }, { "basename": "mbio.02716-21-sf004.pdf", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mbio.02716-21-sf004.pdf" }, { "basename": "mbio.02716-21-st001.xlsx", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mbio.02716-21-st001.xlsx" }, { "basename": "mbio.02716-21-st002.xlsx", "url": "https://authors.library.caltech.edu/records/3g66e-qr348/files/mbio.02716-21-st002.xlsx" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Phan, Quynh T.; Lin, Jianfeng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jt523-xd767", "eprint_id": 111925, "eprint_status": "archive", "datestamp": "2023-10-05 22:28:57", "lastmod": "2023-12-22 23:42:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Ruiz-Lopez-Nallely-M", "name": { "family": "Ruiz-Lopez", "given": "Nallely M." } }, { "id": "Houerbi-Nadia", "name": { "family": "Houerbi", "given": "Nadia" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Impacts of p97 on Proteome Changes in Human Cells during Coronaviral Replication", "ispublished": "pub", "full_text_status": "public", "keywords": "coronavirus; p97; ATPase; proteomics; inhibitor", "note": "\u00a9 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived: 15 September 2021; Accepted: 25 October 2021; Published: 29 October 2021. \n\nThis research was funded by the National Institute of Neurological Disorders and Stroke, grant number R01NS102279, and the Merkin Institute for Translational Research at Caltech. \n\nSupplementary Materials: The following are available online at https://www.mdpi.com/article/10.3390/cells10112953/s1, Figure S1: Full blot images of results shown in Figure 1B; Figure S2: Cell viability of HCoV-infected H1299 cells in the presence of CB-5083; Figure S3: Full blot images of results shown in Figure 2B; Figure S4: Cell viability of HCoV-infected H1299 cells in the stage-limited inhibition assay; Figure S5: Full blot images of results shown in Figure 3B; Figure S6: Knockdown of p97 expression in H1299 cells; Figure S7: Cell viability of H1299 cells with inducible control shRNA (Ctrl shRNA) or p97 shRNA after HCoV infection; Figure S8: Full blot images of results shown in Figure 4B; Figure S9: Overlapping host responses in cells after HCoV-229E, HCoV-OC43, or SARS-CoV-2 infection; Figure S10: Proteins enriched in \"Cellular responses to stress\"; Figure S11: Proteins enriched \"Host interactions of HIV factors\"; Figure S12: Proteins enriched \"Mitotic anaphases\"; Table S1: TagMan probes list; Table S2: Proteomics of H1299 cells with control shRNA and p97 shRNA after HCoV-229E infection; Table S3: Proteomics of H1299 cells with control shRNA and p97 shRNA after HCoV-OC43 infection; Table S4: Reactome pathway enrichment analysis; Table S5: Multi-list Reactome pathway enrichment analysis. \n\nAuthor Contributions: T.-F.C. conceived and supervised the project. K.-W.C. designed and performed experiments. S.L. and F.W. assisted in sample preparation for proteomics. N.M.R.-L. provided technique support for RNA extraction and real-time PCR. S.L., F.W. and N.H. assisted in proteomics data analysis and provided suggestions. K.-W.C. wrote the manuscript with support from T.-F.C., N.M.R.-L. and N.H. edited the manuscript. All authors have read and agreed to the published version of the manuscript. \n\nInstitutional Review Board Statement: Not applicable. \n\nInformed Consent Statement: Not applicable. \n\nData Availability Statement: All relevant data generated during this study are included in the article and the supplementary information. The mass spectrometry raw data are deposited to the ProteomeXchance Consortium (https://www.ebi.ac.uk/pride/ (accessed on 21 October 2021)) via the PRIDE repository with the dataset identifier PXD026216 and 10.6019/PXD026216). Additional raw data generated during the current study and relevant information are available from the corresponding authors upon request. \n\nThe authors declare no conflict of interest.\n\nPublished - cells-10-02953-v2.pdf
Supplemental Material - cells-10-02953-s001.zip
", "abstract": "Human coronavirus (HCoV) similar to other viruses rely on host cell machinery for both replication and to spread. The p97/VCP ATPase is associated with diverse pathways that may favor HCoV replication. In this study, we assessed the role of p97 and associated host responses in human lung cell line H1299 after HCoV-229E or HCoV-OC43 infection. Inhibition of p97 function by small molecule inhibitors shows antiviral activity, particularly at early stages of the virus life cycle, during virus uncoating and viral RNA replication. Importantly, p97 activity inhibition protects human cells against HCoV-induced cytopathic effects. The p97 knockdown also inhibits viral production in infected cells. Unbiased quantitative proteomics analyses reveal that HCoV-OC43 infection resulted in proteome changes enriched in cellular senescence and DNA repair during virus replication. Further analysis of protein changes between infected cells with control and p97 shRNA identifies cell cycle pathways for both HCoV-229E and HCoV-OC43 infection. Together, our data indicate a role for the essential host protein p97 in supporting HCoV replication, suggesting that p97 is a therapeutic target to treat HCoV infection.", "date": "2021-10-29", "date_type": "published", "publication": "Cells", "volume": "10", "number": "11", "publisher": "MDPI", "pagerange": "Art. No. 2953", "id_number": "CaltechAUTHORS:20211117-180505059", "issn": "2073-4409", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211117-180505059", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01NS102279" }, { "agency": "Caltech Merkin Institute for Translational Research" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.3390/cells10112953", "pmcid": "PMC8616207", "primary_object": { "basename": "cells-10-02953-s001.zip", "url": "https://authors.library.caltech.edu/records/jt523-xd767/files/cells-10-02953-s001.zip" }, "related_objects": [ { "basename": "cells-10-02953-v2.pdf", "url": "https://authors.library.caltech.edu/records/jt523-xd767/files/cells-10-02953-v2.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Cheng, Kai-Wen; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pkzqz-wsp80", "eprint_id": 110799, "eprint_status": "archive", "datestamp": "2023-08-20 05:03:49", "lastmod": "2023-12-22 23:19:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Xiaoyi", "name": { "family": "Zhang", "given": "Xiaoyi" }, "orcid": "0000-0001-9732-1449" }, { "id": "Gui-Lin", "name": { "family": "Gui", "given": "Lin" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Nandi-Purbasha", "name": { "family": "Nandi", "given": "Purbasha" }, "orcid": "0000-0002-8047-2029" }, { "id": "Columbres-Rod-Carlo-A", "name": { "family": "Columbres", "given": "Rod Carlo" } }, { "id": "Wong-Daniel-E", "name": { "family": "Wong", "given": "Daniel E." } }, { "id": "Moen-Derek-R", "name": { "family": "Moen", "given": "Derek R." } }, { "id": "Lin-Henry-J", "name": { "family": "Lin", "given": "Henry J." } }, { "id": "Chiu-Po-Lin", "name": { "family": "Chiu", "given": "Po-Lin" }, "orcid": "0000-0001-8608-7650" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Conserved L464 in p97 D1\u2013D2 linker is critical for p97 cofactor regulated ATPase activity", "ispublished": "pub", "full_text_status": "public", "keywords": "anti-caner, cryo-electron microscopy, enzyme kinetics, p97/VCP", "note": "\u00a9 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society. \n\nReceived: April 27 2021; Revision Received: August 10 2021; Accepted: August 18 2021; Accepted Manuscript online: August 18 2021. \n\nCryo-EM data collection was by the use of the Titan Krios TEM at the Eyring Materials Center at Arizona State University, with funding for the instrumentation by NSF MRI 1531991. Special thanks to Dewight Williams for assisting cryo-EM data collection. Computation for image processing was partly supported by the NVIDIA GPU Grant Program. Molecular graphics and analyses performed with the UCSF ChimeraX was supported by NIH R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, NIAID. This project was supported in part with funds from the National Institute of Neurological Disorders and Stroke, R01NS100815 and R01NS102279. \n\nData availability: Cryo-EM density maps were deposited in the Electron Microscopy Data Bank (EMDB) under accession numbers of EMD-23775 and EMD-23776 (symmetrized) and the Protein Data Bank (PDB) under accession numbers of 7MDM and 7MDO (symmetrized). All data are available from the corresponding author upon request. \n\nAuthor Contributions: XZ, LG, SL, PN, PLC, TFC designed the research. XZ, LG, SL, PN, RCC, DEW and DRM performed the research. LG, XZ, SL, PN, DEW, DRM, HJL, PLC and TFC analyzed the data and composed the paper. \n\nThe authors have no competing financial interests to disclose.\n\nAccepted Version - bcj-2021-0288.pdf
Accepted Version - nihms-1797719.pdf
", "abstract": "p97 protein is a highly conserved, abundant, functionally diverse, structurally dynamic homohexameric AAA enzyme-containing N, D1, and D2 domains. A truncated p97 protein containing the N and D1 domains and the D1\u2013D2 linker (ND1L) exhibits 79% of wild-type (WT) ATPase activity whereas the ND1 domain alone without the linker only has 2% of WT activity. To investigate the relationship between the D1\u2013D2 linker and the D1 domain, we produced p97 ND1L mutants and demonstrated that this 22-residue linker region is essential for D1 ATPase activity. The conserved amino acid leucine 464 (L464) is critical for regulating D1 and D2 ATPase activity by p97 cofactors p37, p47, and Npl4\u2013Ufd1 (NU). Changing leucine to alanine, proline, or glutamate increased the maximum rate of ATP turnover (k_(cat)) of p47-regulated ATPase activities for these mutants, but not for WT. p37 and p47 increased the k_(cat) of the proline substituted linker, suggesting that they induced linker conformations facilitating ATP hydrolysis. NU inhibited D1 ATPase activities of WT and mutant ND1L proteins, but activated D2 ATPase activity of full-length p97. To further understand the mutant mechanism, we used single-particle cryo-EM to visualize the full-length p97^(L464P) and revealed the conformational change of the D1\u2013D2 linker, resulting in a movement of the helix-turn-helix motif (543\u2013569). Taken together with the biochemical and structural results we conclude that the linker helps maintain D1 in a competent conformation and relays the communication to/from the N-domain to the D1 and D2 ATPase domains, which are \u223c50 \u00c5 away.", "date": "2021-09-07", "date_type": "published", "publication": "Biochemical Journal", "volume": "478", "number": "17", "publisher": "Biochemical Society", "pagerange": "3185-3204", "id_number": "CaltechAUTHORS:20210910-171152306", "issn": "0264-6021", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210910-171152306", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "MRI-1531991" }, { "agency": "NVIDIA Corporation" }, { "agency": "NIH", "grant_number": "R01-GM129325" }, { "agency": "NIH", "grant_number": "R01NS100815" }, { "agency": "NIH", "grant_number": "R01NS102279" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1042/bcj20210288", "pmcid": "PMC9041309", "primary_object": { "basename": "nihms-1797719.pdf", "url": "https://authors.library.caltech.edu/records/pkzqz-wsp80/files/nihms-1797719.pdf" }, "related_objects": [ { "basename": "bcj-2021-0288.pdf", "url": "https://authors.library.caltech.edu/records/pkzqz-wsp80/files/bcj-2021-0288.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Zhang, Xiaoyi; Gui, Lin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wd2ea-4j472", "eprint_id": 110190, "eprint_status": "archive", "datestamp": "2023-08-20 04:40:20", "lastmod": "2023-12-22 23:24:06", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Le-Steven-Q", "name": { "family": "Le", "given": "Steven Q." } }, { "id": "Kan-Shih-hsin", "name": { "family": "Kan", "given": "Shih-hsin" } }, { "id": "Nu\u00f1ez-Marie", "name": { "family": "Nu\u00f1ez", "given": "Marie" } }, { "id": "Dearborn-Joshua-T", "name": { "family": "Dearborn", "given": "Joshua T." }, "orcid": "0000-0003-0335-1087" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Snella-Elizabeth-M", "name": { "family": "Snella", "given": "Liz" }, "orcid": "0000-0003-1482-2876" }, { "id": "Jens-Jackie-K", "name": { "family": "Jens", "given": "Jackie K." } }, { "id": "Valentine-Bethann-N", "name": { "family": "Valentine", "given": "Bethann N." } }, { "id": "Nelvagal-Hemanth-R", "name": { "family": "Nelvagal", "given": "Hemanth R." }, "orcid": "0000-0003-2407-4517" }, { "id": "Sorensen-Alexander", "name": { "family": "Sorensen", "given": "Alexander" } }, { "id": "Cooper-Jonathan-D", "name": { "family": "Cooper", "given": "Jonathan D." }, "orcid": "0000-0003-1339-4750" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Ellinwood-N-Matthew", "name": { "family": "Ellinwood", "given": "N. Matthew" }, "orcid": "0000-0002-1701-5052" }, { "id": "Smith-Jodi-D", "name": { "family": "Smith", "given": "Jodi D." }, "orcid": "0000-0001-7952-8024" }, { "id": "Sands-Mark-S", "name": { "family": "Sands", "given": "Mark S." }, "orcid": "0000-0002-5559-0832" }, { "id": "Dickson-Patricia-I", "name": { "family": "Dickson", "given": "Patricia I." } } ] }, "title": "Recombinant NAGLU-IGF2 prevents physical and neurological disease and improves survival in Sanfilippo B syndrome", "ispublished": "unpub", "full_text_status": "public", "keywords": "mucopolysaccharidosis, enzyme replacement therapy, glycosaminoglycan, proteomics, lysosomal storage disease", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nVersion 1 - August 8, 2021; Version 2 - September 15, 2021; Version 3 - September 16, 2021. \n\nP.I.D., J.T.D., M.S.S., and J.D.C. designed experiments and prepared the manuscript. S.Q.L., S.-h.K., M.N., and J.T.D. performed mouse experiments. S.Q.L, A.S., H.R.N., and J.D.C. performed quantitative immunofluorescence. L.S., B.N.V., N.M.E., J.J., and J.D.S. performed canine experiments. F.W., S.L, S.Q.L., and T.F.C. performed enzyme assays and/or proteomics on canine tissues. We gratefully acknowledge the assistance and support of Soila Sukipolvi, Irina Zhuravka, George Lopez, Ling Wang, Valentina Sanguez, and Catalina Guerra. BioMarin Pharmaceutical provided vehicle, rhNAGLU, and rhNAGLU-IGF2. BioMarin provided HS measurement of mouse brain and heart tissues. We gratefully acknowledge Roger Lawrence and Brett Crawford for their specific assistance with these assays. \n\nResearch was supported by R01 NS088766 to P.I.D. The Washington University Animal Behavioral services are supported by the Eunice Kennedy Shriver National Institute Of Child Health & Human Development of the National Institutes of Health under Award Number P50 HD103525 to the Intellectual and Developmental Disabilities Research Center at Washington University. A traineeship from 5T32 GM8243-28 (to S.-h.K.) The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The UCLA Behavioral Testing Core is supported by the UCLA Bioscience Core Funding Initiative. Immunofluorescence imaging was performed in part through the use of Washington University Center for Cellular Imaging (WUCCI) supported by Washington University School of Medicine, The Children's Discovery Institute of Washington University and St. Louis Children's Hospital (CDI-CORE-2015-505 and CDI-CORE-2019-813) and the\nFoundation for Barnes-Jewish Hospital (3770 and 4642). \n\nConflicts of Interest: BioMarin Pharmaceutical Inc provided research materials for this study. Dr. Dickson receives research support from Genzyme and research materials from M6P Therapeutics.\n\nSubmitted - 2021.08.06.455469v3.full.pdf
Supplemental Material - media-1.docx
Supplemental Material - media-2.xlsx
", "abstract": "Recombinant human alpha-N-acetylglucosaminidase-insulin-like growth factor-2 (rhNAGLU-IGF2) is an investigational enzyme replacement therapy for Sanfilippo B, a lysosomal storage disease. Because recombinant human NAGLU (rhNAGLU) is poorly mannose 6-phosphorylated, we generated a fusion protein of NAGLU with IGF2 to permit its binding to the cation-independent mannose 6-phosphate receptor. We previously administered rhNAGLU-IGF2 intracerebroventricularly to Sanfilippo B mice, and demonstrated therapeutic restoration of NAGLU, normalization of lysosomal storage, and improvement in markers of neurodegeneration and inflammation. Here, we studied intracerebroventricular rhNAGLU-IGF2 delivery in both murine and canine Sanfilippo B to determine potential effects on their behavioral phenotypes and survival. Treated mice showed improvement in disease markers such as heparan sulfate glycosaminoglycans, beta-hexosaminidase, microglial activation, and lysosomal-associated membrane protein-1. Sanfilippo B mice treated with rhNAGLU-IGF2 displayed partial normalization of their stretch attend postures, a defined fear pose in mice (p<0.001). We found a more normal dark/light activity pattern in Sanfilippo B mice treated with rhNAGLU-IGF2 compared to vehicle-treated Sanfilippo B mice (p=0.025). We also found a 61% increase in survival in Sanfilippo B mice treated with rhNAGLU-IGF2 (mean 53w, median 48w) compared to vehicle-treated Sanfilippo B mice (mean 33w, median 37w; p<0.001). In canine Sanfilippo B, we found that rhNAGLU-IGF2 administered into cerebrospinal fluid normalized HS and beta-hexosaminidase activity in gray and white matter brain regions. Proteomic analysis of cerebral cortex showed restoration of protein expression levels in pathways relevant to cognitive function, synapse, and the lysosome. These data suggest that treatment with rhNAGLU-IGF2 may improve the phenotype of Sanfilippo B disease.", "date": "2021-08-11", "date_type": "published", "id_number": "CaltechAUTHORS:20210810-163528980", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210810-163528980", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 NS088766" }, { "agency": "NIH", "grant_number": "P50 HD103525" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32 GM8243-28" }, { "agency": "UCLA" }, { "agency": "Washington University" }, { "agency": "Children's Discovery Institute" }, { "agency": "St. Louis Children's Hospital Foundation", "grant_number": "CDI-CORE-2015-505" }, { "agency": "St. Louis Children's Hospital Foundation", "grant_number": "CDI-CORE-2019-813" }, { "agency": "Foundation for Barnes-Jewish Hospital", "grant_number": "3770" }, { "agency": "Foundation for Barnes-Jewish Hospital", "grant_number": "4642" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.08.06.455469", "primary_object": { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/wd2ea-4j472/files/media-2.xlsx" }, "related_objects": [ { "basename": "2021.08.06.455469v3.full.pdf", "url": "https://authors.library.caltech.edu/records/wd2ea-4j472/files/2021.08.06.455469v3.full.pdf" }, { "basename": "media-1.docx", "url": "https://authors.library.caltech.edu/records/wd2ea-4j472/files/media-1.docx" } ], "resource_type": "monograph", "pub_year": "2021", "author_list": "Le, Steven Q.; Kan, Shih-hsin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rz697-6hm65", "eprint_id": 109168, "eprint_status": "archive", "datestamp": "2023-10-03 22:43:11", "lastmod": "2023-12-22 23:14:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Michels-Dana-E", "name": { "family": "Michels", "given": "Dana E." } }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" } }, { "id": "Sweredoski-Michael-J", "name": { "family": "Sweredoski", "given": "Michael J." }, "orcid": "0000-0003-0878-3831" }, { "id": "Pasulka-Alexis", "name": { "family": "Pasulka", "given": "Alexis" }, "orcid": "0000-0001-5930-8825" } ] }, "title": "Amino Acid Analog Induces Stress Response in Marine Synechococcus", "ispublished": "pub", "full_text_status": "public", "keywords": "BONCAT, picocyanobacteria, proteomics, synechococcus", "note": "\u00a9 2021 American Society for Microbiology. \n\nReceived 27 January 2021; Accepted 8 May 2021; Accepted manuscript posted online 14 May 2021; Published 13 July 2021. \n\nWe thank Pete Countway (NCMA at the Bigelow Laboratory) for kindly providing all algal cultures, Jeff Jones (Proteomic Exploration Laboratory at California Institute of Technology) for his thoughtful insights into proteomic data analysis and interpretation, and Victoria Orphan (California Institute of Technology) for her continued professional support. We also thank Cal Poly undergraduate students Julia Kallet, Will Hammond, Ardea Batiste, and Mark Dizon for assistance with algal culturing, experiments, and sample processing. \n\nThis study was funded by the Research Scholarly and Creative Activities Grant program at Cal Poly, the Dr. Earl H. Myers & Ethel M. Myers Oceanographic & Marine Biology Trust, and the Cal Poly Baker and Koob Endowment. \n\nData availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (76) with the data set identifier PXD023371.\n\nPublished - AEM00200-21.pdf
Accepted Version - Applied_and_Environmental_Microbiology-2021-Michels-AEM00200-21full.pdf
", "abstract": "Characterizing the cell-level metabolic trade-offs that phytoplankton exhibit in response to changing environmental conditions is important for predicting the impact of these changes on marine food web dynamics and biogeochemical cycling. The time-selective proteome-labeling approach, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to provide insight into differential allocation of resources at the cellular level, especially when coupled with proteomics. However, the application of this technique in marine phytoplankton remains limited. We demonstrate that the marine cyanobacteria Synechococcus sp. and two groups of eukaryotic algae take up the modified amino acid l-homopropargylglycine (HPG), suggesting that BONCAT can be used to detect translationally active phytoplankton. However, the impact of HPG addition on growth dynamics varied between groups of phytoplankton. In addition, proteomic analysis of Synechococcus cells grown with HPG revealed a physiological shift in nitrogen metabolism, general protein stress, and energy production, indicating a potential limitation for the use of BONCAT in understanding the cell-level response of Synechococcus sp. to environmental change. Variability in HPG sensitivity between algal groups and the impact of HPG on Synechococcus physiology indicates that particular considerations should be taken when applying this technique to other marine taxa or mixed marine microbial communities.", "date": "2021-08", "date_type": "published", "publication": "Applied and Environmental Microbiology", "volume": "87", "number": "15", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e00200-21", "id_number": "CaltechAUTHORS:20210518-092014570", "issn": "0099-2240", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210518-092014570", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "California Polytechnic State University" }, { "agency": "Dr. Earl H. Myers & Ethel M. Myers Oceanographic & Marine Biology Trust" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/aem.00200-21", "primary_object": { "basename": "AEM00200-21.pdf", "url": "https://authors.library.caltech.edu/records/rz697-6hm65/files/AEM00200-21.pdf" }, "related_objects": [ { "basename": "Applied_and_Environmental_Microbiology-2021-Michels-AEM00200-21full.pdf", "url": "https://authors.library.caltech.edu/records/rz697-6hm65/files/Applied_and_Environmental_Microbiology-2021-Michels-AEM00200-21full.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Michels, Dana E.; Lomenick, Brett; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/re22y-aq279", "eprint_id": 110339, "eprint_status": "archive", "datestamp": "2023-08-22 10:36:21", "lastmod": "2023-12-22 23:24:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nandi-Purbasha", "name": { "family": "Nandi", "given": "Purbasha" }, "orcid": "0000-0002-8047-2029" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Columbres-Rod-Carlo-A", "name": { "family": "Columbres", "given": "Rod Carlo A." } }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Williams-Dewight-R", "name": { "family": "Williams", "given": "Dewight R." } }, { "id": "Poh-Yu-Ping", "name": { "family": "Poh", "given": "Yu-Ping" }, "orcid": "0000-0001-6709-2147" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Chiu-Po-Lin", "name": { "family": "Chiu", "given": "Po-Lin" }, "orcid": "0000-0001-8608-7650" } ] }, "title": "Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes", "ispublished": "pub", "full_text_status": "public", "keywords": "p97 ATPase; p97^(R155H) mutation; p47 cofactor; arginine finger; IBMPFD; single-particle cryo-EM", "note": "\u00a9 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\nReceived: 2 July 2021; Accepted: 25 July 2021; Published: 28 July 2021. \n\nWe thank Ellen Zhong (Massachusetts Institute of Technology) for the brief discussion on the data analysis using cryoDRGN neural networks. We thank Xiaoyi Zhang, Gui Lin, and Daniel Wong for preliminary ATPase activity determination for p97 mutants. We thank Andrey Malyutin for assisting in sample screening at the Beckman Caltech Cryo-EM Center. \n\nWe acknowledge using the Titan Krios TEM in the Eyring Materials Center (EMC) at Arizona State University (ASU) and funding for the instrumentation from grant number NSF MRI 1531991. We thank the NVIDIA GPU Grant Program to P.-L.C for GPU device support. The project was partially supported by a grant from the National Institute of Neurological Disorders and Stroke (NINDS) (R01NS102279) to T.-F.C. and the ASU startup fund to P.-L.C. \n\nAuthor Contributions: Conceptualization, T.-F.C. and P.-L.C.; investigation, formal analysis, and data curation, P.N., S.L., R.C.A.C., F.W., Y.-P.P., D.R.W. and P.-L.C.; supervision and validation, T.-F.C. and P.-L.C.; writing, P.N., T.-F.C. and P.-L.C. All authors have read and agreed to the published version of the manuscript. \n\nInstitutional Review Board Statement: Not applicable. \n\nInformed Consent Statement: Not applicable. \n\nData Availability Statement: Cryo-EM density maps have been deposited in the Electron Microscopy Data Bank (EMDB) under accession numbers EMD-24302 (p97^(R155H)|ATP\u03b3S-p47), EMD-24305 (p97^(R155H)-p47), EMD-23191 (p97^(R155H) dodecamer), EMD-24304 (p97^(R155H)|ADP-p47), and EMD-23192 (p97^(R155H) dodecamer II). Model coordinates were deposited in the Protein Data Bank (PDB) under accession numbers 7R7S (p97^(R155H)|ATP\u03b3S-p47), 7R7U (p97^(R155H)-p47), 7L5W (p97^(R155H) dodecamer), and 7R7T (p97^(R155H)|ADP-p47). All data are available from the corresponding authors upon request.\n\nPublished - ijms-22-08079-v2.pdf
Supplemental Material - ijms-22-08079-s001.zip
", "abstract": "IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation alters the ATPase regulation, we assembled a full-length p97^(R155H) with its p47 cofactor and first visualized their structures using single-particle cryo-EM. More than one-third of the population was the dodecameric form. Nucleotide presence dissociates the dodecamer into two hexamers for its highly elevated function. The N-domains of the p97^(R155H) mutant all show up configurations in ADP- or ATP\u03b3S-bound states. Our functional and structural analyses showed that the p47 binding is likely to impact the p97^(R155H) ATPase activities via changing the conformations of arginine fingers. These functional and structural analyses underline the ATPase dysregulation with the miscommunication between the functional modules of the p97^(R155H).", "date": "2021-07-28", "date_type": "published", "publication": "International Journal of Molecular Sciences", "volume": "22", "number": "15", "publisher": "MDPI", "pagerange": "Art. No. 8079", "id_number": "CaltechAUTHORS:20210820-234106808", "issn": "1422-0067", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210820-234106808", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "MRI-1531991" }, { "agency": "NVIDIA Corporation" }, { "agency": "NIH", "grant_number": "R01NS102279" }, { "agency": "Arizona State University" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.3390/ijms22158079", "pmcid": "PMC8347982", "primary_object": { "basename": "ijms-22-08079-s001.zip", "url": "https://authors.library.caltech.edu/records/re22y-aq279/files/ijms-22-08079-s001.zip" }, "related_objects": [ { "basename": "ijms-22-08079-v2.pdf", "url": "https://authors.library.caltech.edu/records/re22y-aq279/files/ijms-22-08079-v2.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Nandi, Purbasha; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/a8drt-w9233", "eprint_id": 110204, "eprint_status": "archive", "datestamp": "2023-08-20 04:17:38", "lastmod": "2023-12-22 23:24:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wani-Abubakar", "name": { "family": "Wani", "given": "Abubakar" }, "orcid": "0000-0001-7079-3278" }, { "id": "Zhu-Jiang", "name": { "family": "Zhu", "given": "Jiang" } }, { "id": "Ulrich-Jason-D", "name": { "family": "Ulrich", "given": "Jason D." }, "orcid": "0000-0002-4743-926X" }, { "id": "Eteleeb-Abdallah", "name": { "family": "Eteleeb", "given": "Abdallah" } }, { "id": "Sauerbeck-Andrew-D", "name": { "family": "Sauerbeck", "given": "Andrew D." } }, { "id": "Reitz-Sydney-J", "name": { "family": "Reitz", "given": "Sydney J." } }, { "id": "Arhzaouy-Khalid", "name": { "family": "Arhzaouy", "given": "Khalid" } }, { "id": "Ikenaga-Chiseko", "name": { "family": "Ikenaga", "given": "Chiseko" }, "orcid": "0000-0003-2264-1696" }, { "id": "Yuede-Carla-M", "name": { "family": "Yuede", "given": "Carla M." }, "orcid": "0000-0001-6362-4767" }, { "id": "Pittman-Sara-K", "name": { "family": "Pittman", "given": "Sara K." } }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Benitez-Bruno-A", "name": { "family": "Benitez", "given": "Bruno A." }, "orcid": "0000-0002-2699-3878" }, { "id": "Cruchaga-Carlos", "name": { "family": "Cruchaga", "given": "Carlos" }, "orcid": "0000-0002-0276-2899" }, { "id": "Kummer-Terrance-T", "name": { "family": "Kummer", "given": "Terrance T." }, "orcid": "0000-0001-8938-8280" }, { "id": "Harari-Oscar", "name": { "family": "Harari", "given": "Oscar" }, "orcid": "0000-0002-2635-6975" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Schr\u00f6der-Rolf", "name": { "family": "Schr\u00f6der", "given": "Rolf" }, "orcid": "0000-0002-2772-2615" }, { "id": "Clemen-Christoph-S", "name": { "family": "Clemen", "given": "Christoph S." }, "orcid": "0000-0002-1291-4219" }, { "id": "Weihl-Conrad-C", "name": { "family": "Weihl", "given": "Conrad C." }, "orcid": "0000-0002-3816-6124" } ] }, "title": "Neuronal VCP loss of function recapitulates FTLD-TDP pathology", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). \n\nReceived 4 January 2021, Revised 6 April 2021, Accepted 22 June 2021, Available online 21 July 2021. \n\nThis work was supported by NIH grants K24AR073317 and R01AG031867 (to C.C.W.); I01BX005204 to (T.T.K.); R01AG044546, P01AG003991, P30AG066444, RF1AG053303, RF1AG058501, and U01AG058922 (to C.C.); R01AG057777 (to O.H.); R01NS118146 (to B.A.B.); and R01NS102279 (to T.F.C. and C.C.W.). O.H. is supported as an Archer Foundation Research Scientist. \n\nAuthor contributions: A.W., J.Z., J.D.U., A.E., A.D.S., S.J.R., K.A., S.K.P., F.W., S.L., and B.A.B. performed experiments. A.W., J.Z., J.D.U., A.E., A.D.S., C.I., C.M.Y., C.C., T.T.K., O.H., T.-F.C., R.S., C.S.C., and C.C.W. analyzed data. C.C.W. and O.H. guided experiments. C.C.W. and A.W. wrote the initial manuscript and edited subsequent versions of the manuscript. O.H., J.D.U., T.T.K., and T.-F.C. wrote critical sections of the manuscript. C.C.W. edited and wrote the final version of the manuscript. All authors reviewed and edited the final version of the manuscript. C.C.W. conceived the project and directed all experiments. \n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S221112472100797X-main.pdf
Supplemental Material - 1-s2.0-S221112472100797X-mmc1.pdf
Supplemental Material - 1-s2.0-S221112472100797X-mmc2.xlsx
Supplemental Material - 1-s2.0-S221112472100797X-mmc3.xlsx
Supplemental Material - 1-s2.0-S221112472100797X-mmc4.xlsx
", "abstract": "The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivate VCP in murine postnatal forebrain neurons (VCP conditional knockout [cKO]). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction, and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulates features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency.", "date": "2021-07-20", "date_type": "published", "publication": "Cell Reports", "volume": "36", "number": "3", "publisher": "Cell Press", "pagerange": "Art. No. 109399", "id_number": "CaltechAUTHORS:20210811-212815828", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210811-212815828", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K24AR073317" }, { "agency": "NIH", "grant_number": "R01AG031867" }, { "agency": "NIH", "grant_number": "I01BX005204" }, { "agency": "NIH", "grant_number": "R01AG044546" }, { "agency": "NIH", "grant_number": "P01AG003991" }, { "agency": "NIH", "grant_number": "P30AG066444" }, { "agency": "NIH", "grant_number": "RF1AG053303" }, { "agency": "NIH", "grant_number": "RF1AG058501" }, { "agency": "NIH", "grant_number": "U01AG058922" }, { "agency": "NIH", "grant_number": "R01AG057777" }, { "agency": "NIH", "grant_number": "R01NS118146" }, { "agency": "NIH", "grant_number": "R01NS102279" }, { "agency": "Archer Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.celrep.2021.109399", "pmcid": "PMC8383344", "primary_object": { "basename": "1-s2.0-S221112472100797X-main.pdf", "url": "https://authors.library.caltech.edu/records/a8drt-w9233/files/1-s2.0-S221112472100797X-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S221112472100797X-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/a8drt-w9233/files/1-s2.0-S221112472100797X-mmc1.pdf" }, { "basename": "1-s2.0-S221112472100797X-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/a8drt-w9233/files/1-s2.0-S221112472100797X-mmc2.xlsx" }, { "basename": "1-s2.0-S221112472100797X-mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/a8drt-w9233/files/1-s2.0-S221112472100797X-mmc3.xlsx" }, { "basename": "1-s2.0-S221112472100797X-mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/a8drt-w9233/files/1-s2.0-S221112472100797X-mmc4.xlsx" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Wani, Abubakar; Zhu, Jiang; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8zw84-m8x34", "eprint_id": 108705, "eprint_status": "archive", "datestamp": "2023-08-22 10:28:35", "lastmod": "2023-12-22 23:13:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Gang", "name": { "family": "Zhang", "given": "Gang" }, "orcid": "0000-0003-0774-5710" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" } }, { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors", "ispublished": "pub", "full_text_status": "public", "keywords": "AAA ATPases; Small molecule inhibitors; p97; RUVBL1/2; ATAD2", "note": "\u00a9 2021 Elsevier Masson SAS. \n\nReceived 6 October 2020, Revised 21 March 2021, Accepted 30 March 2021, Available online 10 April 2021. \n\nAAA ATPase related work in the Chou lab was funded in part by the National Institutes of Health, National Institute of Neurological Disorders and Stroke, R01NS100815 and R01NS102279; National Institute of Child Health and Human Development R01 HD086596. Work on p97 in the authors' laboratories has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024, Task Order No. 75N091019F00129. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the U.S. Government. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nAccepted Version - nihms-1692797.pdf
", "abstract": "ATPases Associated with Diverse Cellular Activity (AAA ATPase) are essential enzymes found in all organisms. They are involved in various processes such as DNA replication, protein degradation, membrane fusion, microtubule serving, peroxisome biogenesis, signal transduction, and the regulation of gene expression. Due to the importance of AAA ATPases, several researchers identified and developed small-molecule inhibitors against these enzymes. We discuss six AAA ATPases that are potential drug targets and have well-developed inhibitors. We compare available structures that suggest significant differences of the ATP binding pockets among the AAA ATPases with or without ligand. The distances from ADP to the His20 in the His-Ser-His motif and the Arg finger (Arg353 or Arg378) in both RUVBL1/2 complex structures bound with or without ADP have significant differences, suggesting dramatically different interactions of the binding site with ADP. Taken together, the inhibitors of six well-studied AAA ATPases and their structural information suggest further development of specific AAA ATPase inhibitors due to difference in their structures. Future chemical biology coupled with proteomic approaches could be employed to develop variant specific, complex specific, and pathway specific inhibitors or activators for AAA ATPase proteins.", "date": "2021-07-05", "date_type": "published", "publication": "European Journal of Medicinal Chemistry", "volume": "219", "publisher": "Elsevier", "pagerange": "Art. No. 113446", "id_number": "CaltechAUTHORS:20210413-071559531", "issn": "0223-5234", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210413-071559531", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01NS100815" }, { "agency": "NIH", "grant_number": "R01NS102279" }, { "agency": "NIH", "grant_number": "R01 HD086596" }, { "agency": "NIH", "grant_number": "75N91019D00024" }, { "agency": "NIH", "grant_number": "75N091019F00129" }, { "agency": "National Cancer Institute" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.ejmech.2021.113446", "pmcid": "PMC8165034", "primary_object": { "basename": "nihms-1692797.pdf", "url": "https://authors.library.caltech.edu/records/8zw84-m8x34/files/nihms-1692797.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Zhang, Gang; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/mt5z7-xxt77", "eprint_id": 109679, "eprint_status": "archive", "datestamp": "2023-08-22 10:15:28", "lastmod": "2023-12-22 23:13:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yang-Xiaohong", "name": { "family": "Yang", "given": "Xiaohong" } }, { "id": "Yang-Xiaoxiao", "name": { "family": "Yang", "given": "Xiaoxiao" } }, { "id": "Yu-Hai", "name": { "family": "Yu", "given": "Hai" } }, { "id": "Na-Lan", "name": { "family": "Na", "given": "Lan" } }, { "id": "Ghosh-Tamashree", "name": { "family": "Ghosh", "given": "Tamashree" } }, { "id": "McArthur-John-B", "name": { "family": "McArthur", "given": "John B." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Dickson-Patricia", "name": { "family": "Dickson", "given": "Patricia" } }, { "id": "Chen-Xi-CHEM", "name": { "family": "Chen", "given": "Xi" }, "orcid": "0000-0002-3160-614X" } ] }, "title": "A GH89 human \u03b1-N-acetylglucosaminidase (hNAGLU) homologue from gut microbe Bacteroides thetaiotaomicron capable of hydrolyzing heparosan oligosaccharides", "ispublished": "pub", "full_text_status": "public", "keywords": "\u03b1-N-Acetylglucosaminidase; NAGLU; Bacterial glycoside hydrolases; Heparosan oligosaccharides; Bacteroides thetaiotaomicron", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 07 June 2021; Accepted 15 June 2021; Published 24 June 2021. \n\nThis work was financially supported in part by the United States (US) National Institutes of Health (NIH) Grant Number U01GM125288 (to HY) and Million Dollar Bike Ride Grant Program form the Orphan Disease Center in the University of Pennsylvania (to PD). \n\nAvailability of data and materials: All data generated or analyzed during this study are included in this published article. \n\nEthics approval and consent to participation: Not applicable. \n\nConsent for publication: Not applicable. \n\nThe authors declare no competing interests.\n\nPublished - Yang2021_Article_AGH89Human\u0391-N-acetylglucosamin.pdf
", "abstract": "Carbohydrate-Active enZYme (CAZY) GH89 family enzymes catalyze the cleavage of terminal \u03b1-N-acetylglucosamine from glycans and glycoconjugates. Although structurally and mechanistically similar to the human lysosomal \u03b1-N-acetylglucosaminidase (hNAGLU) in GH89 which is involved in the degradation of heparan sulfate in the lysosome, the reported bacterial GH89 enzymes characterized so far have no or low activity toward \u03b1-N-acetylglucosamine-terminated heparosan oligosaccharides, the preferred substrates of hNAGLU. We cloned and expressed several soluble and active recombinant bacterial GH89 enzymes in Escherichia coli. Among these enzymes, a truncated recombinant \u03b1-N-acetylglucosaminidase from gut symbiotic bacterium Bacteroides thetaiotaomicron \u220622Bt3590 was found to catalyze the cleavage of the terminal \u03b11\u20134-linked N-acetylglucosamine (GlcNAc) from a heparosan disaccharide with high efficiency. Heparosan oligosaccharides with lengths up to decasaccharide were also suitable substrates. This bacterial \u03b1-N-acetylglucosaminidase could be a useful catalyst for heparan sulfate analysis.", "date": "2021-06-24", "date_type": "published", "publication": "AMB Express", "volume": "11", "publisher": "Springer", "pagerange": "Art. No. 94", "id_number": "CaltechAUTHORS:20210630-194140069", "issn": "2191-0855", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210630-194140069", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U01GM125288" }, { "agency": "University of Pennsylvania" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1186/s13568-021-01253-1", "pmcid": "PMC8225759", "primary_object": { "basename": "Yang2021_Article_AGH89Human\u0391-N-acetylglucosamin.pdf", "url": "https://authors.library.caltech.edu/records/mt5z7-xxt77/files/Yang2021_Article_AGH89Human\u0391-N-acetylglucosamin.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Yang, Xiaohong; Yang, Xiaoxiao; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rbtj2-3s832", "eprint_id": 109997, "eprint_status": "archive", "datestamp": "2023-08-20 03:32:12", "lastmod": "2023-12-22 23:23:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cheng-Kai-Wen", "name": { "family": "Cheng", "given": "Kai-Wen" }, "orcid": "0000-0001-9888-9773" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Lopez-George-A", "name": { "family": "Lopez", "given": "George A." } }, { "id": "Singamsetty-Srikanth", "name": { "family": "Singamsetty", "given": "Srikanth" } }, { "id": "Wood-Jill", "name": { "family": "Wood", "given": "Jill" } }, { "id": "Dickson-Patricia-I", "name": { "family": "Dickson", "given": "Patricia I." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Evaluation of artificial signal peptides for secretion of two lysosomal enzymes in CHO cells", "ispublished": "pub", "full_text_status": "public", "keywords": "N-acetyl-\u03b1-glucosaminidase (NAGLU), enzyme replacement therapy, mucopolysaccharidosis, N-acetylglucosamine-6-sulfatase (GNS), signal peptide", "note": "\u00a9 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society. \n\nReceived: January 12 2021; Revision Received: May 24 2021; Accepted: May 24 2021; Accepted Manuscript online: May 25 2021. \n\nThis project was supported in part by the National Institute of Neurological Disorders and Stroke U44NS089061 to Phoenix Nest Inc. We thank William Rosencrans and Nadia Houerbi for proofreading our final manuscript. \n\nAuthor contributions statement: T.-F. Chou conceived the project. K.-W. Cheng designed and performed experiments. F. Wang constructed the pOptiVEC-TOPO-rhGNS-TEV-myc plasmid. G. A. Lopez constructed the pOptiVECTOPO-rhNAGLU-myc plasmid. F. Wang and G. A. Lopez assisted in eliminating problems during experiments and provided suggestions. K.-W. Cheng, and T.-F. Chou wrote the manuscript. S. Singamsetty, J. Wood, and P.I. Dickson, and T.-F. Chou provided suggestions, edited the manuscript and obtained funding for this work. \n\nThe authors declare no conflicts of interest. \n\nDisclosure: SS, and JW are Phoenix Nest Inc. employees. \n\nData availability statement: Most data generated during this study are included in the article and its Supplementary Information. \n\nUncropped images of all gels and blots can be found in Supplementary Figures 1 to 3. Additional measurements such as protein concentrations and enzymatic activities generated during the current study and relevant information are available from the corresponding authors upon request.\n\nAccepted Version - bcj-2021-0015.pdf
Accepted Version - nihms-1797714.pdf
", "abstract": "Enzyme replacement therapy (ERT) is a scientifically rational and clinically proven treatment for lysosomal storage diseases. Most enzymes used for ERT are purified from the culture supernatant of mammalian cells. However, it is challenging to purify lysosomal enzymes with sufficient quality and quantity for clinical use due to their low secretion levels in mammalian cell systems. To improve the secretion efficiency of recombinant lysosomal enzymes, we evaluated the impact of artificial signal peptides on the production of recombinant lysosomal enzymes in Chinese hamster ovary (CHO) cell lines. We engineered two recombinant human lysosomal enzymes, N-acetyl-\u03b1-glucosaminidase (rhNAGLU) and glucosamine (N-acetyl)-6-sulfatase (rhGNS), by replacing their native signal peptides with nine different signal peptides derived from highly secretory proteins and expressed them in CHO K1 cells. When comparing the native signal peptides, we found that rhGNS was secreted into media at higher levels than rhNAGLU. The secretion of rhNAGLU and rhGNS can, however, be carefully controlled by altering signal peptides. The secretion of rhNAGLU was relatively higher with murine Ig\u03ba light chain and human chymotrypsinogen B1 signal peptides, whereas Ig\u03ba light chain signal peptide 1 and human chymotrypsinogen B1 signal peptides were more effective for rhGNS secretion, suggesting that human chymotrypsinogen B1 signal peptide is the most appropriate for increasing lysosomal enzyme secretion. Collectively, our results indicate that altering signal peptide can modulate the secretion of recombinant lysosome enzymes and will enable lysosomal enzyme production for clinical use.", "date": "2021-06", "date_type": "published", "publication": "Biochemical Journal", "volume": "478", "number": "12", "publisher": "Biochemical Society", "pagerange": "2309-2319", "id_number": "CaltechAUTHORS:20210723-172036186", "issn": "0264-6021", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210723-172036186", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U44NS089061" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1042/bcj20210015", "pmcid": "PMC9074758", "primary_object": { "basename": "bcj-2021-0015.pdf", "url": "https://authors.library.caltech.edu/records/rbtj2-3s832/files/bcj-2021-0015.pdf" }, "related_objects": [ { "basename": "nihms-1797714.pdf", "url": "https://authors.library.caltech.edu/records/rbtj2-3s832/files/nihms-1797714.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Cheng, Kai-Wen; Wang, Feng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5b58b-qz615", "eprint_id": 107308, "eprint_status": "archive", "datestamp": "2023-08-22 09:12:23", "lastmod": "2023-12-22 23:23:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Gang", "name": { "family": "Zhang", "given": "Gang" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" } }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Jones-Amanda-C", "name": { "family": "Jones", "given": "Amanda C." }, "orcid": "0000-0001-7445-8311" }, { "id": "Goldberg-Alexander-F-G", "name": { "family": "Goldberg", "given": "Alexander F. G." } }, { "id": "Lin-Benjamin", "name": { "family": "Lin", "given": "Benjamin" }, "orcid": "0000-0002-0580-6818" }, { "id": "Virgil-Scott-C", "name": { "family": "Virgil", "given": "Scott" }, "orcid": "0000-0001-8586-5641" }, { "id": "Stoltz-B-M", "name": { "family": "Stoltz", "given": "Brian M." }, "orcid": "0000-0001-9837-1528" }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "A covalent p97/VCP ATPase inhibitor can overcome resistance to CB-5083 and NMS-873 in colorectal cancer cells", "ispublished": "pub", "full_text_status": "public", "keywords": "P97; Covalent inhibitor; ATPase Activity; Organic Synthesis; Docking; Anti-proliferative activity; Proteomics", "note": "\u00a9 2021 Elsevier Masson SAS. \n\nReceived 22 November 2020, Revised 16 December 2020, Accepted 28 December 2020, Available online 2 January 2021. \n\nWe thank M. S. Cohen, J. Taunton, and K. Shokat for providing compounds 4,5,6, M. Smythe and C. Crews for YU101, A. M. Weissman for PYR-41, C. C. Wu for \u03b2-nitrostyrene analogues (compounds 7, 9,10,11,12), Y. Ye at NIDDK/NIH for providing yeast Cdc48 and hamster NSF plasmids. A.C.J. was supported by NIH Grant F32GM082000; A.F.G.G thanks the Natural Sciences and Engineering Research Council (NSERC) of Canada for a PGS D scholarship; R.J.D. was an HHMI Investigator, and this work was funded in part by HHMI; This work was funded in part by the NIH-NINDS (R01NS102279) to T.F.C. and NIH-NIGMS (R01GM080269) to B.M.S. We thank the anonymous reviewers for constructive criticism. \n\nAuthor contributions: Gang Zhang wrote the manuscript and analyzed the potential interaction between PPA and p97 by molecular docking. Shan Li and Feng Wang performed the anti-proliferative assay and proteomics study. Amanda C. Jones, Alexander F. G. Goldberg, and Scott Virgil synthesized and characterized the target compounds. Tsui-Fen Chou performed experiments in Table 1, Table 2, Table 3, Table 4; Fig. 2, Fig. 4. Amanda C. Jones, Brian M. Stoltz, Raymond J. Deshaies, and Tsui-Fen Chou conceived the project and made the major contribution in the design of the initial work. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nAccepted Version - nihms-1659547.pdf
Supplemental Material - 1-s2.0-S022352342031120X-mmc1.docx
", "abstract": "Small-molecule inhibitors of p97 are useful tools to study p97 function. Human p97 is an important AAA ATPase due to its diverse cellular functions and implication in mediating the turnover of proteins involved in tumorigenesis and virus infections. Multiple p97 inhibitors identified from previous high-throughput screening studies are thiol-reactive compounds targeting Cys522 in the D2 ATP-binding domain. Thus, these findings suggest a potential strategy to develop covalent p97 inhibitors. We first used purified p97 to assay several known covalent kinase inhibitors to determine if they can inhibit ATPase activity. We evaluated their selectivity using our dual reporter cells that can distinguish p97 dependent and independent degradation. We selected a \u03b2-nitrostyrene scaffold to further study the structure-activity relationship. In addition, we used p97 structures to design and synthesize analogues of pyrazolo[3,4-d]pyrimidine (PP). We incorporated electrophiles into a PP-like compound 17 (4-amino-1-tert-butyl-3-phenyl pyrazolo[3,4-d]pyrimidine) to generate eight compounds. A selective compound 18 (N-(1-(tert-butyl)-3-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl)acrylamide, PPA) exhibited excellent selectivity in an in vitro ATPase activity assay: IC50 of 0.6 \u03bcM, 300 \u03bcM, and 100 \u03bcM for wild type p97, yeast Cdc48, and N-ethylmaleimide sensitive factor (NSF), respectively. To further examine the importance of Cys522 on the active site pocket during PPA inhibition, C522A and C522T mutants of p97 were purified and shown to increase IC50 values by 100-fold, whereas replacement of Thr532 of yeast Cdc48 with Cysteine decreased the IC50 by 10-fold. The molecular modeling suggested the hydrogen bonds and hydrophobic interactions in addition to the covalent bonding at Cys522 between WT-p97 and PPA. Furthermore, tandem mass spectrometry confirmed formation of a covalent bond between Cys522 and PPA. An anti-proliferation assay indicated that the proliferation of HCT116, HeLa, and RPMI8226 was inhibited by PPA with IC50 of 2.7 \u03bcM, 6.1 \u03bcM, and 3.4 \u03bcM, respectively. In addition, PPA is able to inhibit proliferation of two HCT116 cell lines that are resistant to CB-5083 and NMS-873, respectively. Proteomic analysis of PPA-treated HCT116 revealed Gene Ontology enrichment of known p97 functional pathways such as the protein ubiquitination and the ER to Golgi transport vesicle membrane. In conclusion, we have identified and characterized PPA as a selective covalent p97 inhibitor, which will allow future exploration to improve the potency of p97 inhibitors with different mechanisms of action.", "date": "2021-03-05", "date_type": "published", "publication": "European Journal of Medicinal Chemistry", "volume": "213", "publisher": "Elsevier", "pagerange": "Art. No. 113148", "id_number": "CaltechAUTHORS:20210104-164231600", "issn": "0223-5234", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210104-164231600", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32GM082000" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R01NS102279" }, { "agency": "NIH", "grant_number": "R01GM080269" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.ejmech.2020.113148", "pmcid": "PMC7954469", "primary_object": { "basename": "1-s2.0-S022352342031120X-mmc1.docx", "url": "https://authors.library.caltech.edu/records/5b58b-qz615/files/1-s2.0-S022352342031120X-mmc1.docx" }, "related_objects": [ { "basename": "nihms-1659547.pdf", "url": "https://authors.library.caltech.edu/records/5b58b-qz615/files/nihms-1659547.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Zhang, Gang; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/e4szt-jrf66", "eprint_id": 107103, "eprint_status": "archive", "datestamp": "2023-08-20 01:20:25", "lastmod": "2023-12-22 23:23:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Moen-Derek-R", "name": { "family": "Moen", "given": "Derek R." } }, { "id": "Sauni-Chelsee", "name": { "family": "Sauni", "given": "Chelsee" } }, { "id": "Kan-Shih-hsin", "name": { "family": "Kan", "given": "Shih-hsin" }, "orcid": "0000-0003-0209-4963" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" } }, { "id": "Le-Steven-Q", "name": { "family": "Le", "given": "Steven Q." }, "orcid": "0009-0005-2703-9057" }, { "id": "Lomenick-Brett", "name": { "family": "Lomenick", "given": "Brett" }, "orcid": "0000-0002-5023-9998" }, { "id": "Zhang-Xiaoyi", "name": { "family": "Zhang", "given": "Xiaoyi" }, "orcid": "0000-0001-9732-1449" }, { "id": "Ekins-Sean", "name": { "family": "Ekins", "given": "Sean" }, "orcid": "0000-0002-5691-5790" }, { "id": "Singamsetty-Srikanth", "name": { "family": "Singamsetty", "given": "Srikanth" } }, { "id": "Wood-Jill", "name": { "family": "Wood", "given": "Jill" }, "orcid": "0000-0002-0262-4285" }, { "id": "Dickson-Patricia-I", "name": { "family": "Dickson", "given": "Patricia I." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Enzyme Replacement Therapy for Mucopolysaccharidosis IIID using Recombinant Human \u03b1-N-Acetylglucosamine-6-Sulfatase in Neonatal Mice", "ispublished": "pub", "full_text_status": "public", "keywords": "MPS IIID, enzyme replacement therapy, GNS, CHO cells, recombinant protein production, DHFR", "note": "\u00a9 2020 American Chemical Society. \n\nReceived: August 12, 2020; Revised: November 24, 2020; Accepted: November 30, 2020; Published: December 15, 2020. \n\nThis study was supported by grants from the National Institutes of Health 1R41NS89061, R42NS089061, R44NS089061, and U44NS089061 to Phoenix Nest Inc. and R01NS088766 to P.I.D. S.-h.K. was supported by a T32 fellowship in the UCLA Medical Genetics Training Program (GM008243). The MPS IIID mouse model was developed by Taconic as a generous prize to Jonah's Just Begun as part of the Rare Disease Science Challenge 2012, hosted by Assay Depot and the Rare Genomics Institute. The authors gratefully acknowledge the monthly meetings and encouragement of Dr. Emily Caporello, Dr. Jill Morris, and colleagues (NIH/NINDS). The authors appreciate Ms. Rachel Dokko and Caitlin Yumori for their initial work on this project. The authors also kindly acknowledge the support of MPSIIID families and the MPS Society. The authors would like to thank the anonymous reviewers for constructive criticism. \n\nAuthor Contributions. F.W., D.R.M., C.S., and S.-h.K. contributed equally to this study. \n\nThe authors declare the following competing financial interest(s): C.S., D.R.M., and S.E. are former Phoenix Nest Inc. employees. S.S. and J.W. are current Phoenix Nest Inc. employees.\n\nAccepted Version - nihms-1728712.pdf
Supplemental Material - mp0c00831_si_001.pdf
", "abstract": "There is currently no cure or effective treatment available for mucopolysaccharidosis type IIID (MPS IIID, Sanfilippo syndrome type D), a lysosomal storage disorder (LSD) caused by the deficiency of \u03b1-N-acetylglucosamine-6-sulfatase (GNS). The clinical symptoms of MPS IIID, like other subtypes of Sanfilippo syndrome, are largely localized to the central nervous system (CNS), and any treatments aiming to ameliorate or reverse the catastrophic and fatal neurologic decline caused by this disease need to be delivered across the blood\u2013brain barrier. Here, we report a proof-of-concept enzyme replacement therapy (ERT) for MPS IIID using recombinant human \u03b1-N-acetylglucosamine-6-sulfatase (rhGNS) via intracerebroventricular (ICV) delivery in a neonatal MPS IIID mouse model. We overexpressed and purified rhGNS from CHO cells with a specific activity of 3.9 \u00d7 10\u2074 units/mg protein and a maximal enzymatic activity at lysosomal pH (pH 5.6), which was stable for over one month at 4 \u00b0C in artificial cerebrospinal fluid (CSF). We demonstrated that rhGNS was taken up by MPS IIID patient fibroblasts via the mannose 6-phosphate (M6P) receptor and reduced intracellular glycosaminoglycans to normal levels. The delivery of 5 \u03bcg of rhGNS into the lateral cerebral ventricle of neonatal MPS IIID mice resulted in normalization of the enzymatic activity in brain tissues; rhGNS was found to be enriched in lysosomes in MPS IIID-treated mice relative to the control. Furthermore, a single dose of rhGNS was able to reduce the accumulated heparan sulfate and \u03b2-hexosaminidase. Our results demonstrate that rhGNS delivered into CSF is a potential therapeutic option for MPS IIID that is worthy of further development.", "date": "2021-01-04", "date_type": "published", "publication": "Molecular Pharmaceutics", "volume": "18", "number": "1", "publisher": "American Chemical Society", "pagerange": "214-227", "id_number": "CaltechAUTHORS:20201215-141038657", "issn": "1543-8384", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201215-141038657", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1R41NS89061" }, { "agency": "NIH", "grant_number": "R42NS089061" }, { "agency": "NIH", "grant_number": "R44NS089061" }, { "agency": "NIH", "grant_number": "U44NS089061" }, { "agency": "NIH", "grant_number": "R01NS088766" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM008243" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1021/acs.molpharmaceut.0c00831", "pmcid": "PMC8362844", "primary_object": { "basename": "mp0c00831_si_001.pdf", "url": "https://authors.library.caltech.edu/records/e4szt-jrf66/files/mp0c00831_si_001.pdf" }, "related_objects": [ { "basename": "nihms-1728712.pdf", "url": "https://authors.library.caltech.edu/records/e4szt-jrf66/files/nihms-1728712.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Wang, Feng; Moen, Derek R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vyzbv-daf40", "eprint_id": 106783, "eprint_status": "archive", "datestamp": "2023-08-20 00:25:24", "lastmod": "2023-12-13 16:46:45", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Arango-Gonzalez-Bianca", "name": { "family": "Arango-Gonzalez", "given": "Blanca" }, "orcid": "0000-0002-9045-182X" }, { "id": "Sen-Merve", "name": { "family": "Sen", "given": "Merve" } }, { "id": "Guarascio-Rosellina", "name": { "family": "Guarascio", "given": "Rosellina" } }, { "id": "Ziaka-Kalliopi", "name": { "family": "Ziaka", "given": "Kalliopi" } }, { "id": "del-Amo-E-M", "name": { "family": "del Amo", "given": "Eva M." }, "orcid": "0000-0002-5705-4515" }, { "id": "Hau-Kwan", "name": { "family": "Hau", "given": "Kwan" } }, { "id": "Poultney-Hannah", "name": { "family": "Poultney", "given": "Hannah" } }, { "id": "Asfahani-Rowan", "name": { "family": "Asfahani", "given": "Rowan" } }, { "id": "Urtti-Arto", "name": { "family": "Urtti", "given": "Arto" }, "orcid": "0000-0001-6064-3102" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Bolz-Sylvia", "name": { "family": "Bolz", "given": "Sylvia" } }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" }, { "id": "Haq-Wadood", "name": { "family": "Haq", "given": "Wadood" } }, { "id": "Cheetham-M-E", "name": { "family": "Cheetham", "given": "Michael E." }, "orcid": "0000-0001-6429-654X" }, { "id": "Ueffing-Marius", "name": { "family": "Ueffing", "given": "Marius" }, "orcid": "0000-0003-2209-2113" } ] }, "title": "Inhibition of VCP preserves retinal structure and function in autosomal dominant retinal degeneration", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nThis version posted November 19, 2020. \n\nThis study was supported by funds (to M.Ue. and B.A-G) from FFB (Grant PPA-0717-0719-RAD), Kerstan Foundation, European Union's Horizon 2020 research and innovation programme under the Marie Sk\u0142odowska-Curie (Grant agreement No. 722717 \u2013 project OCUTHER) and ProRetina Foundation. The personnel of the animal husbandry at the Universit\u00e4tsklinikums T\u00fcbingen and Norman Rieger are acknowledged for the animal care. Christine Henes is acknowledged for her skilled technical assistance with the experiments. Ellen Kilger and Sally Williamson are gratefully acknowledged for language editing and proofreading. \n\nAuthors contributions: B.A.-G. designed experiments, carried out and treated organotypic cultures, performed intravitreal injections, prepared, stained, and imaged histological samples, analyzed the experimental data, and wrote the manuscript. M.S. carried out and treated organotypic cultures, prepared, stained, and imaged histological samples. M.S. and W.H. planned and carried out the ex-vivo light stimulation and activity recordings of the retinal explants. M.S. and E.M.A. performed the in silico calculations. R.G., K.H, K.Z., H.P., R.A., and. M.C. performed intravitreal injections and corresponding ERG and contributed to study planning therein. S.B. performed the EM and prepared histological samples. T.-F.C., R.D., A.U. participated in planning the study, and M.Ue. designed and coordinated the project, participated in designing the experiments, wrote the manuscript, and acquired funding for the studies. All authors have provided feedback on the results, read and approved the final manuscript.\nB.A.-G. and M.S. are co-first authors. B.A.-G. is listed first because she contributed more to the conception of the project and the writing of the manuscript.\n\nSubmitted - 2020.11.17.384669v1.full.pdf
Supplemental Material - media-1.docx
Supplemental Material - media-2.docx
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Supplemental Material - media-5.docx
", "abstract": "Due to continuously high production rates of rhodopsin (RHO) and high metabolic activity, photoreceptor neurons are especially vulnerable to defects in proteostasis. A proline to histidine substitution at position 23 (P23H) leads to production of structurally misfolded RHO, causing the most common form of autosomal dominant Retinitis Pigmentosa (adRP) in North America. The AAA-ATPase valosin-containing protein (VCP) extracts misfolded proteins from the ER membrane for cytosolic degradation. Here, we provide the first evidence that inhibition of VCP activity rescues degenerating P23H rod cells and improves their functional properties in P23H transgenic rat and P23H knock-in mouse retinae, both in vitro and in vivo. This improvement correlates with the restoration of the physiological RHO localization to rod outer segments (OS) and properly-assembled OS disks. As a single intravitreal injection suffices to deliver a long-lasting benefit in vivo, we suggest VCP inhibition as a potential therapeutic strategy for adRP patients carrying mutations in the RHO gene.", "date": "2020-11-23", "date_type": "published", "id_number": "CaltechAUTHORS:20201123-120919400", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201123-120919400", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Foundation Fighting Blindness", "grant_number": "PPA-0717-0719-RAD" }, { "agency": "Kerstan Foundation" }, { "agency": "Marie Curie Fellowship", "grant_number": "722717" }, { "agency": "ProRetina Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2020.11.17.384669", "primary_object": { "basename": "media-2.docx", "url": "https://authors.library.caltech.edu/records/vyzbv-daf40/files/media-2.docx" }, "related_objects": [ { "basename": "media-3.docx", "url": "https://authors.library.caltech.edu/records/vyzbv-daf40/files/media-3.docx" }, { "basename": "media-4.docx", "url": "https://authors.library.caltech.edu/records/vyzbv-daf40/files/media-4.docx" }, { "basename": "media-5.docx", "url": "https://authors.library.caltech.edu/records/vyzbv-daf40/files/media-5.docx" }, { "basename": "2020.11.17.384669v1.full.pdf", "url": "https://authors.library.caltech.edu/records/vyzbv-daf40/files/2020.11.17.384669v1.full.pdf" }, { "basename": "media-1.docx", "url": "https://authors.library.caltech.edu/records/vyzbv-daf40/files/media-1.docx" } ], "resource_type": "monograph", "pub_year": "2020", "author_list": "Arango-Gonzalez, Blanca; Sen, Merve; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/xxjmp-jst31", "eprint_id": 104581, "eprint_status": "archive", "datestamp": "2023-08-22 05:41:33", "lastmod": "2023-12-22 23:14:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Yu-Chuan", "name": { "family": "Chen", "given": "Yu-Chuan" } }, { "id": "Navarrete-M-S", "name": { "family": "Navarrete", "given": "Marian S." } }, { "id": "Wang-Ying", "name": { "family": "Wang", "given": "Ying" } }, { "id": "McClintock-N-C", "name": { "family": "McClintock", "given": "Natalie C." } }, { "id": "Sakurai-Reiko", "name": { "family": "Sakurai", "given": "Reiko" } }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Chen-Kathryn-T", "name": { "family": "Chen", "given": "Kathryn T." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" } }, { "id": "Rehan-V-K", "name": { "family": "Rehan", "given": "Virender K." } }, { "id": "Lee-Delphine-J", "name": { "family": "Lee", "given": "Delphine J." } }, { "id": "Diaz-Bego\u00f1a", "name": { "family": "Diaz", "given": "Bego\u00f1a" }, "orcid": "0000-0002-7892-6319" } ] }, "title": "N-myristoyltransferase-1 is necessary for lysosomal degradation and mTORC1 activation in cancer cells", "ispublished": "pub", "full_text_status": "public", "keywords": "Cancer; Cell biology", "note": "\u00a9 The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 28 March 2020; Accepted 25 June 2020; Published 20 July 2020. \n\nData availability: Materials and data generated during the current study are available from the corresponding author on reasonable request. \n\nWe thank Dr. Shawn Ferguson for sharing the TFE3-GFP plasmid. We thank Isabel Mejia for help with TFE3-GFP DNA purification, Mishal I. Syed for help with colony assays in Supplementary Figures, and Stacy Behare for technical assistance with animal experiments. We thank Guillermina Garcia at the Sanford-Burnham Prebys Medical Discovery Institute Histopathology Service (La Jolla), and Catalina Guerra and Jenny Dancourt at the Lundquist Institute Bioresources Center for valuable technical support. We are thankful to Dr. Samuel W. French (Harbor-UCLA Medical Center) for expert histopathological evaluation of H&E stained mouse organs. We are grateful to Dr. Sara Courtneidge (OHSU) and Dr. David Shackelford (UCLA) for useful critical comments on the manuscript. This work has been supported by grants NIH HL127237 and TRDRP 27IP-0050 to VKR, and The Lundquist Institute Grant to BD. \n\nAuthor Contributions: Y.C. performed and analyzed WB, proliferation, colony assays, IF, and animal experiments; M.N. performed and analyzed IHC on tumor sections and quantified IF experiments; Y.W. designed, performed and interpreted animal experiments; N.M. assisted with animal experiments; R.S. assisted with animal experiments and performed WB of tumors; F.W. designed, performed and interpreted NMTi viability experiments to calculate EC\u2085\u2080; K.T.C. performed and interpreted animal experiments; T.C. designed and interpreted NMTi viability experiments to calculate EC\u2085\u2080; V.K.R. designed and interpreted animal experiments; D.J.L. designed and interpreted IHC experiments; B.D. conceived the project, designed and performed experiments, coordinated and supervised the project, analyzed and interpreted data, and wrote the manuscript. All authors read and approved the manuscript. \n\nThe authors declare no competing interests.\n\nPublished - s41598-020-68615-w.pdf
Supplemental Material - 41598_2020_68615_MOESM1_ESM.pdf
", "abstract": "N-myristoyltransferase-1 (NMT1) catalyzes protein myristoylation, a lipid modification that is elevated in cancer cells. NMT1 sustains proliferation and/or survival of cancer cells through mechanisms that are not completely understood. We used genetic and pharmacological inhibition of NMT1 to further dissect the role of this enzyme in cancer, and found an unexpected essential role for NMT1 at promoting lysosomal metabolic functions. Lysosomes mediate enzymatic degradation of vesicle cargo, and also serve as functional platforms for mTORC1 activation. We show that NMT1 is required for both lysosomal functions in cancer cells. Inhibition of NMT1 impaired lysosomal degradation leading to autophagy flux blockade, and simultaneously caused the dissociation of mTOR from the surface of lysosomes leading to decreased mTORC1 activation. The regulation of lysosomal metabolic functions by NMT1 was largely mediated through the lysosomal adaptor LAMTOR1. Accordingly, genetic targeting of LAMTOR1 recapitulated most of the lysosomal defects of targeting NMT1, including defective lysosomal degradation. Pharmacological inhibition of NMT1 reduced tumor growth, and tumors from treated animals had increased apoptosis and displayed markers of lysosomal dysfunction. Our findings suggest that compounds targeting NMT1 may have therapeutic benefit in cancer by preventing mTORC1 activation and simultaneously blocking lysosomal degradation, leading to cancer cell death.", "date": "2020-07-20", "date_type": "published", "publication": "Scientific Reports", "volume": "10", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 11952", "id_number": "CaltechAUTHORS:20200727-084934912", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200727-084934912", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HL127237" }, { "agency": "California Tobacco-Related Disease Research Program", "grant_number": "27IP-0050" }, { "agency": "Lundquist Institute" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41598-020-68615-w", "primary_object": { "basename": "41598_2020_68615_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/xxjmp-jst31/files/41598_2020_68615_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "s41598-020-68615-w.pdf", "url": "https://authors.library.caltech.edu/records/xxjmp-jst31/files/s41598-020-68615-w.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Chen, Yu-Chuan; Navarrete, Marian S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8517g-b9a69", "eprint_id": 101920, "eprint_status": "archive", "datestamp": "2023-08-22 04:42:02", "lastmod": "2023-12-22 23:19:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Gan-Taiping", "name": { "family": "Gan", "given": "Taiping" } }, { "id": "Stott-Gordon-M", "name": { "family": "Stott", "given": "Gordon M." }, "orcid": "0000-0002-9148-6100" }, { "id": "Flint-Andrew-J", "name": { "family": "Flint", "given": "Andrew J." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Allosteric p97 inhibitors can overcome resistance to ATP-competitive p97 inhibitors for potential anti-cancer therapy", "ispublished": "pub", "full_text_status": "public", "keywords": "p97 VCP; resistance; small molecule inhibitor; ATPase; cancer", "note": "\u00a9 2020 Wiley\u2010VCH Verlag GmbH & Co. KGaA, Weinheim. \n\nAccepted manuscript online: 11 March 2020; Manuscript accepted: 05 March 2020; Manuscript revised: 15 February 2020; Manuscript received: 21 December 2019. \n\nWe thank the University of Kansas Specialized Chemistry Center for providing DeBQ, ML240, ML241 and University of Pittsburgh Chemical Diversity Center for providing UPCDC-30245. We thank Jingying Xu for helping on maintaining the CB-5083 resistant line, Xiaoyi Zhang and Lin Gui for assistance with preparing samples to determine intracellular compound concentration, and Paul Sternberg for editorial suggestions. We thank Quintara Discovery for LC-MS/MS analysis. We thank Neal Green for helpful suggestion. The project was supported in part with funds from the National Cancer Institute, National Institutes of Health, under Contract No. HHSN261200800001E, through the NExT Chemical Biology Consortium.\n\nAccepted Version - nihms-1577759.pdf
Supplemental Material - cmdc201900722-s1-supporting_information_for_accepted_article.pdf
", "abstract": "A major challenge of targeted cancer therapy is the selection for drug\u2010resistant mutations in tumor cells leading to loss of treatment effectiveness. p97/VCP is a central regulator of protein homeostasis and a promising anti\u2010cancer target because of its vital role in cell growth and survival. One ATP\u2010competitive p97 inhibitor, CB\u20105083, has entered clinical trials. Selective pressure on HCT116 cells treated with CB\u20105083 identified 5 different resistant mutants. Identification of p97 inhibitors with different mechanisms of action would offer the potential to overcome this class of resistance mutations. Our results demonstrate that two CB\u20105083 resistant p97 mutants, N660K and T688A, were also resistant to several other ATP\u2010competitive p97 inhibitors, whereas inhibition by two allosteric p97 inhibitors NMS\u2010873 and UPCDC\u201030245 were unaffected by these mutations. We also established a CB\u20105083 resistant cell line that harbors a new p97 double mutation (D649A/T688A). While CB\u20105083, NMS\u2010873, and UPCDC\u201030245 all effectively inhibited proliferation of the parental HCT116 cell line, NMS\u2010873 and UPCDC\u201030245 were 30\u2010fold more potent than CB\u20105083 in inhibiting the CB\u20105083 resistant D649A/T688A double mutant. Our results suggest that allosteric p97 inhibitors are promising alternatives when resistance to ATP\u2010competitive p97 inhibitors arises during anti\u2010cancer treatment.", "date": "2020-04-20", "date_type": "published", "publication": "ChemMedChem", "volume": "15", "number": "8", "publisher": "Wiley", "pagerange": "685-694", "id_number": "CaltechAUTHORS:20200316-130434745", "issn": "1860-7179", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200316-130434745", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HHSN261200800001E" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1002/cmdc.201900722", "pmcid": "PMC9049325", "primary_object": { "basename": "cmdc201900722-s1-supporting_information_for_accepted_article.pdf", "url": "https://authors.library.caltech.edu/records/8517g-b9a69/files/cmdc201900722-s1-supporting_information_for_accepted_article.pdf" }, "related_objects": [ { "basename": "nihms-1577759.pdf", "url": "https://authors.library.caltech.edu/records/8517g-b9a69/files/nihms-1577759.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Wang, Feng; Li, Shan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4570v-77h57", "eprint_id": 89092, "eprint_status": "archive", "datestamp": "2023-08-22 00:19:50", "lastmod": "2023-10-18 22:30:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Jing", "name": { "family": "Li", "given": "Jing" } }, { "id": "Zhang-Yaru", "name": { "family": "Zhang", "given": "Yaru" } }, { "id": "Da-Silva-Sil-Dos-Santos-Bruno", "name": { "family": "Da Silva Sil Dos Santos", "given": "Bruno" } }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Ma-Yuyong", "name": { "family": "Ma", "given": "Yuyong" } }, { "id": "Perez-Christian", "name": { "family": "Perez", "given": "Christian" } }, { "id": "Yang-Yanling", "name": { "family": "Yang", "given": "Yanling" } }, { "id": "Peng-Junmin", "name": { "family": "Peng", "given": "Junmin" } }, { "id": "Cohen-Seth-M", "name": { "family": "Cohen", "given": "Seth M." }, "orcid": "0000-0002-5233-2280" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Hilton-Stephen-T", "name": { "family": "Hilton", "given": "Stephen T." } }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" } ] }, "title": "Epidithiodiketopiperazines Inhibit Protein Degradation by Targeting Proteasome Deubiquitinase Rpn11", "ispublished": "pub", "full_text_status": "public", "keywords": "proteasome; Rpn11; POH1; PSMD14; ubiquitin; Capzimin; epidithiodiketopiperazine; gliotoxin; protein degradation; JAMM protease", "note": "\u00a9 2018 Elsevier Ltd. Under an Elsevier user license. \n\nReceived 15 February 2018, Revised 23 May 2018, Accepted 25 July 2018, Available online 23 August 2018. \n\nWe thank J.M. Huibregtse (The University of Texas at Austin) for the vector expressing GST-Wbp2-C-K222, Rsp5, and Rsp5-E6AP, A. Martin (University of California, Berkeley) for the pETDuet-1 vector expressing the Rpn11-Rpn8 dimer, T.M. Kapoor (The Rockefeller University) for providing the RPE1 WT and BTZ-resistant cell lines, H. Park for testing the cell lines for mycoplasma contamination, A. Bowers (University of North Carolina) for the stimulating discussion on gliotoxin, and D. Sherman (Amgen Inc.) for critical reading of our manuscript. This work was supported by grants from the Caltech Gates Grubstake Fund and Amgen to R.J.D. and from the NIH (CA164803) to R.J.D. and S.M.C. S.T.H. and B.D.S.S.D.S. were supported by the funding from FCT (grant no. SFRH/BD/65630/2009). \n\nAuthor Contributions: J.L. designed, executed, and interpreted the experiments using Wbp2 as proteasome activity substrate, in vitro Rpn11 assay and AMSH assay, and western blot. Y.Z. performed and analyzed the in vitro Csn5 assay, real-time qPCR assay, and western blot. B.D.S.S.D.S. and S.T.H. synthesized ETP compounds SOP1-11. Y.Y. and J.P. quantified the linkage type of ubiquitin chain on Wbp2. F.W. and T.-F.C performed and analyzed the UbG76V-GFP degradation assay. Y.M., C.P. and S.M.C. performed and analyzed the hCAII and MMP-2 assay. R.J.D. designed, interpreted, and oversaw the experiments for the entire study. The manuscript was drafted by J.L. and R.J.D with input from all authors. \n\nDeclaration of Interests: R.J.D. is a founder, shareholder, and member of the Scientific Advisory Board of Cleave Biosciences, which is engaged in discovery and development of drugs that target enzymes involved in ubiquitin-dependent protein degradation. R.J.D. is currently Senior Vice President of discovery research at Amgen Inc.. S.M.C. is a co-founder and has an equity interest, and receives income as a member of the Scientific Advisory Board for Cleave Biosciences and is a co-founder, has an equity interest, and a member of the Scientific Advisory Board for Forge Therapeutics. Both companies may potentially benefit from the research results of certain projects in the laboratory of S.M.C. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.\n\nAccepted Version - nihms-1510970.pdf
Supplemental Material - 1-s2.0-S2451945618302642-mmc1.pdf
", "abstract": "The 26S proteasome is the major proteolytic machine for breaking down cytosolic and nuclear proteins in eukaryotes. Due to the lack of a suitable assay, it is difficult to measure routinely and quantitatively the breakdown of proteins by the 26S proteasome in vitro. In the present study, we developed an assay to monitor proteasome-mediated protein degradation. Using this assay, we discovered that epidithiodiketopiperazine (ETPs) blocked the degradation of our model substrate in vitro. Further characterization revealed that ETPs inhibited proteasome function by targeting the essential proteasomal deubiquitinase Rpn11 (POH1/PSMD14). ETPs also inhibited other JAMM (JAB1/MPN/Mov34 metalloenzyme) proteases such as Csn5 and AMSH. An improved ETP with fewer non-specific effects, SOP11, stabilized a subset of proteasome substrates in cells, induced the unfolded protein response, and led to cell death. SOP11 represents a class of Rpn11 inhibitor and provides an alternative route to develop proteasome inhibitors.", "date": "2018-11-15", "date_type": "published", "publication": "Cell Chemical Biology", "volume": "25", "number": "11", "publisher": "Cell Press", "pagerange": "1350-1358", "id_number": "CaltechAUTHORS:20180823-134532623", "issn": "2451-9456", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180823-134532623", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Gates Grubstake Fund" }, { "agency": "Amgen" }, { "agency": "NIH", "grant_number": "CA164803" }, { "agency": "Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia (FCT)", "grant_number": "SFRH/BD/65630/2009" } ] }, "doi": "10.1016/j.chembiol.2018.07.012", "pmcid": "PMC6309308", "primary_object": { "basename": "1-s2.0-S2451945618302642-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/4570v-77h57/files/1-s2.0-S2451945618302642-mmc1.pdf" }, "related_objects": [ { "basename": "nihms-1510970.pdf", "url": "https://authors.library.caltech.edu/records/4570v-77h57/files/nihms-1510970.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Li, Jing; Zhang, Yaru; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/05j1y-ecq55", "eprint_id": 114045, "eprint_status": "archive", "datestamp": "2023-08-22 00:18:00", "lastmod": "2023-10-23 23:20:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "LaPorte-Matthew-G", "name": { "family": "LaPorte", "given": "Matthew G." } }, { "id": "Burnett-James-C", "name": { "family": "Burnett", "given": "James C." } }, { "id": "Colombo-Raffaele", "name": { "family": "Colombo", "given": "Raffaele" } }, { "id": "Bulfer-Stacie-L", "name": { "family": "Bulfer", "given": "Stacie L." }, "orcid": "0000-0002-7274-7213" }, { "id": "Alverez-Celeste", "name": { "family": "Alverez", "given": "Celeste" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Neitz-R-Jeffrey", "name": { "family": "Neitz", "given": "R. Jeffrey" }, "orcid": "0000-0002-2247-9345" }, { "id": "Green-Neal", "name": { "family": "Green", "given": "Neal" }, "orcid": "0000-0001-5851-5152" }, { "id": "Moore-William-J", "name": { "family": "Moore", "given": "William J." }, "orcid": "0000-0002-1140-7661" }, { "id": "Yue-Zhizhou", "name": { "family": "Yue", "given": "Zhizhou" } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Arkin-Michelle-R", "name": { "family": "Arkin", "given": "Michelle R." }, "orcid": "0000-0002-9366-6770" }, { "id": "Wipf-Peter", "name": { "family": "Wipf", "given": "Peter" }, "orcid": "0000-0001-7693-5863" }, { "id": "Huryn-Donna-M", "name": { "family": "Huryn", "given": "Donna M." }, "orcid": "0000-0001-5542-4968" } ] }, "title": "Optimization of Phenyl Indole Inhibitors of the AAA+ ATPase p97", "ispublished": "pub", "full_text_status": "public", "keywords": "AAA+ ATPase; p97; allosteric inhibitor; protein homeostasis modulator; anticancer; phenyl indole; Organic Chemistry; Drug Discovery; Biochemistry", "note": "\u00a9 2018 American Chemical Society. This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. \n\nReceived 15 August 2018. Accepted 18 September 2018. Published online 18 September 2018. Published in issue 8 November 2018. \n\nThe authors gratefully acknowledge Marina Kovaliov (University of Pittsburgh) for technical support and advice; Chaemin Lim (University of Pittsburgh) for data retrieval and collation; Mary Liang (University of Pittsburgh) for compound management and extensive assistance with manuscript preparation; Taber Maskrey (University of Pittsburgh) for analytical chemistry support; Clifford Bryant (UCSF) for preliminary chemistry; Gregory Lee (UCSF) for help with data compilation; Sean Marcsisin, CTP US Army; Jason Sousa and Brittney Potter (WRAIR) for solubility data; AMRI for microsomal stability data; Richard Gussio, CAPT USPHS (NCI) for contributions to computational and molecular modeling studies; and the NCI for access to the NCI-60 cell line. The authors also appreciate the helpful discussion and suggestions of all the CBC p97 project team members, particularly Raymond Deshaies (CalTech), Eric Baldwin (Leidos), Andrew Flint (Leidos), Barbara Mroczowski (NCI), Shizuko Sei (Leidos), Gordon Stott (Leidos), Gunda Georg (University of Minnesota), and Michael Walters (University of Minnesota). \n\nThe project was funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health, under Chemical Biology Consortium Contract No. HHSN261200800001E, Agreement No. 29XS127TO15.\n\nAuthor Contributions:\nThe manuscript was written through contributions of all\nauthors. All authors have given approval to the final version of the manuscript.\n\nThe authors declare no competing financial interest.\n\nPublished - acsmedchemlett.8b00372.pdf
Supplemental Material - ml8b00372_si_001.pdf
", "abstract": "Optimization of the side-chain of a phenyl indole scaffold identified from a high-throughput screening campaign for inhibitors of the AAA+ ATPase p97 is reported. The addition of an N-alkyl piperazine led to high potency of this series in a biochemical assay, activity in cell-based assays, and excellent pharmaceutical properties. Molecular modeling based on a subsequently obtained cryo-EM structure of p97 in complex with a phenyl indole was used to rationalize the potency of these allosteric inhibitors.", "date": "2018-11-08", "date_type": "published", "publication": "ACS Medicinal Chemistry Letters", "volume": "9", "number": "11", "publisher": "American Chemical Society", "pagerange": "1075-1081", "id_number": "CaltechAUTHORS:20220323-565669000", "issn": "1948-5875", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565669000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HHSN261200800001E" }, { "agency": "NIH", "grant_number": "29XS127TO15" } ] }, "doi": "10.1021/acsmedchemlett.8b00372", "pmcid": "PMC6231190", "primary_object": { "basename": "acsmedchemlett.8b00372.pdf", "url": "https://authors.library.caltech.edu/records/05j1y-ecq55/files/acsmedchemlett.8b00372.pdf" }, "related_objects": [ { "basename": "ml8b00372_si_001.pdf", "url": "https://authors.library.caltech.edu/records/05j1y-ecq55/files/ml8b00372_si_001.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "LaPorte, Matthew G.; Burnett, James C.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gpdck-mh575", "eprint_id": 114049, "eprint_status": "archive", "datestamp": "2023-08-21 23:19:44", "lastmod": "2023-10-23 23:20:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sanghez-Valentina", "name": { "family": "Sanghez", "given": "Valentina" }, "orcid": "0000-0002-4131-7480" }, { "id": "Chen-Mengqing", "name": { "family": "Chen", "given": "Mengqing" }, "orcid": "0000-0001-5576-2297" }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" }, "orcid": "0000-0002-0829-1821" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Iacovino-Michelina", "name": { "family": "Iacovino", "given": "Michelina" }, "orcid": "0000-0002-1076-3146" }, { "id": "Lin-Henry-J", "name": { "family": "Lin", "given": "Henry J." } }, { "id": "Lasky-Joseph-L", "name": { "family": "Lasky", "given": "Joseph L." }, "orcid": "0000-0002-2565-1921" }, { "id": "Panosyan-Eduard-H", "name": { "family": "Panosyan", "given": "Eduard H." } } ] }, "title": "Efficacy of Asparaginase Erwinia chrysanthemi With and Without Temozolomide Against Glioma Cells and Intracranial Mouse Medulloblastoma", "ispublished": "pub", "full_text_status": "public", "keywords": "Glioblastoma; medulloblastoma; temozolomide; L-glutamine; L-asparagine; asparaginase; Cancer Research; Oncology; General Medicine", "note": "\u00a9 2018 International Institute of Anticancer Research. \n\nReceived February 27, 2018. Revision received March 21, 2018. Accepted March 29, 2018. \n\nThis study was funded by Jazz Pharmaceuticals (Dublin, Ireland). \n\nWe thank Dr. Harley Kornblum from the UCLA Intellectual and Developmental Disability Research Center for the gliomasphere lines used in these experiments.\n\nPublished - 2627.full.pdf
", "abstract": "Background: Anti-metabolites are less-myelosuppressive than DNA-damaging anticancer drugs and may be useful against brain tumors. \n\nMaterials and Methods: We evaluated the asparagine/glutamine-deaminating agent Erwinaze with/without temozolomide against brain tumor cells and mouse medulloblastomas. \n\nResults. Erwinaze treatment of cell lines and neurospheres led to dose-dependent reductions of cells (reversible by L-glutamine), with half maximal inhibitory concentrations (IC\u2085\u2080s) of 0.12->10 IU/ml. Erwinaze at <1 IU/ml reduced temozolomide IC\u2085\u2080s by 3.6- to 13-fold (300-1,200 \u03bcM to 40-330 \u03bcM). Seven-week-old SMO/SMO mice treated with Erwinaze (regardless of temozolomide treatment) had better survival 11 weeks post-therapy, compared to those not treated with Erwinaze (81.25% vs. 46.15, p=0.08). Temozolomide-treated mice developed 10% weight loss, impairing survival. All 16 mice treated with temozolomide (regardless of Erwinaze treatment) succumbed by 40-weeks of age, whereas 5/8 animals treated with Erwinaze alone and 2/6 controls survived (p=0.035). \n\nConclusion: Erwinaze enhances cytotoxicity of temozolomide in vitro, and improves survival in SMO/SMO mice, likely by reducing cerebrospinal fluid glutamine. Temozolomide-associated toxicity prevented demonstration of any potential combinatorial advantage with Erwinaze in vivo.", "date": "2018-05-02", "date_type": "published", "publication": "Anticancer Research", "volume": "38", "number": "5", "publisher": "International Institute of Anticancer Research", "pagerange": "2627-2634", "id_number": "CaltechAUTHORS:20220323-565878000", "issn": "0250-7005", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565878000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Jazz Pharmaceuticals" } ] }, "doi": "10.21873/anticanres.12504", "primary_object": { "basename": "2627.full.pdf", "url": "https://authors.library.caltech.edu/records/gpdck-mh575/files/2627.full.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Sanghez, Valentina; Chen, Mengqing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ycn2b-f3q28", "eprint_id": 83483, "eprint_status": "archive", "datestamp": "2023-08-21 22:21:24", "lastmod": "2023-10-17 23:09:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nakasone-M-A", "name": { "family": "Nakasone", "given": "Mark A." } }, { "id": "Lewis-T-A", "name": { "family": "Lewis", "given": "Timothy A." } }, { "id": "Walker-O", "name": { "family": "Walker", "given": "Olivier" } }, { "id": "Thakur-A", "name": { "family": "Thakur", "given": "Anita" } }, { "id": "Mansour-W", "name": { "family": "Mansour", "given": "Wissam" } }, { "id": "Casta\u00f1eda-C-A", "name": { "family": "Casta\u00f1eda", "given": "Carlos A." } }, { "id": "Goeckeler-Fried-J-L", "name": { "family": "Goeckeler-Fried", "given": "Jennifer L." } }, { "id": "Parlati-F", "name": { "family": "Parlati", "given": "Frank" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Hayat-O", "name": { "family": "Hayat", "given": "Ortal" } }, { "id": "Zhang-Daoning", "name": { "family": "Zhang", "given": "Daoning" } }, { "id": "Camara-C-M", "name": { "family": "Camara", "given": "Christina M." } }, { "id": "Bonn-S-M", "name": { "family": "Bonn", "given": "Steven M." } }, { "id": "Nowicka-U-K", "name": { "family": "Nowicka", "given": "Urszula K." } }, { "id": "Krueger-S", "name": { "family": "Krueger", "given": "Susan" } }, { "id": "Glickman-M-H", "name": { "family": "Glickman", "given": "Michael H." } }, { "id": "Brodsky-J-L", "name": { "family": "Brodsky", "given": "Jeffrey L." } }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" }, { "id": "Fushman-D", "name": { "family": "Fushman", "given": "David" } } ] }, "title": "Structural Basis for the Inhibitory Effects of Ubistatins in the Ubiquitin-Proteasome Pathway", "ispublished": "pub", "full_text_status": "public", "keywords": "ubiquitin-proteasome system; deubiquitination; ubiquitination; ubistatin; polyubiquitin; NMR; SANS", "note": "\u00a9 2017 Elsevier Ltd. \n\nReceived 21 July 2017, Revised 9 September 2017, Accepted 24 October 2017, Available online 16 November 2017. \n\nWe thank George H. Lorimer and Arnon Henn for access to their fluorimeters, Ananya Majumdar for help with setting up triple-resonance NMR experiments, Rajesh Singh for the Rub1 sample, Allan Weissman for RCC4 cells, and Konstantin Berlin for useful discussions. The project has been funded in part from the NCI Initiative for Chemical Genetics, NIH, under contract no. N01-CO-12400 to Stuart L. Schreiber, by NIH grants GM065334 to D.F. and GM095755 to D.F. and M.H.G., ISF grant 909-14 to M.H.G., and by NIH grants GM075061 and DK079307 and by Cystic Fibrosis Foundation Therapeutics grant BRODSK13XXO to J.L.B., and a Fulbright postdoctoral fellowship to M.A.N., and utilized NMR instrumentation supported in part by NSF grant DBI1040158 and neutron-scattering facilities supported in part by the NSF under agreement no. DMR-0944772. R.J.D. is a founder and shareholder of Cleave Biosciences, which is developing drugs that target the ubiquitin system. \n\nAuthor Contributions: T.A.L. synthesized ubistatin compounds. Rpn11 functional assays were performed by F.P., T.-F.C., R.J.D.; CFTR assays by J.L.B. and J.L.G.-F.; NMR measurements and analysis by M.A.N., U.K.N., O.W., D.Z., C.M.C., S.M.B., D.F.; SANS studies by C.A.C., S.K., D.F.; structure calculations by O.W. and M.A.N.; fluorescence measurements by M.A.N., W.M., A.T., O.H. and analyzed by D.F.; DUB assays by M.A.N., W.M., O.H., and cellular assays by M.A.N., A.T., and M.H.G. All authors contributed to writing the manuscript and revisions.\n\nSupplemental Material - 1-s2.0-S0969212617303350-mmc1.pdf
", "abstract": "The discovery of ubistatins, small molecules that impair proteasomal degradation of proteins by directly binding to polyubiquitin, makes ubiquitin itself a potential therapeutic target. Although ubistatins have the potential for drug development and clinical applications, the lack of structural details of ubiquitin-ubistatin interactions has impeded their development. Here, we characterized a panel of new ubistatin derivatives using functional and binding assays. The structures of ubiquitin complexes with ubistatin B and hemi-ubistatin revealed direct interactions with ubiquitin's hydrophobic surface patch and the basic/polar residues surrounding it. Ubistatin B binds ubiquitin and diubiquitin tighter than a high-affinity ubiquitin receptor and shows strong preference for K48 linkages over K11 and K63. Furthermore, ubistatin B shields ubiquitin conjugates from disassembly by a range of deubiquitinases and by the 26S proteasome. Finally, ubistatin B penetrates cancer cells and alters the cellular ubiquitin landscape. These findings highlight versatile properties of ubistatins and have implications for their future development and use in targeting ubiquitin-signaling pathways.", "date": "2017-12-05", "date_type": "published", "publication": "Structure", "volume": "25", "number": "12", "publisher": "Cell Press", "pagerange": "1839-1855", "id_number": "CaltechAUTHORS:20171128-081216731", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171128-081216731", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "N01-CO-12400" }, { "agency": "NIH", "grant_number": "GM065334" }, { "agency": "NIH", "grant_number": "GM095755" }, { "agency": "Israel Science Foundation", "grant_number": "909-14" }, { "agency": "NIH", "grant_number": "GM075061" }, { "agency": "NIH", "grant_number": "DK079307" }, { "agency": "Cystic Fibrosis Foundation", "grant_number": "BRODSK13XXO" }, { "agency": "Fulbright Foundation" }, { "agency": "NSF", "grant_number": "DBI-1040158" }, { "agency": "NSF", "grant_number": "DMR-0944772" } ] }, "doi": "10.1016/j.str.2017.10.007", "primary_object": { "basename": "1-s2.0-S0969212617303350-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/ycn2b-f3q28/files/1-s2.0-S0969212617303350-mmc1.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Nakasone, Mark A.; Lewis, Timothy A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d17fg-2j273", "eprint_id": 114040, "eprint_status": "archive", "datestamp": "2023-08-21 22:10:09", "lastmod": "2023-10-23 23:20:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bastola-Prabhakar", "name": { "family": "Bastola", "given": "Prabhakar" }, "orcid": "0000-0002-7378-8690" }, { "id": "Wang-Feng", "name": { "family": "Wang", "given": "Feng" } }, { "id": "Schaich-Matthew-A", "name": { "family": "Schaich", "given": "Matthew A." } }, { "id": "Gan-Taiping", "name": { "family": "Gan", "given": "Taiping" } }, { "id": "Freudenthal-Bret-D", "name": { "family": "Freudenthal", "given": "Bret D." }, "orcid": "0000-0003-1449-4710" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Chien-Jeremy", "name": { "family": "Chien", "given": "Jeremy" }, "orcid": "0000-0003-4744-8374" } ] }, "title": "Specific mutations in the D1\u2013D2 linker region of VCP/p97 enhance ATPase activity and confer resistance to VCP inhibitors", "ispublished": "pub", "full_text_status": "public", "keywords": "Cancer Research; Cell Biology; Cellular and Molecular Neuroscience; Immunology", "note": "\u00a9 The Author(s) 2017. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. \n\nReceived 08 August 2017. Accepted 10 August 2017. Published 06 November 2017. \n\nTFC is supported in part by the National Institutes of Health (Grants R01HD086596 and R01NS100815). TFC is a member of the University of California, Los Angeles Jonsson Comprehensive Cancer Center. The study is funded by the University of Kansas Cancer Center Support Grant (P30-CA168524), the American Cancer Society Research Scholar (125618-RSG-14-067-01-TBE, to JC) and the Department of Defense Ovarian Cancer Research Program under award number (W81XWH-17-1-0078, to JC). \n\nViews and opinions of and endorsements by the author(s) do not reflect those of the US Army or the Department of Defense. \n\nContributions. PB and JC conceived the project and designed experiments from Figures 1 to 3; PB performed experiments from Figures 1 to 3; BDF and MAS designed and performed molecular docking studies; TFC, FW and TG designed and performed ATPase activity assay. PB, JC, BDF and TFC wrote the paper. All authors revised the paper. \n\nThe authors declare no conflict of interest.\n\nPublished - cddiscovery201765.pdf
Supplemental Material - 41420_2017_BFcddiscovery201765_MOESM167_ESM.pdf
", "abstract": "Valosin-containing protein (VCP), together with several partner proteins, extracts ubiquitinated client proteins from E3 ligase complex and facilitates their degradation through ubiquitin\u2013proteasome system. Therefore, it plays an important role in regulating protein quality control and various cellular pathways. Recent studies also identified VCP as a lineage-specific essential gene in ovarian cancer. An orally bioavailable VCP inhibitor, CB-5083, is currently in Phase I clinical trials because it shows therapeutic effects in multiple tumor xenograft models. However, the mechanism of resistance to CB-5083 is unknown. Here, we characterized molecular mechanism of resistance to CB-5083. Using incremental exposure to CB-5083, we established CB-5083-resistant ovarian cancer cells that showed five- to six-fold resistance in vitro compared with parental cells. Genomic and complementary DNA sequencing of the VCP coding region revealed a pattern of co-selected mutations: (1) missense mutations at codon 470 in one copy resulting in increased ATPase activity and (2) nonsense or frameshift mutations at codon 606 or codon 616 in another copy causing the loss of allele-specific expression. Unbiased molecular docking studies showed codon 470 as a putative binding site for CB-5083. Furthermore, the analysis of somatic mutations in cancer genomes from the Cancer Genome Atlas (TCGA) indicated that codon 616 contains hotspot mutations in VCP. Thus, identification of these mutations associated with in vitro resistance to VCP inhibitors may be useful as potential theranostic markers while screening for patients to enroll in clinical trials. VCP has emerged as a viable therapeutic target for several cancer types, and therefore targeting such hyperactive VCP mutants should aid in improving the therapeutic outcome in cancer patients.", "date": "2017-11-06", "date_type": "published", "publication": "Cell Death Discovery", "volume": "3", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 17065", "id_number": "CaltechAUTHORS:20220323-565541000", "issn": "2058-7716", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565541000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01HD086596" }, { "agency": "NIH", "grant_number": "R01NS100815" }, { "agency": "Jonsson Comprehensive Cancer Center" }, { "agency": "NIH", "grant_number": "P30-CA168524" }, { "agency": "American Cancer Society", "grant_number": "125618-RSG-14-067-01-TBE" }, { "agency": "Department of Defense", "grant_number": "W81XWH-17-1-0078" } ] }, "doi": "10.1038/cddiscovery.2017.65", "pmcid": "PMC5672561", "primary_object": { "basename": "41420_2017_BFcddiscovery201765_MOESM167_ESM.pdf", "url": "https://authors.library.caltech.edu/records/d17fg-2j273/files/41420_2017_BFcddiscovery201765_MOESM167_ESM.pdf" }, "related_objects": [ { "basename": "cddiscovery201765.pdf", "url": "https://authors.library.caltech.edu/records/d17fg-2j273/files/cddiscovery201765.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Bastola, Prabhakar; Wang, Feng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ppqww-m6w63", "eprint_id": 114032, "eprint_status": "archive", "datestamp": "2023-08-21 21:55:19", "lastmod": "2023-10-23 23:19:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sanghez-Valentina", "name": { "family": "Sanghez", "given": "Valentina" }, "orcid": "0000-0002-4131-7480" }, { "id": "Luzzi-Anna", "name": { "family": "Luzzi", "given": "Anna" } }, { "id": "Clarke-Don", "name": { "family": "Clarke", "given": "Don" } }, { "id": "Kee-Dustin", "name": { "family": "Kee", "given": "Dustin" }, "orcid": "0000-0001-6806-4957" }, { "id": "Beuder-Steven", "name": { "family": "Beuder", "given": "Steven" } }, { "id": "Rux-Danielle", "name": { "family": "Rux", "given": "Danielle" }, "orcid": "0000-0002-9952-4474" }, { "id": "Osawa-Mitsujiro", "name": { "family": "Osawa", "given": "Mitsujiro" } }, { "id": "Madrenas-Joaqu\u00edn", "name": { "family": "Madrenas", "given": "Joaqu\u00edn" }, "orcid": "0000-0001-6191-3733" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Kyba-Michael", "name": { "family": "Kyba", "given": "Michael" }, "orcid": "0000-0002-5579-7534" }, { "id": "Iacovino-Michelina", "name": { "family": "Iacovino", "given": "Michelina" }, "orcid": "0000-0002-1076-3146" } ] }, "title": "Notch activation is required for downregulation of HoxA3-dependent endothelial cell phenotype during blood formation", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2017 Sanghez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: June 9, 2017; Accepted: October 9, 2017; Published: October 26, 2017. \n\nWe thank Dr. Michael Bevan for the OP9-Dll1 cells. \n\nThis research was supported by NIH grants U01 HL100407 and 1R01 HL081186 and by the American Heart Association grant 12SDG9260007. J.M. holds a Tier I Canada Research Chair ih Human Immunology. \n\nAuthor Contributions:\nConceptualization: Valentina Sanghez, Michelina Iacovino.\nData curation: Valentina Sanghez, Anna Luzzi, Don Clarke, Dustin Kee, Steven Beuder, Danielle Rux, Mitsujiro Osawa, Tsui-Fen Chou.\nFormal analysis: Valentina Sanghez, Tsui-Fen Chou, Michelina Iacovino.\nWriting \u00b1 original draft: Valentina Sanghez, Michelina Iacovino.\nWriting \u00b1 review & editing: Don Clarke, Joaquin Madrenas, Michael Kyba.\n\nThe authors have declared that no competing interests exist.\n\nPublished - pone.0186818.pdf
Supplemental Material - pone.0186818.s001.pdf
Supplemental Material - pone.0186818.s002.pdf
Supplemental Material - pone.0186818.s003.pdf
Supplemental Material - pone.0186818.s004.pdf
Supplemental Material - pone.0186818.s005.pdf
Supplemental Material - pone.0186818.s006.pdf
Supplemental Material - pone.0186818.s007.pdf
Supplemental Material - pone.0186818.s008.pdf
Supplemental Material - pone.0186818.s009.pdf
Supplemental Material - pone.0186818.s010.pdf
Supplemental Material - pone.0186818.s011.pdf
", "abstract": "Hemogenic endothelium (HE) undergoes endothelial-to-hematopoietic transition (EHT) to generate blood, a process that requires progressive down-regulation of endothelial genes and induction of hematopoietic ones. Previously, we have shown that the transcription factor HoxA3 prevents blood formation by inhibiting Runx1 expression, maintaining endothelial gene expression and thus blocking EHT. In the present study, we show that HoxA3 also prevents blood formation by inhibiting Notch pathway. HoxA3 induced upregulation of Jag1 ligand in endothelial cells, which led to cis-inhibition of the Notch pathway, rendering the HE nonresponsive to Notch signals. While Notch activation alone was insufficient to promote blood formation in the presence of HoxA3, activation of Notch or downregulation of Jag1 resulted in a loss of the endothelial phenotype which is a prerequisite for EHT. Taken together, these results demonstrate that Notch pathway activation is necessary to downregulate endothelial markers during EHT.", "date": "2017-10", "date_type": "published", "publication": "PLoS ONE", "volume": "12", "number": "10", "publisher": "Public Library of Science", "pagerange": "Art. No. e0186818", "id_number": "CaltechAUTHORS:20220323-565416000", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565416000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HL100407" }, { "agency": "NIH", "grant_number": "HL081186" }, { "agency": "American Heart Association", "grant_number": "12SDG9260007" }, { "agency": "Canada Research Chairs Program" } ] }, "doi": "10.1371/journal.pone.0186818", "pmcid": "PMC5658089", "primary_object": { "basename": "pone.0186818.s003.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s003.pdf" }, "related_objects": [ { "basename": "pone.0186818.s004.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s004.pdf" }, { "basename": "pone.0186818.s005.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s005.pdf" }, { "basename": "pone.0186818.s007.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s007.pdf" }, { "basename": "pone.0186818.s001.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s001.pdf" }, { "basename": "pone.0186818.s002.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s002.pdf" }, { "basename": "pone.0186818.s008.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s008.pdf" }, { "basename": "pone.0186818.s009.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s009.pdf" }, { "basename": "pone.0186818.s010.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s010.pdf" }, { "basename": "pone.0186818.s011.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s011.pdf" }, { "basename": "pone.0186818.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.pdf" }, { "basename": "pone.0186818.s006.pdf", "url": "https://authors.library.caltech.edu/records/ppqww-m6w63/files/pone.0186818.s006.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Sanghez, Valentina; Luzzi, Anna; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m2y4b-t8h14", "eprint_id": 114058, "eprint_status": "archive", "datestamp": "2023-08-21 21:48:20", "lastmod": "2023-10-23 23:21:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shah-Rachit", "name": { "family": "Shah", "given": "Rachit" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Maize-Kimberly-M", "name": { "family": "Maize", "given": "Kimberly M." } }, { "id": "Strom-Alexander", "name": { "family": "Strom", "given": "Alexander" } }, { "id": "Finzel-Barry-C", "name": { "family": "Finzel", "given": "Barry C." } }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Inhibition by divalent metal ions of human histidine triad nucleotide binding protein1 (hHint1), a regulator of opioid analgesia and neuropathic pain", "ispublished": "pub", "full_text_status": "public", "keywords": "Histidine triad nucleotide binding protein1 (Hint1); Phosphoramidase; Human Hint1; Escherichia coli (E.\u00a0coli) Hint; Cell Biology; Molecular Biology; Biochemistry; Biophysics", "note": "\u00a9 2017 Elsevier. \n\nReceived 9 July 2017, Revised 18 July 2017, Accepted 20 July 2017, Available online 21 July 2017, Version of Record 18 August 2017. \n\nThe authors are grateful to Jay Nix of the Molecular Biology Consortium of ALS Beamline 4.2.2 for crystallographic data collection and processing. KMM was supported by the University of Minnesota Frieda Martha Kunze Fellowship and the American Foundation for Pharmaceutical Education. Funding from the University of Maryland Extension is gratefully acknowledged. Funding from the University of Minnesota Foundation is gratefully acknowledged.\n\nSupplemental Material - 1-s2.0-S0006291X17314699-mmc1.docx
Supplemental Material - 1-s2.0-S0006291X17314699-mmc2.pdf
", "abstract": "Human histidine triad nucleotide binding protein 1 (hHint1) is a purine nucleoside phosphoramidase and adenylate hydrolase that has emerged as a potential therapeutic target for the management of pain. However, the molecular mechanism of Hint1 in the signaling pathway has remained less clear. The role of metal ions in regulating postsynaptic transmission is well known, and the active site of hHint1 contains multiple histidines. Here we have investigated the effect of divalent metal ions (Cd\u00b2\u207a, Cu\u00b2\u207a, Mg\u00b2\u207a, Mn\u00b2\u207a, Ni\u00b2\u207a, and Zn\u00b2\u207a) on the structural integrity and catalytic activity of hHint1. With the exception of Mg\u00b2\u207a, all the divalent ions inhibited hHint1, the rank of order was found to be Cu\u00b2\u207a >Zn\u00b2\u207a >Cd2+ \u2265Ni\u00b2\u207a >Mn\u00b2\u207a based on their IC50 and kin/KI values. A crystal structure of hHint1 with bound Cu\u00b2\u207a is described to explain the competitive reversible inactivation of hHint1 by divalent cations. All the metal ions exhibited time- and concentration- dependent inhibition, with the rate of inactivation highly dependent on alterations of the C-terminus. With the exception of Cu\u00b2\u207a; restoration of inhibition was observed for all the metal ions after treatment with EDTA. Our studies reveal a loss in secondary structure and aggregation of hHint1 upon incubation with 10-fold excess of copper. Thus, hHint1 appears to be structurally sensitive to irreversible inactivation by copper, which may be of neurotoxicological and pharmacological significance.", "date": "2017-09-23", "date_type": "published", "publication": "Biochemical and Biophysical Research Communications", "volume": "491", "number": "3", "publisher": "Elsevier", "pagerange": "760-766", "id_number": "CaltechAUTHORS:20220323-565997000", "issn": "0006-291X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565997000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Minnesota" }, { "agency": "American Foundation for Pharmaceutical Education" }, { "agency": "University of Maryland Extension" }, { "agency": "University of Minnesota Foundation" } ] }, "doi": "10.1016/j.bbrc.2017.07.111", "primary_object": { "basename": "1-s2.0-S0006291X17314699-mmc1.docx", "url": "https://authors.library.caltech.edu/records/m2y4b-t8h14/files/1-s2.0-S0006291X17314699-mmc1.docx" }, "related_objects": [ { "basename": "1-s2.0-S0006291X17314699-mmc2.pdf", "url": "https://authors.library.caltech.edu/records/m2y4b-t8h14/files/1-s2.0-S0006291X17314699-mmc2.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Shah, Rachit; Chou, Tsui-Fen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/52jp9-hwh08", "eprint_id": 114050, "eprint_status": "archive", "datestamp": "2023-08-21 20:48:33", "lastmod": "2023-10-23 23:20:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-YouJin", "name": { "family": "Lee", "given": "YouJin" }, "orcid": "0000-0001-7299-935X" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Pittman-Sara-K", "name": { "family": "Pittman", "given": "Sara K." } }, { "id": "Keith-Amy-L", "name": { "family": "Keith", "given": "Amy L." } }, { "id": "Razani-Babak", "name": { "family": "Razani", "given": "Babak" }, "orcid": "0000-0002-7172-9240" }, { "id": "Weihl-Conrad-C", "name": { "family": "Weihl", "given": "Conrad C." }, "orcid": "0000-0002-3816-6124" } ] }, "title": "Keap1/Cullin3 Modulates p62/SQSTM1 Activity via UBA Domain Ubiquitination", "ispublished": "pub", "full_text_status": "public", "keywords": "SQSTM1/p62; ubiquitin; autophagy; neurodegeneration; aggregaphagy; General Biochemistry, Genetics and Molecular Biology", "note": "\u00a9 2017 The Author(s). Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) \n\nReceived 13 September 2016, Revised 30 November 2016, Accepted 8 March 2017, Available online 4 April 2017, Version of Record 4 April 2017. \n\nFunding sources included NIH grants AG031867 and AG042095 (to C.C.W.) and the Muscular Dystrophy Association (416457, to C.C.W.). \n\nAuthor Contributions. Y.L. and C.C.W. designed and wrote the study. Y.L. conducted most of the experiments with support from S.K.P. and A.L.K. T.-F.C. reviewed the paper. B.R. offered reagents.\n\nPublished - 1-s2.0-S2211124717303625-main.pdf
Supplemental Material - 1-s2.0-S2211124717303625-mmc1.pdf
", "abstract": "p62/SQSTM1 (p62) is a scaffolding protein that facilitates the formation and degradation of ubiquitinated aggregates via its self-interaction and ubiquitin binding domains. The regulation of this process is unclear but may relate to the post-translational modification of p62. In the present study, we find that Keap1/Cullin3 ubiquitinates p62 at lysine 420 within its UBA domain. Substitution of lysine 420 with an arginine diminishes p62 sequestration and degradation activity similar what is seen when the UBA domain is deleted. Overexpression of Keap1/Cullin3 in p62-WT-expressing cells increases ubiquitinated inclusion formation and p62's association with LC3 and rescues proteotoxicity. This effect is not seen in cells expressing a mutant p62 that fails to interact with Keap1. Interestingly, p62 disease mutants have diminished or absent UBA domain ubiquitination. These data suggest that the ubiquitination of p62's UBA domain at lysine 420 may regulate p62's function and be disrupted in p62-associated disease.", "date": "2017-04-04", "date_type": "published", "publication": "Cell Reports", "volume": "19", "number": "1", "publisher": "Cell Press", "pagerange": "188-202", "id_number": "CaltechAUTHORS:20220323-565886000", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565886000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AG031867" }, { "agency": "NIH", "grant_number": "AG042095" }, { "agency": "Muscular Dystrophy Association", "grant_number": "416457" } ] }, "doi": "10.1016/j.celrep.2017.03.030", "pmcid": "PMC5395095", "primary_object": { "basename": "1-s2.0-S2211124717303625-main.pdf", "url": "https://authors.library.caltech.edu/records/52jp9-hwh08/files/1-s2.0-S2211124717303625-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S2211124717303625-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/52jp9-hwh08/files/1-s2.0-S2211124717303625-mmc1.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Lee, YouJin; Chou, Tsui-Fen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/h9q0s-2j756", "eprint_id": 114030, "eprint_status": "archive", "datestamp": "2023-08-22 19:54:45", "lastmod": "2023-10-23 23:19:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Segura-Cabrera-Aldo", "name": { "family": "Segura-Cabrera", "given": "Aldo" } }, { "id": "Tripathi-Reshmi", "name": { "family": "Tripathi", "given": "Reshmi" } }, { "id": "Zhang-Xiaoyi", "name": { "family": "Zhang", "given": "Xiaoyi" }, "orcid": "0000-0001-9732-1449" }, { "id": "Gui-Lin", "name": { "family": "Gui", "given": "Lin" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Komurov-Kakajan", "name": { "family": "Komurov", "given": "Kakajan" } } ] }, "title": "A structure- and chemical genomics-based approach for repositioning of drugs against VCP/p97 ATPase", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 The Author(s) 2017. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. \n\nReceived 28 November 2016. Accepted 14 February 2017. Published 21 March 2017. \n\nThis work was supported by grants from the Susan G. Komen Foundation (CCR13263034) and NCI (CA193549) to KK. ASC acknowledges CONACYT-M\u00e9xico for support from \"Estancias Postdoctorales al Extranjero para la Consolidaci\u00f3n de Grupos de Investigaci\u00f3n\" (grant number 238386). \n\nContributions. A.-S.C., K.K. and T.S.C. wrote the manuscript. A.-S.C. and K.K. designed the research. R.T., X.Z., L.G. and A.-S.C. performed the research. A.-S.C., K.K. and T.-S.C analyzed the data. \n\nThe authors declare no competing financial interests.\n\nPublished - srep44912.pdf
Supplemental Material - 41598_2017_BFsrep44912_MOESM69_ESM.xls
", "abstract": "Valosin-containing protein (VCP/p97) ATPase (a.k.a. Cdc48) is a key member of the ER-associated protein degradation (ERAD) pathway. ERAD and VCP/p97 have been implicated in a multitude of human diseases, such as neurodegenerative diseases and cancer. Inhibition of VCP/p97 induces proteotoxic ER stress and cell death in cancer cells, making it an attractive target for cancer treatment. However, no drugs exist against this protein in the market. Repositioning of drugs towards new indications is an attractive alternative to the de novo drug development due to the potential for significantly shorter time to clinical translation. Here, we employed an integrative strategy for the repositioning of drugs as novel inhibitors of the VCP/p97 ATPase. We integrated structure-based virtual screening with the chemical genomics analysis of drug molecular signatures, and identified several candidate inhibitors of VCP/p97 ATPase. Importantly, experimental validation with cell-based and in vitro ATPase assays confirmed three (ebastine, astemizole and clotrimazole) out of seven tested candidates (~40% true hit rate) as direct inhibitors of VCP/p97 and ERAD. This study introduces an effective integrative strategy for drug repositioning, and identified new drugs against the VCP/p97/ERAD pathway in human diseases.", "date": "2017-03-21", "date_type": "published", "publication": "Scientific Reports", "volume": "7", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 44912", "id_number": "CaltechAUTHORS:20220323-564837000", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-564837000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Susan G. Komen Breast Cancer Foundation", "grant_number": "CCR13263034" }, { "agency": "NIH", "grant_number": "CA193549" }, { "agency": "Consejo Nacional de Ciencia y Tecnolog\u00eda (CONACYT)", "grant_number": "238386" } ] }, "doi": "10.1038/srep44912", "pmcid": "PMC5359624", "primary_object": { "basename": "41598_2017_BFsrep44912_MOESM69_ESM.xls", "url": "https://authors.library.caltech.edu/records/h9q0s-2j756/files/41598_2017_BFsrep44912_MOESM69_ESM.xls" }, "related_objects": [ { "basename": "srep44912.pdf", "url": "https://authors.library.caltech.edu/records/h9q0s-2j756/files/srep44912.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Segura-Cabrera, Aldo; Tripathi, Reshmi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/mr2ms-gw797", "eprint_id": 75381, "eprint_status": "archive", "datestamp": "2023-08-19 01:39:37", "lastmod": "2023-10-20 23:27:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Perez-Christian", "name": { "family": "Perez", "given": "Christian" } }, { "id": "Li-Jing", "name": { "family": "Li", "given": "Jing" } }, { "id": "Parlati-Francesco", "name": { "family": "Parlati", "given": "Francesco" } }, { "id": "Rouffet-Matthieu", "name": { "family": "Rouffet", "given": "Matthieu" } }, { "id": "Ma-Yuyong", "name": { "family": "Ma", "given": "Yuyong" } }, { "id": "Zhou-Han-Jie", "name": { "family": "Zhou", "given": "Han-Jie" } }, { "id": "MacKinnon-Andrew-L", "name": { "family": "MacKinnon", "given": "Andrew L." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Deshaies-Raymond-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" }, { "id": "Cohen-Seth-M", "name": { "family": "Cohen", "given": "Seth M." }, "orcid": "0000-0002-5233-2280" } ] }, "title": "Discovery of an Inhibitor of the Proteasome Subunit Rpn11", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 American Chemical Society. \n\nReceived: September 20, 2016; Published: February 13, 2017. \n\nWe acknowledge Dr. Yongxuan Su (U.C. San Diego Molecular Mass Spectrometry Facility) for aid with HR-MS and HPLC fragment purity analysis. We acknowledge Dr. Dave P. Martin and Dr. David T. Puerta for their helpful discussions and assistance with the synthesis and characterization of the [(Tp^(Me,Ph))Zn(8TQ)] metal complex and the U.C. San Diego X-ray diffraction facilities for assistance with experiments. We also thank Dr. Elton Zeqiraj for providing purified BRISC complex. This work was initiated with an American Recovery and Reinvestment Act (ARRA) supplement to R.J.D. (3-R01-GM065997\u201307S1), followed by a grant to S.M.C. and R.J.D. from the National Cancer Institute (R01-CA164803). J.L. was supported in part by a Caltech Grubstake Award and CBEA Award from Amgen. R.J.D. is an Investigator of the Howard Hughes Medical Institute and this work was supported in part by HHMI.\n\nPage 1343. The author list and author affiliations should be\nmodified to include a new author Han-Jie Zhou of Cleave\nBiosciences. The correct author listing is shown above, and the correct author listing with the affiliation symbols and the associated affiliations are shown below. Note that nonaffiliation symbols in the author listing below are defined in the manuscript.\n\nAccepted Version - nihms930851.pdf
Supplemental Material - jm6b01379_si_001.pdf
Supplemental Material - jm6b01379_si_002.csv
", "abstract": "The proteasome plays a crucial role in degradation of normal proteins that happen to be constitutively or inducibly unstable, and in this capacity it plays a regulatory role. Additionally, it degrades abnormal/damaged/mutant/misfolded proteins, which serves a quality-control function. Inhibitors of the proteasome have been validated in the treatment of multiple myeloma, with several FDA-approved therapeutics. Rpn11 is a Zn\u00b2\u207a-dependent metalloisopeptidase that hydrolyzes ubiquitin from tagged proteins that are trafficked to the proteasome for degradation. A fragment-based drug discovery (FBDD) approach was utilized to identify fragments with activity against Rpn11. Screening of a library of metal-binding pharmacophores (MBPs) revealed that 8-thioquinoline (8TQ, IC\u2085\u2080 value \u223c2.5 \u03bcM) displayed strong inhibition of Rpn11. Further synthetic elaboration of 8TQ yielded a small molecule compound (35, IC\u2085\u2080 value \u223c400 nM) that is a potent and selective inhibitor of Rpn11 that blocks proliferation of tumor cells in culture.", "date": "2017-02-23", "date_type": "published", "publication": "Journal of Medicinal Chemistry", "volume": "60", "number": "4", "publisher": "American Chemical Society", "pagerange": "1343-1361", "id_number": "CaltechAUTHORS:20170324-090339100", "issn": "0022-2623", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170324-090339100", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "American Recovery and Reinvestment Act (ARRA)" }, { "agency": "NIH", "grant_number": "3-R01-GM065997-07S1" }, { "agency": "NIH", "grant_number": "R01-CA164803" }, { "agency": "Caltech Grubstake Fund" }, { "agency": "Amgen" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Cancer Institute" } ] }, "doi": "10.1021/acs.jmedchem.6b01379", "pmcid": "PMC5761724", "primary_object": { "basename": "jm6b01379_si_001.pdf", "url": "https://authors.library.caltech.edu/records/mr2ms-gw797/files/jm6b01379_si_001.pdf" }, "related_objects": [ { "basename": "jm6b01379_si_002.csv", "url": "https://authors.library.caltech.edu/records/mr2ms-gw797/files/jm6b01379_si_002.csv" }, { "basename": "nihms930851.pdf", "url": "https://authors.library.caltech.edu/records/mr2ms-gw797/files/nihms930851.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Perez, Christian; Li, Jing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7wryn-5yx47", "eprint_id": 114046, "eprint_status": "archive", "datestamp": "2023-08-22 18:31:04", "lastmod": "2023-10-23 23:20:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bulfer-Stacie-L", "name": { "family": "Bulfer", "given": "Stacie L." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Arkin-Michelle-R", "name": { "family": "Arkin", "given": "Michelle R." }, "orcid": "0000-0002-9366-6770" } ] }, "title": "p97 Disease Mutations Modulate Nucleotide-Induced Conformation to Alter Protein\u2013Protein Interactions", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics, Monomers, Surface plasmon resonance, Conformation, Screening assays; Molecular Medicine; General Medicine; Biochemistry", "note": "\u00a9 2016 American Chemical Society. This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. \n\nReceived 22 April 2016. Accepted 7 June 2016. Published online 13 June 2016. Published in issue 19 August 2016. \n\nThe project was funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under Chemical Biology Consortium Contract No. HHSN261200800001E Agreement No. 29XS127TO15, and from the National Institute of Aging, National Institutes of Health, R01AG044515 and from the LA BioMed Seed Grant program (20826-01). TFC is a member of UCLA Jonsson Comprehensive Cancer Center. \n\nAuthor Contributions:\nThe manuscript was written through contributions of all\nauthors.\n\nThe authors declare no competing financial interest.\n\nPublished - acschembio.6b00350.pdf
Supplemental Material - cb6b00350_si_001.pdf
", "abstract": "The AAA+ ATPase p97/VCP adopts at least three conformations that depend on the binding of ADP and ATP and alter the orientation of the N-terminal protein\u2013protein interaction (PPI) domain into \"up\" and \"down\" conformations. Point mutations that cause multisystem proteinopathy 1 (MSP1) are found at the interface of the N domain and D1-ATPase domain and potentially alter the conformational preferences of p97. Additionally, binding of \"adaptor\" proteins to the N-domain regulates p97's catalytic activity. We propose that p97/adaptor PPIs are coupled to p97 conformational states. We evaluated the binding of nucleotides and the adaptor proteins p37 and p47 to wild-type p97 and MSP1 mutants. Notably, p47 and p37 bind 8-fold more weakly to the ADP-bound conformation of wild-type p97 compared to the ATP-bound conformation. However, MSP1 mutants lose this nucleotide-induced conformational coupling because they destabilize the ADP-bound, \"down\" conformation of the N-domain. Loss in conformation coupling to PPIs could contribute to the mechanism of MSP1.", "date": "2016-08-19", "date_type": "published", "publication": "ACS Chemical Biology", "volume": "11", "number": "8", "publisher": "American Chemical Society", "pagerange": "2112-2116", "id_number": "CaltechAUTHORS:20220323-565696000", "issn": "1554-8929", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565696000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HHSN261200800001E" }, { "agency": "NIH", "grant_number": "29XS127TO15" }, { "agency": "NIH", "grant_number": "R01AG044515" }, { "agency": "LA BioMed Seed Grant", "grant_number": "20826-01" }, { "agency": "UCLA Jonsson Comprehensive Cancer Center" } ] }, "doi": "10.1021/acschembio.6b00350", "pmcid": "PMC5224236", "primary_object": { "basename": "acschembio.6b00350.pdf", "url": "https://authors.library.caltech.edu/records/7wryn-5yx47/files/acschembio.6b00350.pdf" }, "related_objects": [ { "basename": "cb6b00350_si_001.pdf", "url": "https://authors.library.caltech.edu/records/7wryn-5yx47/files/cb6b00350_si_001.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Bulfer, Stacie L.; Chou, Tsui-Fen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gmmgm-m6495", "eprint_id": 114038, "eprint_status": "archive", "datestamp": "2023-08-22 17:57:39", "lastmod": "2023-10-23 23:20:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gui-Lin", "name": { "family": "Gui", "given": "Lin" } }, { "id": "Zhang-Xiaoyi", "name": { "family": "Zhang", "given": "Xiaoyi" } }, { "id": "Li-Kelin", "name": { "family": "Li", "given": "Kelin" } }, { "id": "Frankowski-Kevin-J", "name": { "family": "Frankowski", "given": "Kevin J." } }, { "id": "Li-Shan", "name": { "family": "Li", "given": "Shan" } }, { "id": "Wong-Daniel-E", "name": { "family": "Wong", "given": "Daniel E." } }, { "id": "Moen-Derek-R", "name": { "family": "Moen", "given": "Derek R." } }, { "id": "Porubsky-Patrick-R", "name": { "family": "Porubsky", "given": "Patrick R." } }, { "id": "Lin-Henry-J", "name": { "family": "Lin", "given": "Henry J." } }, { "id": "Schoenen-Frank-J", "name": { "family": "Schoenen", "given": "Frank J." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Evaluating p97 Inhibitor Analogues for Potency against p97-p37 and p97-Npl4-Ufd1 Complexes", "ispublished": "pub", "full_text_status": "public", "keywords": "ATPase; cancer; p97; structure\u2013activity relationships; ubiquitin\u2013proteasome system; Organic Chemistry; General Pharmacology, Toxicology and Pharmaceutics; Molecular Medicine; Drug Discovery; Biochemistry; Pharmacology", "note": "\u00a9 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.\n\nIssue Online: 09 May 2016. Version of Record online: 04 April 2016. Manuscript received: 21 January 2016. \n\nThe authors thank Benjamin Neuenswander (University of Kansas, USA) for compound purification and analysis. The project was supported in part by funds from the US National Institutes of Health (NIH) (U54HG005031 to Jeffrey Aub\u00e9), the US National Cancer Institute (NCI), part of the US NIH, under contract no. HHSN261200800001E, and through the NExT Chemical Biology Consortium. F.J.S. is a member of the University of Kansas NCI-designated Cancer Center. T.F.C. is a member of UCLA Jonsson Comprehensive Cancer Center. T.F.C. was in part supported by LA BioMed through their Seed Grant program (20826-01).\n\nSupplemental Material - cmdc201600036-sup-0001-misc_information.pdf
", "abstract": "We previously found that the p97 cofactor, p47, significantly decreased the potency of some ATP-competitive p97 inhibitors such as ML240 [2-(2-amino-1H-benzo[d]imidazol-1-yl)-N-benzyl-8-methoxyquinazolin-4-amine] and ML241 [2-(2H-benzo[b][1,4]oxazin-4(3H)-yl)-N-benzyl-5,6,7,8 tetrahydroquinazolin-4-amine]. In this study, we aimed to evaluate inhibitor potencies against two additional p97 cofactor complexes, p97\u2013p37 and p97\u2013Npl4\u2013Ufd1. We focused on these two cofactor complexes, because the protein sequence of p37 is 50\u2009% identical to that of p47, and the Npl4\u2013Ufd1 heterodimer (NU) is the most-studied p97 cofactor complex. We screened 200 p97 inhibitor analogues for their ability to inhibit the ATPase activity of p97 alone and of p97\u2013p37 and p97\u2013NU complexes. In contrast to the effect of p47, p37 and NU did not significantly change the potencies of most of the compounds. These results highlight differences among p97 cofactors in influencing p97 conformation and effects of inhibitors on p97 complexes, as compared to p97 alone. Continued efforts are needed to advance the development of complex-specific p97 inhibitors.", "date": "2016-05-06", "date_type": "published", "publication": "ChemMedChem", "volume": "11", "number": "9", "publisher": "Wiley-Blackwell", "pagerange": "953-957", "id_number": "CaltechAUTHORS:20220323-565507000", "issn": "1860-7179", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565507000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54HG005031" }, { "agency": "NIH", "grant_number": "HHSN261200800001E" }, { "agency": "NExT Chemical Biology Consortium" }, { "agency": "Jonsson Comprehensive Cancer Center" }, { "agency": "LA BioMed Seed Grant", "grant_number": "20826-01" } ] }, "doi": "10.1002/cmdc.201600036", "primary_object": { "basename": "cmdc201600036-sup-0001-misc_information.pdf", "url": "https://authors.library.caltech.edu/records/gmmgm-m6495/files/cmdc201600036-sup-0001-misc_information.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Gui, Lin; Zhang, Xiaoyi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vjn8b-2ge15", "eprint_id": 114031, "eprint_status": "archive", "datestamp": "2023-08-22 15:29:58", "lastmod": "2023-10-23 23:19:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Liu-Mingfu", "name": { "family": "Liu", "given": "Mingfu" } }, { "id": "Lin-Lin", "name": { "family": "Lin", "given": "Lin" } }, { "id": "Gebremariam-Teclegiorgis", "name": { "family": "Gebremariam", "given": "Teclegiorgis" } }, { "id": "Luo-Guanpingsheng", "name": { "family": "Luo", "given": "Guanpingsheng" } }, { "id": "Skory-Christopher-D", "name": { "family": "Skory", "given": "Christopher D." }, "orcid": "0000-0001-6268-9104" }, { "id": "French-Samuel-W", "name": { "family": "French", "given": "Samuel W." } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Edwards-John-E-Jr", "name": { "family": "Edwards", "given": "John E., Jr." } }, { "id": "Ibrahim-Ashraf-S", "name": { "family": "Ibrahim", "given": "Ashraf S." } } ] }, "title": "Fob1 and Fob2 Proteins Are Virulence Determinants of Rhizopus oryzae via Facilitating Iron Uptake from Ferrioxamine", "ispublished": "pub", "full_text_status": "public", "keywords": "Virology; Genetics; Molecular Biology; Immunology; Microbiology; Parasitology", "note": "This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. \n\nReceived: May 22, 2014; Accepted: March 31, 2015; Published: May 14, 2015. \n\nThe authors gratefully acknowledge the technical assistance of May Abdallah in isolating the putative ferrioxamine receptors and Hongku Lee in helping with the animal studies. We also would like to thank Pryia Uppuluri and Sameh Soliman for discussions and critical review of the manuscript. Research described in this manuscript was conducted at the research facilities of the Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center. \n\nThis work was supported by Public Health Service grants R01 AI063503 to ASI. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nAuthor Contributions: Conceived and designed the experiments: ML ASI JEE. Performed the experiments: ML LL TG GL SWF TFC ASI. Analyzed the data: ML LL SWF ASI. Contributed reagents/materials/analysis tools: CDS. Wrote the paper: ASI ML. Revised the manuscript: CDS JEE. \n\nThe authors have declared that no competing interests exist.\n\nData Availability Statement: All relevant data are within the paper and its Supporting Information files.\n\nPublished - ppat.1004842.pdf
Supplemental Material - ppat.1004842.s001.tif
Supplemental Material - ppat.1004842.s002.tif
Supplemental Material - ppat.1004842.s003.tif
Supplemental Material - ppat.1004842.s004.tif
Supplemental Material - ppat.1004842.s005.tif
Supplemental Material - ppat.1004842.s006.docx
Supplemental Material - ppat.1004842.s007.docx
Supplemental Material - ppat.1004842.s008.docx
", "abstract": "Dialysis patients with chronic renal failure receiving deferoxamine for treating iron overload are uniquely predisposed for mucormycosis, which is most often caused by Rhizopus oryzae. Although the deferoxamine siderophore is not secreted by Mucorales, previous studies established that Rhizopus species utilize iron from ferrioxamine (iron-rich form of deferoxamine). Here we determined that the CBS domain proteins of Fob1 and Fob2 act as receptors on the cell surface of R. oryzae during iron uptake from ferrioxamine. Fob1 and Fob2 cell surface expression was induced in the presence of ferrioxamine and bound radiolabeled ferrioxamine. A R. oryzae strain with targeted reduced Fob1/Fob2 expression was impaired for iron uptake, germinating, and growing on medium with ferrioxamine as the sole source of iron. This strain also exhibited reduced virulence in a deferoxamine-treated, but not the diabetic ketoacidotic (DKA), mouse model of mucormycosis. The mechanism by which R. oryzae obtains iron from ferrioxamine involves the reductase/permease uptake system since the growth on ferrioxamine supplemented medium is associated with elevated reductase activity and the use of the ferrous chelator bathophenanthroline disulfonate abrogates iron uptake and growth on medium supplemented with ferrioxamine as a sole source of iron. Finally, R. oryzae mutants with reduced copies of the high affinity iron permease (FTR1) or with decreased FTR1 expression had an impaired iron uptake from ferrioxamine in vitro and reduced virulence in the deferoxamine-treated mouse model of mucormycosis. These two receptors appear to be conserved in Mucorales, and can be the subject of future novel therapy to maintain the use of deferoxamine for treating iron-overload.", "date": "2015-05", "date_type": "published", "publication": "PLOS Pathogens", "volume": "11", "number": "5", "publisher": "Public Library of Science", "pagerange": "Art. No. e1004842", "id_number": "CaltechAUTHORS:20220323-565404000", "issn": "1553-7374", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565404000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI063503" } ] }, "doi": "10.1371/journal.ppat.1004842", "pmcid": "PMC4431732", "primary_object": { "basename": "ppat.1004842.s008.docx", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.s008.docx" }, "related_objects": [ { "basename": "ppat.1004842.pdf", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.pdf" }, { "basename": "ppat.1004842.s001.tif", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.s001.tif" }, { "basename": "ppat.1004842.s002.tif", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.s002.tif" }, { "basename": "ppat.1004842.s003.tif", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.s003.tif" }, { "basename": "ppat.1004842.s005.tif", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.s005.tif" }, { "basename": "ppat.1004842.s006.docx", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.s006.docx" }, { "basename": "ppat.1004842.s007.docx", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.s007.docx" }, { "basename": "ppat.1004842.s004.tif", "url": "https://authors.library.caltech.edu/records/vjn8b-2ge15/files/ppat.1004842.s004.tif" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Liu, Mingfu; Lin, Lin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rb69g-9tv93", "eprint_id": 55882, "eprint_status": "archive", "datestamp": "2023-08-22 15:20:15", "lastmod": "2023-10-20 23:21:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Xiaoyi", "name": { "family": "Zhang", "given": "Xiaoyi" }, "orcid": "0000-0001-9732-1449" }, { "id": "Gui-Lin", "name": { "family": "Gui", "given": "Lin" } }, { "id": "Zhang-Xiaoyan", "name": { "family": "Zhang", "given": "Xiaoyan" } }, { "id": "Bulfer-Stacie-L", "name": { "family": "Bulfer", "given": "Stacie L." }, "orcid": "0000-0002-7274-7213" }, { "id": "Sanghez-Valentina", "name": { "family": "Sanghez", "given": "Valentina" }, "orcid": "0000-0002-4131-7480" }, { "id": "Wong-Daniel-E", "name": { "family": "Wong", "given": "Daniel E." } }, { "id": "Lee-YouJin", "name": { "family": "Lee", "given": "YouJin" }, "orcid": "0000-0001-7299-935X" }, { "id": "Lehmann-Lynn", "name": { "family": "Lehmann", "given": "Lynn" } }, { "id": "Lee-James-Siho", "name": { "family": "Lee", "given": "James Siho" } }, { "id": "Shih-Pei-Yin", "name": { "family": "Shih", "given": "Pei-Yin" }, "orcid": "0000-0003-3082-9242" }, { "id": "Lin-Henry-J", "name": { "family": "Lin", "given": "Henry J." } }, { "id": "Iacovino-Michelina", "name": { "family": "Iacovino", "given": "Michelina" }, "orcid": "0000-0002-1076-3146" }, { "id": "Weihl-Conrad-C", "name": { "family": "Weihl", "given": "Conrad C." }, "orcid": "0000-0002-3816-6124" }, { "id": "Arkin-Michelle-R", "name": { "family": "Arkin", "given": "Michelle R." }, "orcid": "0000-0002-9366-6770" }, { "id": "Wang-Yanzhuang", "name": { "family": "Wang", "given": "Yanzhuang" }, "orcid": "0000-0002-1864-7094" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Altered cofactor regulation with disease-associated p97/VCP mutations", "ispublished": "pub", "full_text_status": "public", "keywords": "AAA ATPase; p97/VCP; MSP1; p47; steady-state kinetics", "note": "\u00a9 2015 National Academy of Sciences. Freely available online through the PNAS open access option. \n\nEdited by William J. Lennarz, Stony Brook University, Stony Brook, NY, and approved February 10, 2015 (received for review September 30, 2014) Published online before print March 16, 2015, doi: 10.1073/pnas.1418820112.\n\nT.-F.C. was in part supported by the National Center for Advancing Translational Sciences through UCLA Clinical Translational Science Institute (CTSI) Grant UL1TR000124 and the LA BioMed Seed Grant Program (20826-01). S.L.B. and M.R.A. were funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under Contract HHSN261200800001E, through the NExT Chemical Biology Consortium. (The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government.) Y.W. is supported in part by the National Institutes of Health (Grants GM087364 and GM105920), American Cancer Society (Grant RGS-09-278-01-CSM), MCubed, and the Fastforward Protein Folding Disease Initiative of The University of Michigan. C.C.W. is supported in part by the National Institutes of Health (Grants AG031867 and AG042095). T.-F.C. is a member of the UCLA Jonsson Comprehensive Cancer Center. \n\nAuthor contributions: Xiaoyi Zhang, L.G., Xiaoyan Zhang, S.L.B., Y.L., C.C.W., Y.W., and T.-F.C. designed research; Xiaoyi Zhang, L.G., Xiaoyan Zhang, S.L.B., D.E.W., Y.L., and L.L. performed research; V.S., C.C.W., Y.W., and T.-F.C. contributed new reagents/analytic tools; Xiaoyi Zhang, L.G., Xiaoyan Zhang, S.L.B., V.S., D.E.W., Y.L., L.L., J.S.L., P.-Y.S., H.J.L., M.I., C.C.W., M.R.A., Y.W., and T.-F.C. analyzed data; and S.L.B., D.E.W., J.S.L., P.-Y.S., H.J.L., M.I., C.C.W., M.R.A., Y.W., and T.-F.C. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1418820112/-/DCSupplemental.\n\nPublished - PNAS-2015-Zhang-E1705-14.pdf
Supplemental Material - pnas.1418820112.sapp.pdf
", "abstract": "Dominant mutations in p97/VCP (valosin-containing protein) cause a rare multisystem degenerative disease with varied phenotypes that include inclusion body myopathy, Paget's disease of bone, frontotemporal dementia, and amyotrophic lateral sclerosis. p97 disease mutants have altered N-domain conformations, elevated ATPase activity, and altered cofactor association. We have now discovered a previously unidentified disease-relevant functional property of p97 by identifying how the cofactors p37 and p47 regulate p97 ATPase activity. We define p37 as, to our knowledge, the first known p97-activating cofactor, which enhances the catalytic efficiency (k_(cat)/K_m) of p97 by 11-fold. Whereas both p37 and p47 decrease the K_m of ATP in p97, p37 increases the k_(cat) of p97. In contrast, regulation by p47 is biphasic, with decreased k_(cat) at low levels but increased k_(cat) at higher levels. By deleting a region of p47 that lacks homology to p37 (amino acids 69\u201392), we changed p47 from an inhibitory cofactor to an activating cofactor, similar to p37. Our data suggest that cofactors regulate p97 ATPase activity by binding to the N domain. Induced conformation changes affect ADP/ATP binding at the D1 domain, which in turn controls ATPase cycling. Most importantly, we found that the D2 domain of disease mutants failed to be activated by p37 or p47. Our results show that cofactors play a critical role in controlling p97 ATPase activity, and suggest that lack of cofactor-regulated communication may contribute to p97-associated disease pathogenesis.", "date": "2015-04-07", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "112", "number": "14", "publisher": "National Academy of Sciences", "pagerange": "E1705-E1714", "id_number": "CaltechAUTHORS:20150318-093025125", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150318-093025125", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "UL1TR000124" }, { "agency": "LA BioMed Seed Grant program", "grant_number": "20826-01" }, { "agency": "NIH", "grant_number": "HHSN261200800001E" }, { "agency": "NExT Chemical Biology Consortium" }, { "agency": "NIH", "grant_number": "GM087364" }, { "agency": "NIH", "grant_number": "GM105920" }, { "agency": "American Cancer Society", "grant_number": "RGS-09-278-01-CSM" }, { "agency": "MCubed" }, { "agency": "Fastforward Protein Folding Disease Initiative, University of Michigan" }, { "agency": "NIH", "grant_number": "AG031867" }, { "agency": "NIH", "grant_number": "AG042095" }, { "agency": "UCLA Jonsson Comprehensive Cancer Center" }, { "agency": "National Cancer Institute" } ] }, "doi": "10.1073/pnas.1418820112", "pmcid": "PMC4394316", "primary_object": { "basename": "PNAS-2015-Zhang-E1705-14.pdf", "url": "https://authors.library.caltech.edu/records/rb69g-9tv93/files/PNAS-2015-Zhang-E1705-14.pdf" }, "related_objects": [ { "basename": "pnas.1418820112.sapp.pdf", "url": "https://authors.library.caltech.edu/records/rb69g-9tv93/files/pnas.1418820112.sapp.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Zhang, Xiaoyi; Gui, Lin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p4h35-x2609", "eprint_id": 114052, "eprint_status": "archive", "datestamp": "2023-08-22 15:18:15", "lastmod": "2023-10-23 23:20:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Weihl-Conrad-C", "name": { "family": "Weihl", "given": "Conrad C." }, "orcid": "0000-0002-3816-6124" }, { "id": "Baloh-Robert-H", "name": { "family": "Baloh", "given": "Robert H." }, "orcid": "0000-0002-0100-8376" }, { "id": "Lee-Youjin", "name": { "family": "Lee", "given": "Youjin" }, "orcid": "0000-0001-7299-935X" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Pittman-Sara-K", "name": { "family": "Pittman", "given": "Sara K." } }, { "id": "Lopate-Glenn", "name": { "family": "Lopate", "given": "Glenn" } }, { "id": "Allred-Peggy", "name": { "family": "Allred", "given": "Peggy" } }, { "id": "Jockel-Balsarotti-Jennifer", "name": { "family": "Jockel-Balsarotti", "given": "Jennifer" } }, { "id": "Pestronk-Alan", "name": { "family": "Pestronk", "given": "Alan" }, "orcid": "0000-0002-8991-5770" }, { "id": "Harms-Matthew-B", "name": { "family": "Harms", "given": "Matthew B." }, "orcid": "0000-0002-3395-1633" } ] }, "title": "Targeted sequencing and identification of genetic variants in sporadic inclusion body myositis", "ispublished": "pub", "full_text_status": "public", "keywords": "Inclusion body myositis; VCP; Hereditary inclusion body myopathy; Myofibrillar myopathy; Amyotrophic lateral sclerosis; Genetics(clinical); Clinical Neurology; Neurology; Pediatrics, Perinatology, and Child Health", "note": "\u00a9 2014 Elsevier. \n\nReceived 17 October 2014, Revised 15 December 2014, Accepted 28 December 2014, Available online 6 January 2015. \n\nWe thank Amir Dori, Taha Bali, Cindy Ly, Arun Varadacharry, Paul Cooper, and Leo Wang for help with patient assessment. Supported by a research agreement from Ultragenyx Pharmaceuticals, Novato CA to CCW. Other funding included NIH AG031867 (CCW), AG042095 (CCW), NS055980 (RHB), NS069669 (RHB), and NS075094 (MBH). The Muscular Dystrophy Association (CCW), the Myositis Association (CCW), and the Hope Center for Neurological Disorders (CCW and MBH). RHB holds a Career Award for Medical Scientists from the Burroughs Wellcome Fund. Dr. Weihl had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.\n\nSupplemental Material - 1-s2.0-S0960896614007305-mmc1.zip
Supplemental Material - 1-s2.0-S0960896614007305-mmc2.docx
", "abstract": "Sporadic inclusion body myositis (sIBM) has clinical, pathologic and pathomechanistic overlap with some inherited muscle and neurodegenerative disorders. In this study, DNA from 79 patients with sIBM was collected and the sequencing of 38 genes associated with hereditary inclusion body myopathy (IBM), myofibrillar myopathy, Emery\u2013Dreifuss muscular dystrophy, distal myopathy, amyotrophic lateral sclerosis and dementia along with C9orf72 hexanucleotide repeat analysis was performed. No C9orf72 repeat expansions were identified, but; 27 rare (minor allele frequency <1%) missense coding variants in several other genes were identified. One patient carried a p.R95C missense mutation in VCP and another carried a previously reported p.I27V missense mutation in VCP. Mutations in VCP cause IBM associated with Paget's disease of the bone (PDB) and fronto-temporal dementia (IBMPFD). Neither patient had a family history of weakness or manifested other symptoms reported with VCP mutations such as PDB or dementia. In vitro analysis of these VCP variants found that they both disrupted autophagy similar to other pathogenic mutations. Although no clear genetic etiology has been implicated in sIBM pathogenesis, our study suggests that genetic evaluation in sIBM may be clinically meaningful and lend insight into its pathomechanism.", "date": "2015-04", "date_type": "published", "publication": "Neuromuscular Disorders", "volume": "25", "number": "4", "publisher": "Elsevier", "pagerange": "289-296", "id_number": "CaltechAUTHORS:20220323-565912000", "issn": "0960-8966", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565912000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ultragenyx Pharmaceuticals" }, { "agency": "NIH", "grant_number": "AG031867" }, { "agency": "NIH", "grant_number": "AG042095" }, { "agency": "NIH", "grant_number": "NS055980" }, { "agency": "NIH", "grant_number": "NS069669" }, { "agency": "NIH", "grant_number": "NS075094" }, { "agency": "Muscular Dystrophy Association" }, { "agency": "Myositis Association" }, { "agency": "Hope Center for Neurological Disorders" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1016/j.nmd.2014.12.009", "primary_object": { "basename": "1-s2.0-S0960896614007305-mmc1.zip", "url": "https://authors.library.caltech.edu/records/p4h35-x2609/files/1-s2.0-S0960896614007305-mmc1.zip" }, "related_objects": [ { "basename": "1-s2.0-S0960896614007305-mmc2.docx", "url": "https://authors.library.caltech.edu/records/p4h35-x2609/files/1-s2.0-S0960896614007305-mmc2.docx" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Weihl, Conrad C.; Baloh, Robert H.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/92t4a-nme16", "eprint_id": 114048, "eprint_status": "archive", "datestamp": "2023-08-22 15:12:28", "lastmod": "2023-10-23 23:20:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jerath-Nivedita-U", "name": { "family": "Jerath", "given": "Nivedita U." }, "orcid": "0000-0002-2729-880X" }, { "id": "Crockett-Cameron-D", "name": { "family": "Crockett", "given": "Cameron D." }, "orcid": "0000-0002-0240-2762" }, { "id": "Moore-Steven-A", "name": { "family": "Moore", "given": "Steven A." }, "orcid": "0000-0002-6353-7900" }, { "id": "Shy-Michael-E", "name": { "family": "Shy", "given": "Michael E." }, "orcid": "0000-0001-8460-6971" }, { "id": "Weihl-Conrad-C", "name": { "family": "Weihl", "given": "Conrad C." }, "orcid": "0000-0002-3816-6124" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Grider-Tiffany", "name": { "family": "Grider", "given": "Tiffany" }, "orcid": "0000-0002-2236-9218" }, { "id": "Gonzalez-Michael-A", "name": { "family": "Gonzalez", "given": "Michael A." } }, { "id": "Zuchner-Stephan", "name": { "family": "Zuchner", "given": "Stephan" }, "orcid": "0000-0002-8498-5235" }, { "id": "Swenson-Andrea", "name": { "family": "Swenson", "given": "Andrea" }, "orcid": "0000-0003-1547-7699" } ] }, "title": "Rare Manifestation of a c.290 C>T, p.Gly97Glu VCP Mutation", "ispublished": "pub", "full_text_status": "public", "keywords": "General Engineering", "note": "\u00a9 2015 Nivedita U. Jerath et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nReceived 27 January 2015; Accepted 12 March 2015. \n\nMichael E. Shy would like to acknowledge support from the National Institute of Neurological Disorders and Stroke (NINDS) and Office of Rare Diseases (U54, NS065712) as well as grants from the Muscular Dystrophy Association (MDA) and Charcot Marie Tooth Association (CMTA). Nivedita U. Jerath would like to acknowledge support from an MDA Clinical Research Training grant and a University of Iowa Internal Funding Initiatives award. Cameron D. Crockett received funding by NIH through the Iowa Wellstone Muscular Dystrophy Cooperative Research Center (U54, NS053672). Steven A. Moore is supported in part by NIH through the Iowa Wellstone Muscular Dystrophy Cooperative Research Center (U54, NS053672). Tsui-Fen Chou is supported by the National Center for Advancing Translational Sciences through UCLA CTSI Grant UL1TR000124 and the LA BioMed Seed Grant program (20826-01) and is a member of UCLA Johnson Comprehensive Cancer Center. \n\nInformed consent was obtained from the patient. \n\nThe authors declare that there is no conflict of interests regarding the publication of this paper.\n\nPublished - 239167.pdf
", "abstract": "Introduction. The valosin-containing protein (VCP) regulates several distinct cellular processes. Consistent with this, VCP mutations manifest variable clinical phenotypes among and within families and are a diagnostic challenge. \n\nMethods. A 60-year-old man who played ice hockey into his 50's was evaluated by electrodiagnostics, muscle biopsy, and molecular genetics.Results. With long-standing pes cavus and toe walking, our patient developed progressive weakness, cramps, memory loss, and paresthesias at age 52. An axonal sensorimotor neuropathy was found upon repeated testing at age 58. Neuropathic histopathology was present in the quadriceps, and exome sequencing revealed the VCP mutation c.290 C>T, p.Gly97Glu. \n\nConclusions. Our patient reflects the clinical heterogeneity of VCP mutations, as his neurological localization is a spectrum between a lower motor neuron disorder and a hereditary axonal peripheral neuropathy such as CMT2. Our case demonstrates a rare manifestation of the c.290 C>T, pGly97Glu VCP mutation.", "date": "2015-03-23", "date_type": "published", "publication": "Case Reports in Genetics", "volume": "2015", "publisher": "Hindawi Limited", "pagerange": "Art. No. 239167", "id_number": "CaltechAUTHORS:20220323-565866000", "issn": "2090-6544", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565866000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54 NS065712" }, { "agency": "Muscular Dystrophy Association" }, { "agency": "Charcot Marie Tooth Association" }, { "agency": "University of Iowa" }, { "agency": "NIH", "grant_number": "U54 NS053672" }, { "agency": "NIH", "grant_number": "UL1TR000124" }, { "agency": "LA BioMed Seed Grant", "grant_number": "20826-01" }, { "agency": "UCLA Johnson Comprehensive Cancer Center" } ] }, "doi": "10.1155/2015/239167", "pmcid": "PMC4386706", "primary_object": { "basename": "239167.pdf", "url": "https://authors.library.caltech.edu/records/92t4a-nme16/files/239167.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Jerath, Nivedita U.; Crockett, Cameron D.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6x60v-c4g35", "eprint_id": 114039, "eprint_status": "archive", "datestamp": "2023-08-22 14:40:12", "lastmod": "2023-10-23 23:20:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fang-Chen-Jie", "name": { "family": "Fang", "given": "Chen-Jie" }, "orcid": "0000-0003-1450-1271" }, { "id": "Gui-Lin", "name": { "family": "Gui", "given": "Lin" } }, { "id": "Zhang-Xiaoyi", "name": { "family": "Zhang", "given": "Xiaoyi" }, "orcid": "0000-0001-9732-1449" }, { "id": "Moen-Derek-R", "name": { "family": "Moen", "given": "Derek R." } }, { "id": "Li-Kelin", "name": { "family": "Li", "given": "Kelin" } }, { "id": "Frankowski-Kevin-J", "name": { "family": "Frankowski", "given": "Kevin J." }, "orcid": "0000-0002-7173-6352" }, { "id": "Lin-Henry-J", "name": { "family": "Lin", "given": "Henry J." } }, { "id": "Schoenen-Frank-J", "name": { "family": "Schoenen", "given": "Frank J." }, "orcid": "0000-0003-2711-1117" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" } ] }, "title": "Evaluating p97 Inhibitor Analogues for Their Domain Selectivity and Potency against the p97-p47 Complex", "ispublished": "pub", "full_text_status": "public", "keywords": "AAA ATPase; antitumor agents; p97; proteasomes; structure\u2013activity relationships; ubiquitin; Organic Chemistry; General Pharmacology, Toxicology and Pharmaceutics; Molecular Medicine; Drug Discovery; Biochemistry; Pharmacology", "note": "\u00a9 2015 WILEY-VCH. \n\nIssue Online: 23 December 2014. Version of Record online: 06 November 2014. Manuscript received: 14 October 2014. \n\nThe authors thank Benjamin Neuenswander (University of Kansas, USA) and Patrick R. Porubsky (University of Kansas, USA) for managing compounds. The project was in part supported by the US National Center for Advancing Translational Sciences through UCLA CTSI Grant UL1TR000124 and the LA BioMed Seed Grant program (20826-01). This work was supported by a grant from the US National Institutes of Health Molecular Libraries Probe Production Centers Network to Jeffrey Aub\u00e9 at the University of Kansas (PI) (5U54HG005031). FJS thanks the University of Kansas (Lawrence, KS, USA) for support of this research through a KU Research Achievement Award. CJF thanks The Beijing Teachers Training Center for Higher Education for financial support (Grant No. 067135300100). FJS is a member of the University of Kansas Cancer Center. TFC is a member of UCLA Jonsson Comprehensive Cancer Center.\n\nAccepted Version - nihms647576.pdf
Supplemental Material - cmdc_201402420_sm_miscellaneous_information.pdf
", "abstract": "We previously found that p97 ATPase inhibitors 2-(2-amino-1H-benzo[d]imidazol-1-yl)-N-benzyl-8-methoxyquinazolin-4-amine (ML240) and 2-(2H-benzo[b][1,4]oxazin-4(3H)-yl)-N-benzyl-5,6,7,8-tetrahydroquinazolin-4-amine (ML241) specifically target the D2 domain of wild-type p97. In addition, one of the major p97 cofactors, p47, decreases their potencies by \u223c50-fold. In contrast, N2,N4-dibenzylquinazoline-2,4-diamine (DBeQ) targets both the D1 and D2 domains and shows only a four- to sixfold decrease in potency against the p97\u2013p47 complex. To elucidate structure\u2013activity relationships for the inhibitors, we screened 200 p97 inhibitor analogues for their ability to inhibit the ATPase activity of either or both of the D1 or D2 domains, as well for their effects on p47 potency. The selectivity of 29 of these compounds was further examined by eight-dose titrations. Four compounds showed modest selectivity for inhibiting the ATPase activity of D1. Eleven compounds inhibited D2 with greater potencies, and four showed similar potencies against D1 and D2. p47 decreased the potencies of the majority of the compounds and increased the potencies of five compounds. These results highlight the possibility of developing domain-selective and complex-specific p97 inhibitors in order to further elucidate the physiological roles of p97 and its cofactors.", "date": "2015-01", "date_type": "published", "publication": "ChemMedChem", "volume": "10", "number": "1", "publisher": "Wiley-Blackwell", "pagerange": "52-56", "id_number": "CaltechAUTHORS:20220323-565532000", "issn": "1860-7179", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565532000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "UL1TR000124" }, { "agency": "LA BioMed Seed Grant", "grant_number": "20826-01" }, { "agency": "NIH", "grant_number": "5U54HG005031" }, { "agency": "University of Kansas" }, { "agency": "Beijing Teachers Training Center for Higher Education", "grant_number": "067135300100" }, { "agency": "Jonsson Comprehensive Cancer Center" } ] }, "doi": "10.1002/cmdc.201402420", "pmcid": "PMC4280364", "primary_object": { "basename": "cmdc_201402420_sm_miscellaneous_information.pdf", "url": "https://authors.library.caltech.edu/records/6x60v-c4g35/files/cmdc_201402420_sm_miscellaneous_information.pdf" }, "related_objects": [ { "basename": "nihms647576.pdf", "url": "https://authors.library.caltech.edu/records/6x60v-c4g35/files/nihms647576.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Fang, Chen-Jie; Gui, Lin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qc0ec-yqr06", "eprint_id": 52399, "eprint_status": "archive", "datestamp": "2023-08-20 03:56:21", "lastmod": "2023-10-18 19:49:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kato-Mihoko", "name": { "family": "Kato", "given": "Mihoko" }, "orcid": "0000-0003-3827-8879" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Yu-Collin-Z", "name": { "family": "Yu", "given": "Collin Z." } }, { "id": "DeModena-J-A", "name": { "family": "DeModena", "given": "John A." } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "LINKIN, a new transmembrane protein necessary for cell adhesion", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 eLife Sciences Publications.\n\nReceived: 21 August 2014;\nAccepted: 28 November 2014;\nPublished: 1 December 2014.\n\nWe are grateful to Amir Sapir, Hillel Schwartz, and Srimoyee Ghosh for critical reading of the manuscript, and to TFC's postdocs, Xiaoyi Zhaang and Lin Gui, for assistance with IP/Western blot analysis experiments. Caltech protein expression facility expressed and purified LNKN-1 extracellular domain. Mass spectrometry experiments were performed at the Caltech protein exploration laboratory directed by Dr. Sonja Hess and Prof. Ray Deshaies. Wormbase (wormbase.org) was a valuable resource for C. elegans information as was the British Columbia C. elegans Gene Expression Consortium (http://elegans.bcgsc.ca/home/ge_consortium.html) GFP expression pattern database. The monoclonal antibody developed by Frankel, J. and Nelsen, E.M. was obtained from the Developmental Studies Hydridoma Bank, created by the NICHD of the NIH and maintained at the University of Iowa. Nematode strains were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources. C.Z.Y. was funded by a CIRM pre-doctoral training grant. P.W.S. in an investigator with the Howard Hughes Medical Institute, which supported this work.\n\nAuthor contributions:\n\nMK, T-FC, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting\nor revising the article; CZY, JD, Acquisition of data, Analysis and interpretation of data; PWS,\nConception and design, Analysis and interpretation of data, Drafting or revising the article.\n\nSupplemental Material - elife04449_Supplemental_files.zip
", "abstract": "In epithelial collective migration, leader and follower cells migrate while maintaining cell-cell adhesion and tissue polarity. We have identified a conserved protein and interactors required for maintaining cell adhesion during a simple collective migration in the developing C. elegans male gonad. LINKIN is a previously uncharacterized, transmembrane protein conserved throughout Metazoa. We identified seven atypical FG-GAP domains in the extracellular domain, which potentially folds into a \u03b2-propeller structure resembling the \u03b1-integrin ligand-binding domain. C. elegans LNKN-1 localizes to the plasma membrane of all gonadal cells, with apical and lateral bias. We identified the LINKIN interactors RUVBL1, RUVBL2, and \u03b1-tubulin by using SILAC mass spectrometry on human HEK 293T cells and testing candidates for lnkn-1-like function in C. elegans male gonad. We propose that LINKIN promotes adhesion between neighboring cells through its extracellular domain and regulates microtubule dynamics through RUVBL proteins at its intracellular domain.", "date": "2014-12-01", "date_type": "published", "publication": "eLife", "volume": "2014", "number": "3", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e04449", "id_number": "CaltechAUTHORS:20141204-125558317", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141204-125558317", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "California Institute for Regenerative Medicine (CIRM)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.7554/eLife.04449", "pmcid": "PMC4275582", "primary_object": { "basename": "elife04449_Supplemental_files.zip", "url": "https://authors.library.caltech.edu/records/qc0ec-yqr06/files/elife04449_Supplemental_files.zip" }, "resource_type": "article", "pub_year": "2014", "author_list": "Kato, Mihoko; Chou, Tsui-Fen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/07qc6-h3m41", "eprint_id": 114044, "eprint_status": "archive", "datestamp": "2023-08-22 14:07:30", "lastmod": "2023-10-23 23:20:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gonzalez-Michael-A", "name": { "family": "Gonzalez", "given": "Michael A." } }, { "id": "Feely-Shawna-M", "name": { "family": "Feely", "given": "Shawna M." } }, { "id": "Speziani-Fiorella", "name": { "family": "Speziani", "given": "Fiorella" } }, { "id": "Strickland-Alleene-V", "name": { "family": "Strickland", "given": "Alleene V." } }, { "id": "Danzi-Matt", "name": { "family": "Danzi", "given": "Matt" } }, { "id": "Bacon-Chelsea", "name": { "family": "Bacon", "given": "Chelsea" } }, { "id": "Lee-YouJin", "name": { "family": "Lee", "given": "Youjin" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Blanton-Susan-H", "name": { "family": "Blanton", "given": "Susan H." } }, { "id": "Weihl-Conrad-C", "name": { "family": "Weihl", "given": "Conrad C." }, "orcid": "0000-0002-3816-6124" }, { "id": "Zuchner-Stephan", "name": { "family": "Zuchner", "given": "Stephan" } }, { "id": "Shy-Michael-E", "name": { "family": "Shy", "given": "Michael E." } } ] }, "title": "A novel mutation in VCP causes Charcot\u2013Marie\u2013Tooth Type 2 disease", "ispublished": "pub", "full_text_status": "public", "keywords": "neuropathy, whole-exome sequencing, autophagy, hereditary motor and sensory neuropathies, neurodegeneration; Neurology (clinical)", "note": "\u00a9 The Author (2014). Published by Oxford University Press on behalf of the Guarantors of Brain. \n\nReceived: 16 April 2014. Revision received: 23 June 2014. Accepted: 07 July 2014. Published: 14 August 2014. \n\nWe deeply appreciate the commitment of the family studied and we are also thankful for conceptual discussions with Dr Steven Baker, McMaster University, Ontario, Canada. \n\nThis study was supported by NIH (R01NS075764 and U54NS065712 to M.S. and S.Z.; AG031867 and AG042095 to C.C.W.); the CMT Association (M.S. and S.Z.); the Muscular Dystrophy Association (C.C.W.); the Hope Center for Neurological Disorders (C.C.W.); TFC was supported by the National Center for Advancing Translational Sciences through UCLA CTSI (Grant UL1TR000124) and the LA BioMed Seed Grant program (20826-01) and is a member of UCLA Jonsson Comprehensive Cancer Center.\n\nSupplemental Material - awu224_Supplementary_Data.zip
", "abstract": "Mutations in VCP have been reported to account for a spectrum of phenotypes that include inclusion body myopathy with Paget's disease of the bone and frontotemporal dementia, hereditary spastic paraplegia, and 1\u20132% of familial amyotrophic lateral sclerosis. We identified a novel VCP mutation (p.Glu185Lys) segregating in an autosomal dominant Charcot\u2013Marie\u2013Tooth disease type 2 family. Functional studies showed that the Glu185Lys variant impaired autophagic function leading to the accumulation of immature autophagosomes. VCP mutations should thus be considered for genetically undefined Charcot\u2013Marie\u2013Tooth disease type 2.", "date": "2014-11", "date_type": "published", "publication": "Brain", "volume": "137", "number": "11", "publisher": "Oxford University Press", "pagerange": "2897-2902", "id_number": "CaltechAUTHORS:20220323-565646000", "issn": "1460-2156", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565646000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01NS075764" }, { "agency": "NIH", "grant_number": "U54NS065712" }, { "agency": "NIH", "grant_number": "AG031867" }, { "agency": "NIH", "grant_number": "AG042095" }, { "agency": "Charcot-Marie-Tooth Association" }, { "agency": "Muscular Dystrophy Association" }, { "agency": "Hope Center for Neurological Disorders" }, { "agency": "NIH", "grant_number": "UL1TR000124" }, { "agency": "LA BioMed Seed Grant", "grant_number": "20826-01" }, { "agency": "UCLA Jonsson Comprehensive Cancer Center" } ] }, "doi": "10.1093/brain/awu224", "pmcid": "PMC4208462", "primary_object": { "basename": "awu224_Supplementary_Data.zip", "url": "https://authors.library.caltech.edu/records/07qc6-h3m41/files/awu224_Supplementary_Data.zip" }, "resource_type": "article", "pub_year": "2014", "author_list": "Gonzalez, Michael A.; Feely, Shawna M.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/d6fcr-wag21", "eprint_id": 49244, "eprint_status": "archive", "datestamp": "2023-08-22 13:41:08", "lastmod": "2023-10-17 21:14:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sapir-A", "name": { "family": "Sapir", "given": "Amir" }, "orcid": "0000-0001-9888-1800" }, { "id": "Tsur-A", "name": { "family": "Tsur", "given": "Assaf" } }, { "id": "Koorman-T", "name": { "family": "Koorman", "given": "Thijs" }, "orcid": "0000-0002-6064-3353" }, { "id": "Ching-Kaitlin", "name": { "family": "Ching", "given": "Kaitlin" }, "orcid": "0000-0002-0517-2421" }, { "id": "Mishra-P", "name": { "family": "Mishra", "given": "Prashant" } }, { "id": "Bardenheier-A", "name": { "family": "Bardenheier", "given": "Annabelle" } }, { "id": "Podolsky-L", "name": { "family": "Podolsky", "given": "Lisa" } }, { "id": "Bening-Abu-Schach-U", "name": { "family": "Bening-Abu-Schach", "given": "Ulrike" } }, { "id": "Boxem-M", "name": { "family": "Boxem", "given": "Mike" }, "orcid": "0000-0003-3966-4173" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Broday-L", "name": { "family": "Broday", "given": "Limor" } }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging", "ispublished": "pub", "full_text_status": "public", "keywords": "HMG-CoA synthase; sterol synthesis; yeast two-hybrid", "note": "\u00a9 2014 National Academy of Sciences. \n\nContributed by Paul W. Sternberg, August 6, 2014 (sent for review July 3, 2014). Published online before print September 3, 2014, doi: 10.1073/pnas.1414748111. \n\nWe thank Shohei Mitani for a knockout allele, Ann Wang for the ulp-4 RNAi in the ulp-4::gfp experiments, Adam Kolawa and Kevin Yu for their help with worm functional assays, Robyn Branicky and William Schafer for sharing the clh-3::mCherry worms, Brian Williams for total human RNA, David Chan for use of his Seahorse oxygen consumption analyzer, Domenico Fasci for his help with in vitro sumoylation assays, and Jennifer Watt for fat measurements. We also thank WormBase and the Caenorhabditis Genetics Center for C. elegans genetic annotation and strains. The Henry L. Guenther Foundation supported the Q-Exactive mass spectrometer. This research was supported by the Howard Hughes Medical Institute (of which P.W.S. is an Investigator), the Israel Cancer Research Fund PG -11-3086 (to L.B.), and Israel Science Foundation Grant ISF 1617/11 (to L.B.). A.T. was supported by the Ori Foundation-In Memory of Ori Levi, the Israeli Mitochondrial Disease Foundation (www.orifund.org). T.-F.C. is a member of University of California, Los Angeles's Jonsson Comprehensive Cancer Center. P.M. is supported by a Baxter Senior Postdoctoral Fellowship. \n\nAuthor contributions: A.S., M.B., T.-F.C., L.B., and P.W.S. designed research; A.S., A.T., T.K., K.C., P.M., A.B., L.P., U.B.-A.-S., T.-F.C., and L.B. performed research; A.S., A.T., T.K., P.M., M.B., T.-F.C., and L.B. analyzed data; and A.S., K.C., L.B., and P.W.S. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1414748111/-/DCSupplemental.\n\nPublished - E3880.full.pdf
Supplemental Material - pnas.1414748111.sd01.xlsx
Supplemental Material - pnas.1414748111.sm01.avi
Supplemental Material - pnas.1414748111.sm02.avi
Supplemental Material - pnas.201414748SI.pdf
", "abstract": "Many metabolic pathways are critically regulated during development and aging but little is known about the molecular mechanisms underlying this regulation. One key metabolic cascade in eukaryotes is the mevalonate pathway. It catalyzes the synthesis of sterol and nonsterol isoprenoids, such as cholesterol and ubiquinone, as well as other metabolites. In humans, an age-dependent decrease in ubiquinone levels and changes in cholesterol homeostasis suggest that mevalonate pathway activity changes with age. However, our knowledge of the mechanistic basis of these changes remains rudimentary. We have identified a regulatory circuit controlling the sumoylation state of Caenorhabditis elegans HMG-CoA synthase (HMGS-1). This protein is the ortholog of human HMGCS1 enzyme, which mediates the first committed step of the mevalonate pathway. In vivo, HMGS-1 undergoes an age-dependent sumoylation that is balanced by the activity of ULP-4 small ubiquitin-like modifier protease. ULP-4 exhibits an age-regulated expression pattern and a dynamic cytoplasm-to-mitochondria translocation. Thus, spatiotemporal ULP-4 activity controls the HMGS-1 sumoylation state in a mechanism that orchestrates mevalonate pathway activity with the age of the organism. To expand the HMGS-1 regulatory network, we combined proteomic analyses with knockout studies and found that the HMGS-1 level is also governed by the ubiquitin\u2013proteasome pathway. We propose that these conserved molecular circuits have evolved to govern the level of mevalonate pathway flux during aging, a flux whose dysregulation is associated with numerous age-dependent cardiovascular and cancer pathologies.", "date": "2014-09-16", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "111", "number": "37", "publisher": "National Academy of Sciences", "pagerange": "E3880-E3889", "id_number": "CaltechAUTHORS:20140904-122954030", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140904-122954030", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Henry L. Guenther Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Israel Cancer Research Fund", "grant_number": "PG-11-3086" }, { "agency": "Israel Science Foundation", "grant_number": "ISF 1617/11" }, { "agency": "Ori Foundation" }, { "agency": "Israeli Mitochondrial Disease Foundation" }, { "agency": "Baxter Foundation" } ] }, "doi": "10.1073/pnas.1414748111", "pmcid": "PMC4169931", "primary_object": { "basename": "E3880.full.pdf", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/E3880.full.pdf" }, "related_objects": [ { "basename": "pnas.1414748111.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/pnas.1414748111.sd01.xlsx" }, { "basename": "pnas.1414748111.sm01.avi", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/pnas.1414748111.sm01.avi" }, { "basename": "pnas.1414748111.sm02.avi", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/pnas.1414748111.sm02.avi" }, { "basename": "pnas.201414748SI.pdf", "url": "https://authors.library.caltech.edu/records/d6fcr-wag21/files/pnas.201414748SI.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Sapir, Amir; Tsur, Assaf; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6wvcy-70d51", "eprint_id": 46152, "eprint_status": "archive", "datestamp": "2023-08-22 13:16:23", "lastmod": "2023-10-26 18:43:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Bulfer-S-L", "name": { "family": "Bulfer", "given": "Stacie L." } }, { "id": "Weihl-C-C", "name": { "family": "Weihl", "given": "Conrad C." } }, { "id": "Li-Kelin", "name": { "family": "Li", "given": "Kelin" } }, { "id": "Lis-L-G", "name": { "family": "Lis", "given": "Lev G." } }, { "id": "Walters-M-A", "name": { "family": "Walters", "given": "Michael A." } }, { "id": "Schoenen-F-J", "name": { "family": "Schoenen", "given": "Frank J." } }, { "id": "Lin-Henry-J", "name": { "family": "Lin", "given": "Henry J." } }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" }, { "id": "Arkin-M-R", "name": { "family": "Arkin", "given": "Michelle R." } } ] }, "title": "Specific Inhibition of p97/VCP ATPase and Kinetic Analysis Demonstrate Interaction between D1 and D2 ATPase domains", "ispublished": "pub", "full_text_status": "public", "keywords": "p97/VCP AAA ATPase; IBMPFD/ALS; steady-state kinetics; SPR; p97 inhibitor", "note": "\u00a9 2014 Elsevier. \n\nReceived date: 6 February 2014. Revised date: 21 May 2014. Accepted date: 22 May 2014. Available online 27 May 2014. \n\nWe thank Michelina Iacovino for critical reading and suggestions on this manuscript. We thank David Myszka for assistance in fitting SPR data in CLAMP. The project was in part supported by the National Center for Advancing Translational Sciences through UCLA CTSI Grant UL1TR000124 and the LA BioMed Seed Grant program (20826-01). This project has been funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under Chemical Biology Consortium Contract No. HHSN261200800001E and by the National Human Genome Research Institute of the National Institutes of Health under Award Number U54HG005031 (Jeffrey Aub\u00e9, PI). The content of this publication does not\nnecessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. government. RJD is an Investigator of the Howard Hughes Medical Institute, and TFC is a member of UCLA Jonsson Comprehensive Cancer Center.\n\nAccepted Version - nihms606788.pdf
", "abstract": "The p97 AAA (ATPase associated with diverse cellular activities), also called VCP (valosin-containing protein), is an important therapeutic target for cancer and neurodegenerative diseases. p97 forms a hexamer composed of two AAA domains (D1 and D2) that form two stacked rings, and an N-terminal domain that binds numerous cofactor proteins. The interplay between the three domains in p97 is complex, and a deeper biochemical understanding is needed in order to design selective p97 inhibitors as therapeutic agents. It is clear that the D2 ATPase domain hydrolyzes ATP in vitro, but whether D1 contributes to ATPase activity is controversial. Here, we use Walker A and B mutants to demonstrate that D1 is capable of hydrolyzing ATP, and show for the first time that nucleotide binding in the D2 domain increases the catalytic efficiency (k_(cat)/K_m) of D1 ATP hydrolysis 280-fold, by increasing k_(cat) 7-fold and decreasing K_m about 40-fold. We further show that an ND1 construct lacking D2 but including the linker between D1 and D2 is catalytically active, resolving a conflict in the literature. Applying enzymatic observations to small-molecule inhibitors, we show that four p97 inhibitors (DBeQ, ML240, ML241, and NMS-873) have differential responses to Walker A and B mutations, to disease-causing IBMPFD mutations, and to the presence of the N-domain binding cofactor protein p47. These differential effects provide the first evidence that p97 cofactors and disease mutations can alter p97 inhibitor potency and suggest the possibility of developing context-dependent inhibitors of p97.", "date": "2014-07-29", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "426", "number": "15", "publisher": "Elsevier", "pagerange": "2886-2899", "id_number": "CaltechAUTHORS:20140609-114312310", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140609-114312310", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "UL1TR000124" }, { "agency": "LA BioMed Seed Grant program", "grant_number": "20826-01" }, { "agency": "NIH", "grant_number": "HHSN261200800001E" }, { "agency": "NIH", "grant_number": "U54HG005031" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.jmb.2014.05.022", "pmcid": "PMC4102644", "primary_object": { "basename": "nihms606788.pdf", "url": "https://authors.library.caltech.edu/records/6wvcy-70d51/files/nihms606788.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Chou, Tsui-Fen; Bulfer, Stacie L.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/s7fx1-vwn02", "eprint_id": 54415, "eprint_status": "archive", "datestamp": "2023-08-20 00:15:55", "lastmod": "2023-10-20 16:25:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond" }, "orcid": "0000-0002-3671-9354" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Li-Jing", "name": { "family": "Li", "given": "Jing" } }, { "id": "Mackinnon-A", "name": { "family": "Mackinnon", "given": "Andy" } }, { "id": "Parlati-F", "name": { "family": "Parlati", "given": "Francesco" } } ] }, "title": "Exploiting protein homeostasis for cancer therapy", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2014 Federation of American Societies for Experimental Biology.", "abstract": "Cancer cells often harbor numerous genomic insults and an altered metabolism.\nTogether, these changes impede protein folding and assembly. As a result, cancer\ncells can have an elevated dependence on mechanisms that sustain protein\nassembly and quality control. To test whether cancer cells are hypersensitive to\ninhibition of protein homeostasis pathways, we seek to develop small molecule\nantagonists of ubiquitin system enzymes involved in protein quality control. In\nparticular, we have been pursuing the proteasome, the COP9-Signalosome, and\nthe ubiquitin-selective 'segregase' p97/VCP. Over the past 5 years we have carried\nout HTS against these targets through the NIH's Molecular Libraries Program.\nAnalysis of structure-activity relationships for the resulting hits has led to enzyme\ninhibitors with IC50 ~0.1-1 \u03bcM that are active in cells. These compounds are\nuseful tools for basic research and represent starting points for drug discovery. My\ntalk will focus on our recent progress in developing novel small molecule probes\nfor UPS enzymes.", "date": "2014-04", "date_type": "published", "publication": "FASEB Journal", "volume": "28", "number": "1", "publisher": "Federation of American Societies for Experimental Biology", "pagerange": "472.2", "id_number": "CaltechAUTHORS:20150205-100227097", "issn": "0892-6638", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150205-100227097", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2014", "author_list": "Deshaies, Raymond; Chou, Tsui-Fen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tsc8g-mpt51", "eprint_id": 114042, "eprint_status": "archive", "datestamp": "2023-08-22 09:24:36", "lastmod": "2023-10-23 23:20:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhou-Xin", "name": { "family": "Zhou", "given": "Xin" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Aubol-Brandon-E", "name": { "family": "Aubol", "given": "Brandon E." } }, { "id": "Park-Chin-Ju", "name": { "family": "Park", "given": "Chin Ju" }, "orcid": "0000-0002-7750-1554" }, { "id": "Wolfenden-Richard", "name": { "family": "Wolfenden", "given": "Richard" }, "orcid": "0000-0002-3745-9099" }, { "id": "Adams-Joseph-D", "name": { "family": "Adams", "given": "Joseph" }, "orcid": "0000-0001-7645-8913" }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Kinetic Mechanism of Human Histidine Triad Nucleotide Binding Protein 1", "ispublished": "pub", "full_text_status": "public", "keywords": "Kinetic parameters, Peptides and proteins, Monomers, Hydrolysis, Viscosity; Biochemistry", "note": "\u00a9 2013 American Chemical Society. \n\nReceived 2 December 2012. Revised 8 March 2013. Published online 7 May 2013. Published in issue 21 May 2013. \n\nThe authors declare no competing financial interest.\n\nAccepted Version - nihms477319.pdf
Supplemental Material - bi301616c_si_001.pdf
", "abstract": "Human histidine triad nucleotide binding protein 1 (hHint1) is a member of a ubiquitous and ancient branch of the histidine triad protein superfamily. hHint1 is a homodimeric protein that catalyzes the hydrolysis of model substrates, phosphoramidate and acyl adenylate, with a high efficiency. Recently, catalytically inactive hHint1 has been identified as the cause of inherited peripheral neuropathy [Zimon, M., et al. (2012) Nat. Genet. 44, 1080\u20131083]. We have conducted the first detailed kinetic mechanistic studies of hHint1 and have found that the reaction mechanism is consistent with a double-displacement mechanism, in which the active site nucleophile His112 is first adenylylated by the substrate, followed by hydrolysis of the AMP\u2013enzyme intermediate. A transient burst phase followed by a linear phase from the stopped-flow fluorescence assay indicated that enzyme adenylylation was faster than the subsequent intermediate hydrolysis and product release. Solvent viscosity experiments suggested that both chemical transformation and diffusion-sensitive events (product release or protein conformational change) limit the overall turnover. The catalytic trapping experiments and data simulation indicated that the true k_(off) rate of the final product AMP is unlikely to control the overall k_(cat). Therefore, a protein conformational change associated with product release is likely rate-limiting. In addition, the rate of Hint1 adenylylation was found to be dependent on two residues with pK\u2090 values of 6.5 and 8, with the former pK\u2090 agreeing well with the nuclear magnetic resonance titration results for the pK\u2090 of the active site nucleophile His112. In comparison to the uncatalyzed rates, hHint1 was shown to enhance acyl-AMP and AMP phosphoramidate hydrolysis by 10\u2076\u201310\u2078-fold. Taken together, our analysis indicates that hHint1 catalyzes the hydrolysis of phosphoramidate and acyl adenylate with high efficiency, through a mechanism that relies on rapid adenylylation of the active residue, His112, while being partially rate-limited by intermediate hydrolysis and product release associated with a conformational change. Given the high degree of sequence homology of Hint proteins across all kingdoms of life, it is likely that their kinetic and catalytic mechanisms will be similar to those elucidated for hHint1.", "date": "2013-05-21", "date_type": "published", "publication": "Biochemistry", "volume": "52", "number": "20", "publisher": "American Chemical Society", "pagerange": "3588-3600", "id_number": "CaltechAUTHORS:20220323-565578000", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565578000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1021/bi301616c", "pmcid": "PMC3835729", "primary_object": { "basename": "bi301616c_si_001.pdf", "url": "https://authors.library.caltech.edu/records/tsc8g-mpt51/files/bi301616c_si_001.pdf" }, "related_objects": [ { "basename": "nihms477319.pdf", "url": "https://authors.library.caltech.edu/records/tsc8g-mpt51/files/nihms477319.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Zhou, Xin; Chou, Tsui-Fen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1jp9m-9wp37", "eprint_id": 44489, "eprint_status": "archive", "datestamp": "2023-08-19 19:34:32", "lastmod": "2023-10-26 14:20:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shi-Yihui", "name": { "family": "Shi", "given": "Yihui" } }, { "id": "Liu-Xiaohe", "name": { "family": "Liu", "given": "Xiaohe" } }, { "id": "Calaogan-J", "name": { "family": "Calaoagan", "given": "Joy" } }, { "id": "Samuelson-S", "name": { "family": "Samuelson", "given": "Steven" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" }, { "id": "Sambucetti-L-C", "name": { "family": "Sambucetti", "given": "Lidia C." } } ] }, "title": "Development of functional assays for p97/VCP inhibition", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2013 American Association for Cancer Research. Funded by NExT Chemical Biology Consortium, NCI Contract No. HHSN261200800001E.", "abstract": "p97 (also called VCP in metazoans and CDC48 in yeast) is a highly conserved, ubiquitously expressed, and essential AAA ATPase. p97 plays a key role in endoplasmic reticulum-associated degradation of misfolded secretory and membrane proteins as well as ubiquitin-dependent turnover of a subset of cytoplasmic substrates of the ubiquitin-proteasome system.", "date": "2013-04-15", "date_type": "published", "publication": "Cancer Research", "volume": "73", "number": "8", "publisher": "American Association for Cancer Research", "pagerange": "Art. No. 2146", "id_number": "CaltechAUTHORS:20140325-082556135", "issn": "0008-5472", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140325-082556135", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NExT Chemical Biology Consortium" }, { "agency": "National Cancer Institute", "grant_number": "HHSN261200800001E" } ] }, "doi": "10.1158/1538-7445.AM2013-2146", "resource_type": "article", "pub_year": "2013", "author_list": "Shi, Yihui; Liu, Xiaohe; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rqt83-93q76", "eprint_id": 37218, "eprint_status": "archive", "datestamp": "2023-08-19 14:30:53", "lastmod": "2023-10-23 17:15:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Li-Kelin", "name": { "family": "Li", "given": "Kelin" } }, { "id": "Frankowski-K-J", "name": { "family": "Frankowski", "given": "Kevin J." } }, { "id": "Schoenen-F-J", "name": { "family": "Schoenen", "given": "Frank J." } }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" } ] }, "title": "Structure\u2013Activity Relationship Study Reveals ML240 and ML241 as Potent and Selective Inhibitors of p97 ATPase", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Wiley-VCH Verlag GmbH& Co. KGaA, Weinheim. \n\nReceived: November 8, 2012. Revised: December 7, 2012. Published online on January 11, 2013. \n\nWe thank B. E. Nordin and M. P. Patricelli (ActivX Biosciences La Jolla, CA, USA) for analyzing the ACJI-47 positive control free of\ncharge in the kinase profiling experiments. Ki determinations and receptor binding profiles were generously provided by the National Institute of Mental Health's Psychoactive Drug Screening Program, Contract no. HHSN-271-2008-00025-C (NIMH PDSP). The NIMH PDSP is Directed by Bryan L. Roth, MD PhD (University of North Carolina, Chapel Hill, NC, USA) and Project Officer Jamie Driscol (NIMH, Bethesda MD, USA). The NCI 60-cell-line screen was performed by the Developmental Therapeutics Program at the NCI. We thank Jeffrey Aub\u00e9 (University of Kansas, Lawrence, KS, USA) for helpful discussions, P. Porubsky (University of Kansas) for compound management, Ben Neuenswander (University of Kansas) for compound purification and high-resolution mass determination,\nJustin Douglas and Sarah Neuenswander (University of Kansas) for NMR assistance, R. Weinberg (Massachusetts Institute of Technology, Cambridge, MA, USA) via H. Chang (Stanford University, CA, USA) for providing PHMLEB and PHMLER cells, K. S. Osthoff (Eberhard Karls University, T\u00fcbingen, Germany) via G. M. Cohen (University of Leicester, UK) for caspase 9-/- cells, G. Salvesen (Sanford-Burnham Medical Research Institute) for caspase 8-/- cells, and H. Park, R. Oania, and D. Shimoda for technical assistance. This work was supported by a grant from the NIH Molecular Libraries Probe Production Centers Network to Jeffrey Aub\u00e9 (PI) (5U54HG005031). R.J.D. and T.-F.C. were supported by the Howard Hughes Medical Institute, of which R.J.D. is an Investigator.\n\nSupplemental Material - cmdc_201200520_sm_miscellaneous_information.pdf
Supplemental Material - cmdc_201200520_sm_supporting_information.xls
", "abstract": "To discover more potent p97 inhibitors, we carried out a structure\u2013activity relationship study of the quinazoline scaffold previously identified from our HTS campaigns. Two improved inhibitors, ML240 and ML241, inhibit p97 ATPase with IC_(50) values of 100 nM. Both compounds inhibited degradation of a p97-dependent but not a p97-independent proteasome substrate in a dual-reporter cell line. They also impaired the endoplasmic-reticulum-associated degradation (ERAD) pathway. Unexpectedly, ML240 potently stimulated accumulation of LC3-II within minutes, inhibited cancer cell growth, and rapidly mobilized the executioner caspases 3 and 7, whereas ML241 did not. The behavior of ML240 suggests that disruption of the protein homeostasis function of p97 leads to more rapid activation of apoptosis than is observed with a proteasome inhibitor. Further characterization revealed that ML240 has broad antiproliferative activity toward the NCI-60 panel of cancer cell lines, but slightly lower activity toward normal cells. ML240 also synergizes with the proteasome inhibitor MG132 to kill multiple colon cancer cell lines. Meanwhile, both probes have low off-target activity toward a panel of protein kinases and central nervous system targets. Our results nominate ML240 as a promising starting point for the development of a novel agent for the chemotherapy of cancer, and provide a rationale for developing pathway-specific p97 inhibitors.", "date": "2013-02", "date_type": "published", "publication": "ChemMedChem", "volume": "8", "number": "2", "publisher": "Wiley-Blackwell", "pagerange": "297-312", "id_number": "CaltechAUTHORS:20130301-075535357", "issn": "1860-7179", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130301-075535357", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "5U54HG005031" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "HHSN-271-2008-00025-C" } ] }, "doi": "10.1002/cmdc.201200520", "pmcid": "PMC3662613", "primary_object": { "basename": "cmdc_201200520_sm_miscellaneous_information.pdf", "url": "https://authors.library.caltech.edu/records/rqt83-93q76/files/cmdc_201200520_sm_miscellaneous_information.pdf" }, "related_objects": [ { "basename": "cmdc_201200520_sm_supporting_information.xls", "url": "https://authors.library.caltech.edu/records/rqt83-93q76/files/cmdc_201200520_sm_supporting_information.xls" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Chou, Tsui-Fen; Li, Kelin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/drs94-py641", "eprint_id": 25504, "eprint_status": "archive", "datestamp": "2023-08-19 07:52:30", "lastmod": "2023-10-24 15:55:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" } ] }, "title": "Development of p97 AAA ATPase inhibitors", "ispublished": "pub", "full_text_status": "restricted", "keywords": "p97/VCP, chemical inhibitor, caspase, high-throughput screening, cancer therapeutic, DBeQ, autophagy, ERAD", "note": "\u00a9 2011 Landes Bioscience. Submitted: 04-28-11. Revised: 05-03-11. Accepted: 05-13-11. We thank H. Park, R. Oania and D. Shimoda for technical assistance. T.F.C. was supported by a 2008 Fellows Grant Program Award from the Multiple Myeloma Research Foundation, the Howard Hughes Medical Institute (HHMI) and the Weston Havens Foundation. R.J.D. is an HHMI Investigator, and this work was funded\nin part by HHMI and in part by a National Institutes of Health R03 grant (MH085687).", "abstract": "Specific p97 inhibitors are valuable research tools to carry out mechanistic and cellular investigations of p97 biology. p97 is an abundant, ubiquitin-selective chaperone that has multiple functions and is essential for life. Therefore, genetic methods that require long incubations like siRNA or expression of dominant-negative p97 mutants are likely to generate complicated outcomes due to secondary consequences that arise upon slow depletion of p97 activity. We recently identified a small molecule p97 inhibitor, N^2,N^4-dibenzylquinazoline-2,4-diamine (DBeQ), and documented its effects on blocking autophagic degradation of LC3-II and proteasomal degradation of a p97-dependent ubiquitin-proteasome system (UPS) substrate. What distinguishes DBeQ from conventional proteasome inhibitors is that DBeQ affects both the UPS and autophagic protein degradation pathways and rapidly activates cell death. Whether DBeQ activates autophagic and/or apoptotic cell death will require further work to evaluate its detailed mechanism of action. An exciting goal for the future will be to generate p97 inhibitors that affect one or the other pathway. We propose that generation of 'separation of function' inhibitors will be a challenging adventure for chemical biologists but will yield extremely powerful tools to study p97 and enable evaluation of the therapeutic potential of targeting distinct p97 complexes.", "date": "2011-09", "date_type": "published", "publication": "Autophagy", "volume": "7", "number": "9", "publisher": "Landes Bioscience", "pagerange": "1091-1092", "id_number": "CaltechAUTHORS:20110930-072701050", "issn": "1554-8627", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110930-072701050", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Multiple Myeloma Research Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Weston Havens Foundation" }, { "agency": "NIH", "grant_number": "R03 MH085687" } ] }, "doi": "10.4161/auto.7.9.16489", "pmcid": "PMC3210319", "resource_type": "article", "pub_year": "2011", "author_list": "Chou, Tsui-Fen and Deshaies, Raymond J." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/sx9fr-y2s19", "eprint_id": 114033, "eprint_status": "archive", "datestamp": "2023-08-22 03:07:43", "lastmod": "2023-10-23 23:19:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bardaweel-Sanaa", "name": { "family": "Bardaweel", "given": "Sanaa" }, "orcid": "0000-0002-4823-0708" }, { "id": "Ghosh-Brahma", "name": { "family": "Ghosh", "given": "Brahma" }, "orcid": "0000-0003-2288-8293" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Sadowsky-Michael-J", "name": { "family": "Sadowsky", "given": "Michael J." }, "orcid": "0000-0001-8779-2781" }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "E. coli Histidine Triad Nucleotide Binding Protein 1 (ecHinT) Is a Catalytic Regulator of D-Alanine Dehydrogenase (DadA) Activity In Vivo", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2011 Bardaweel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: March 11, 2011; Accepted: May 11, 2011; Published: July 6, 2011. \n\nWe thank Dr. Masayuki Sugawara for his help in conducting the Biolog screening experiments and for his helpful discussions. \n\nFunding was provided by the University of Minnesota. No external funding sources for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nAuthor Contributions. Conceived and designed the experiments: SB MS CRW. Performed the experiments: SB BG TFC. Analyzed the data: SB BG TFC MS CRW. Wrote the paper: SB MS CRW. \n\nThe authors have declared that no competing interests exist.\n\nPublished - pone.0020897.pdf
Supplemental Material - pone.0020897.s001.doc
Supplemental Material - pone.0020897.s002.doc
Supplemental Material - pone.0020897.s003.doc
Supplemental Material - pone.0020897.s004.doc
Supplemental Material - pone.0020897.s005.doc
", "abstract": "Histidine triad nucleotide binding proteins (Hints) are highly conserved members of the histidine triad (HIT) protein superfamily. Hints comprise the most ancient branch of this superfamily and can be found in Archaea, Bacteria, and Eukaryota. Prokaryotic genomes, including a wide diversity of both Gram-negative and Gram-positive bacteria, typically have one Hint gene encoded by hinT (ycfF in E. coli). Despite their ubiquity, the foundational reason for the wide-spread conservation of Hints across all kingdoms of life remains a mystery. In this study, we used a combination of phenotypic screening and complementation analyses with wild-type and hinT knock-out Escherichia coli strains to show that catalytically active ecHinT is required in E. coli for growth on D-alanine as a sole carbon source. We demonstrate that the expression of catalytically active ecHinT is essential for the activity of the enzyme D-alanine dehydrogenase (DadA) (equivalent to D-amino acid oxidase in eukaryotes), a necessary component of the D-alanine catabolic pathway. Site-directed mutagenesis studies revealed that catalytically active C-terminal mutants of ecHinT are unable to activate DadA activity. In addition, we have designed and synthesized the first cell-permeable inhibitor of ecHinT and demonstrated that the wild-type E. coli treated with the inhibitor exhibited the same phenotype observed for the hinT knock-out strain. These results reveal that the catalytic activity and structure of ecHinT is essential for DadA function and therefore alanine metabolism in E. coli. Moreover, they provide the first biochemical evidence linking the catalytic activity of this ubiquitous protein to the biological function of Hints in Escherichia coli.", "date": "2011-07", "date_type": "published", "publication": "PLoS ONE", "volume": "6", "number": "7", "publisher": "Public Library of Science", "pagerange": "Art. No. e20897", "id_number": "CaltechAUTHORS:20220323-565437000", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565437000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Minnesota" } ] }, "doi": "10.1371/journal.pone.0020897", "pmcid": "PMC3130732", "primary_object": { "basename": "pone.0020897.pdf", "url": "https://authors.library.caltech.edu/records/sx9fr-y2s19/files/pone.0020897.pdf" }, "related_objects": [ { "basename": "pone.0020897.s001.doc", "url": "https://authors.library.caltech.edu/records/sx9fr-y2s19/files/pone.0020897.s001.doc" }, { "basename": "pone.0020897.s002.doc", "url": "https://authors.library.caltech.edu/records/sx9fr-y2s19/files/pone.0020897.s002.doc" }, { "basename": "pone.0020897.s003.doc", "url": "https://authors.library.caltech.edu/records/sx9fr-y2s19/files/pone.0020897.s003.doc" }, { "basename": "pone.0020897.s004.doc", "url": "https://authors.library.caltech.edu/records/sx9fr-y2s19/files/pone.0020897.s004.doc" }, { "basename": "pone.0020897.s005.doc", "url": "https://authors.library.caltech.edu/records/sx9fr-y2s19/files/pone.0020897.s005.doc" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Bardaweel, Sanaa; Ghosh, Brahma; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4n2xk-6xn86", "eprint_id": 23913, "eprint_status": "archive", "datestamp": "2023-09-14 19:01:30", "lastmod": "2023-10-23 20:47:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" } ] }, "title": "Quantitative Cell-based Protein Degradation Assays to Identify and Classify Drugs That Target the Ubiquitin-Proteasome System", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 The American Society for Biochemistry and Molecular Biology, Inc. Free via Creative Commons: CC. Creative Commons Attribution Non-Commercial License applies to Author Choice Articles. \n\nReceived for publication, December 22, 2010, and in revised form, February 14, 2011 Published, JBC Papers in Press, February 22, 2011. \n\nWe thank M. Smythe and C. Crews for YU101, A. M. Weissman for PYR-41, Y. Ye for EerI, Millennium Pharmaceuticals for MLN4924, K. Vousden for JNJ26854165, J. Huang for SMER3, and C. C. Wu for 3,4-methylenedioxycinnamic acid (compound 18). We thank P. I. Hanson, A. T. Brunger, and A. L. King for providing plasmids and M. G. Masucci, N. P. Dantuma, R. R. Kopito, and D. Baltimore for providing cell lines. We thank F. Parlati for critical reading of the manuscript; H. Park, R. Oania, and D. Shimoda for technical assistance; and the members of the Molecular Libraries Probe Production Centers Network at The Scripps Research Institute and Kansas University for advice and guidance on the implementation of the ATPase assay and discussions. This work was supported, in whole or in part, by National Institutes of Health Grant R03 MH085687. This work was also supported by the Howard Hughes Medical Institute.\n\nPublished - Chou2011p14027J_Biol_Chem.pdf
Supplemental Material - jbc.M110.215319-1.pdf
", "abstract": "We have generated a set of dual-reporter human cell lines and devised a chase protocol to quantify proteasomal degradation of a ubiquitin fusion degradation (UFD) substrate, a ubiquitin ligase CRL2^(VHL) substrate, and a ubiquitin-independent substrate. Well characterized inhibitors that target different aspects of the ubiquitin-proteasome system can be distinguished by their distinctive patterns of substrate stabilization, enabling assignment of test compounds as inhibitors of the proteasome, ubiquitin chain formation or perception, CRL activity, or the UFD-p97 pathway. We confirmed that degradation of the UFD but not the CRL2^(VHL) or ubiquitin-independent substrates depends on p97 activity. We optimized our suite of assays to establish conditions suitable for high-throughput screening and then validated their performance by screening against 160 cell-permeable protein kinase inhibitors. This screen identified Syk inhibitor III as an irreversible p97/vasolin containing protein inhibitor (IC_(50) = 1.7 \u03bcm) that acts through Cys-522 within the D2 ATPase domain. Our work establishes a high-throughput screening-compatible pipeline for identification and classification of small molecules, cDNAs, or siRNAs that target components of the ubiquitin-proteasome system.", "date": "2011-05-13", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "286", "number": "19", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "16546-16554", "id_number": "CaltechAUTHORS:20110606-105141967", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110606-105141967", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R03 MH085687" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Multiple Myeloma Research Foundation" }, { "agency": "Weston Havens Foundation" } ] }, "doi": "10.1074/jbc.M110.215319", "pmcid": "PMC3089497", "primary_object": { "basename": "Chou2011p14027J_Biol_Chem.pdf", "url": "https://authors.library.caltech.edu/records/4n2xk-6xn86/files/Chou2011p14027J_Biol_Chem.pdf" }, "related_objects": [ { "basename": "jbc.M110.215319-1.pdf", "url": "https://authors.library.caltech.edu/records/4n2xk-6xn86/files/jbc.M110.215319-1.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Chou, Tsui-Fen and Deshaies, Raymond J." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2900a-syw74", "eprint_id": 114047, "eprint_status": "archive", "datestamp": "2023-08-22 02:41:48", "lastmod": "2023-10-23 17:01:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Birkus-Gabriel", "name": { "family": "Birkus", "given": "Gabriel" }, "orcid": "0000-0002-5537-9447" }, { "id": "Kutty-Nilima", "name": { "family": "Kutty", "given": "Nilima" } }, { "id": "Frey-Christian-R", "name": { "family": "Frey", "given": "Christian R." } }, { "id": "Shribata-Riri", "name": { "family": "Shribata", "given": "Riri" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsuifen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston" }, "orcid": "0000-0001-7927-719X" }, { "id": "McDermott-Martin", "name": { "family": "McDermott", "given": "Martin" } }, { "id": "Cihlar-Tomas", "name": { "family": "Cihlar", "given": "Tomas" } } ] }, "title": "Role of Cathepsin A and Lysosomes in the Intracellular Activation of Novel Antipapillomavirus Agent GS-9191", "ispublished": "pub", "full_text_status": "public", "keywords": "Infectious Diseases; Pharmacology (medical); Pharmacology", "note": "\u00a9 2011 American Society for Microbiology. \n\nReceived: 18 November 2010. Returned for modification: 23 December 2010. Accepted: 28 February 2011. Published online: 28 April 2011.\n\nPublished - AAC.01603-10.pdf
", "abstract": "GS-9191, a bis-amidate prodrug of the nucleotide analog 9-(2-phosphonylmethoxyethyl)-N\u2076-cyclopropyl-2,6-diaminopurine (cPrPMEDAP), was designed as a topical agent for the treatment of papillomavirus-associated proliferative disorders, such as genital warts. In this study, we investigated the mechanism of conversion of GS-9191 to cPrPMEDAP. We observed that GS-9191 is hydrolyzed in the presence of the lysosomal carboxypeptidase cathepsin A (CatA) in vitro and is less efficiently metabolized in CatA-deficient fibroblasts than in control cells. In addition, knockdown of CatA by small interfering RNA (siRNA) reduced the intracellular accumulation of GS-9191 metabolites. However, intracellular CatA levels did not correlate with the susceptibility of tested cell lines to GS-9191, indicating that the CatA step is unlikely to be rate limiting for the activation of GS-9191. Further analysis showed that upon the hydrolysis of the carboxylester bond in one of the GS-9191 amidate moieties, the unmasked carboxyl group displaces L-phenylalanine 2-methylpropyl ester from the other amidate moiety. The cPrPMEDAP\u2013L-phenylalanine conjugate (cPrPMEDAP-Phe) formed is not metabolized by Hint1 (histidine triad nucleotide binding protein 1) phosphoramidase but undergoes spontaneous degradation to cPrPMEDAP in acidic pH that can be significantly enhanced by the addition of SiHa cell extract. Pretreatment of SiHa cells with bafilomycin A or chloroquine resulted in an 8-fold increase in the intracellular concentration of cPrPMEDAP-Phe metabolite and the accumulation of GS-9191 metabolites in the lysosomal/endosomal fraction. Together, these observations indicate that the conversion of GS-9191 to cPrPMEDAP occurs in lysosomes via CatA-mediated ester cleavage, followed by the release of cPrPMEDAP, most likely through the combination of enzyme-driven and spontaneous pH-driven hydrolysis of a cPrPMEDAP-Phe intermediate.", "date": "2011-05", "date_type": "published", "publication": "Antimicrobial Agents and Chemotherapy", "volume": "55", "number": "5", "publisher": "American Society for Microbiology", "pagerange": "2166-2173", "id_number": "CaltechAUTHORS:20220323-565704000", "issn": "0066-4804", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565704000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1128/aac.01603-10", "pmcid": "PMC3088193", "primary_object": { "basename": "AAC.01603-10.pdf", "url": "https://authors.library.caltech.edu/records/2900a-syw74/files/AAC.01603-10.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Birkus, Gabriel; Kutty, Nilima; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/yvmyy-ta554", "eprint_id": 23315, "eprint_status": "archive", "datestamp": "2023-08-22 02:17:34", "lastmod": "2023-10-23 19:00:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Brown-S-J", "name": { "family": "Brown", "given": "Steve J." } }, { "id": "Minond-D", "name": { "family": "Minond", "given": "Dmitriy" } }, { "id": "Nordin-B-E", "name": { "family": "Nordin", "given": "Brian E." } }, { "id": "Li-Kelin", "name": { "family": "Li", "given": "Kelin" } }, { "id": "Jones-A-C", "name": { "family": "Jones", "given": "Amanda C." }, "orcid": "0000-0001-8426-8407" }, { "id": "Chase-P", "name": { "family": "Chase", "given": "Peter" } }, { "id": "Porubsky-P-R", "name": { "family": "Porubsky", "given": "Patrick R." } }, { "id": "Stoltz-B-M", "name": { "family": "Stoltz", "given": "Brian M." }, "orcid": "0000-0001-9837-1528" }, { "id": "Schoenen-F-J", "name": { "family": "Schoenen", "given": "Frank J." } }, { "id": "Patricelli-M-P", "name": { "family": "Patricelli", "given": "Matthew P." } }, { "id": "Hodder-P", "name": { "family": "Hodder", "given": "Peter" } }, { "id": "Rosen-H", "name": { "family": "Rosen", "given": "Hugh" } }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "Raymond J." }, "orcid": "0000-0002-3671-9354" } ] }, "title": "Reversible inhibitor of p97, DBeQ, impairs both ubiquitin-dependent and autophagic protein clearance pathways", "ispublished": "pub", "full_text_status": "public", "keywords": "apoptosis; autophagy; unfolded protein response", "note": "\u00a9 2011 National Academy of Sciences. \n\nEdited by Randy King, Harvard University, Cambridge, MA, and accepted by the Editorial Board February 4, 2011 (received for review October 12, 2010). Published online before print March 7, 2011. \n\nWe thank A. Brunger for providing plasmids; G. Georg for a useful suggestion regarding high-throughput screen validation; C. Weihl for helpful discussions; P. Baillargeon and L. DeLuca for compound management; F. Parlati for critical reading of the manuscript; and H. Park, R. Oania, and D. Shimoda for technical assistance. National Institutes of Health (NIH) U54 Grant MH074404 funded Scripps personnel. The University of Kansas was supported by Award U54 HG005031-02 administered by the National Human Genome Research Institute on behalf of the NIH Roadmap Molecular Libraries Program. A.C.J. was supported by NIH Grant F32GM082000. T.-F.C. was supported by a 2008 Fellows Grant Program Award from the Multiple Myeloma Research Foundation, the Howard Hughes Medical Institute (HHMI), and the Weston Havens Foundation. R.J.D. is an HHMI Investigator, and this work was funded in part by HHMI and in part by NIH R03 Grant MH085687. \n\nAuthor contributions: T.-F.C., B.M.S., F.J.S., M.P.P., P.H., H.R., and R.J.D. designed research; T.-F.C., S.J.B., D.M., B.E.N., K.L., A.C.J., P.C., and P.R.P. performed research; T.-F.C. and R.J.D. analyzed data; and T.-F.C. and R.J.D. wrote the paper.\n\nPublished - Chou2011p13345P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - pnas.201015312SI.pdf
Supplemental Material - sd01.xls
", "abstract": "A specific small-molecule inhibitor of p97 would provide an important tool to investigate diverse functions of this essential ATPase associated with diverse cellular activities (AAA) ATPase and to evaluate its potential to be a therapeutic target in human disease. We carried out a high-throughput screen to identify inhibitors of p97 ATPase activity. Dual-reporter cell lines that simultaneously express p97-dependent and p97-independent proteasome substrates were used to stratify inhibitors that emerged from the screen. N^2,N^4-dibenzylquinazoline-2,4-diamine (DBeQ) was identified as a selective, potent, reversible, and ATP-competitive p97 inhibitor. DBeQ blocks multiple processes that have been shown by RNAi to depend on p97, including degradation of ubiquitin fusion degradation and endoplasmic reticulum-associated degradation pathway reporters, as well as autophagosome maturation. DBeQ also potently inhibits cancer cell growth and is more rapid than a proteasome inhibitor at mobilizing the executioner caspases-3 and -7. Our results provide a rationale for targeting p97 in cancer therapy.", "date": "2011-03-22", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "108", "number": "12", "publisher": "National Academy of Sciences", "pagerange": "4834-4839", "id_number": "CaltechAUTHORS:20110414-085357247", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110414-085357247", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54 MH074404" }, { "agency": "NIH", "grant_number": "U54 HG005031-02" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32GM082000" }, { "agency": "Multiple Myeloma Research Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Weston Havens Foundation" }, { "agency": "NIH", "grant_number": "R03 MH085687" }, { "agency": "National Human Genome Research Institute" } ] }, "doi": "10.1073/pnas.1015312108", "pmcid": "PMC3064330", "primary_object": { "basename": "Chou2011p13345P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/yvmyy-ta554/files/Chou2011p13345P_Natl_Acad_Sci_Usa.pdf" }, "related_objects": [ { "basename": "pnas.201015312SI.pdf", "url": "https://authors.library.caltech.edu/records/yvmyy-ta554/files/pnas.201015312SI.pdf" }, { "basename": "sd01.xls", "url": "https://authors.library.caltech.edu/records/yvmyy-ta554/files/sd01.xls" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Chou, Tsui-Fen; Brown, Steve J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w5cpc-hkm93", "eprint_id": 114053, "eprint_status": "archive", "datestamp": "2023-08-22 01:34:24", "lastmod": "2023-10-23 23:20:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bardaweel-Sanaa", "name": { "family": "Bardaweel", "given": "Sanaa" }, "orcid": "0000-0002-4823-0708" }, { "id": "Pace-James", "name": { "family": "Pace", "given": "James" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Cody-Vivian", "name": { "family": "Cody", "given": "Vivian" } }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Probing the Impact of the echinT C-Terminal Domain on Structure and Catalysis", "ispublished": "pub", "full_text_status": "public", "keywords": "histidine triad nucleotide binding protein (Hint); E. coli Hint; crystal structure; C-terminal loop; lysyl-tRNA synthetase (LysRS); Molecular Biology; Structural Biology", "note": "\u00a9 2010 Elsevier. \n\nReceived 10 July 2010, Revised 28 September 2010, Accepted 30 September 2010, Available online 8 October 2010. \n\nV.C. thanks Dr. Edward Snell for his help with data processing and for his helpful discussions on data collection and refinement. Funding from the University of Minnesota Seed Grant Program is gratefully acknowledged. \n\nPDB accession numbers. Coordinates for wt echinT and H101A echinT have been deposited in the PDB with accession codes 3N1S and 3N1T, respectively.\n\nSupplemental Material - 1-s2.0-S0022283610010843-mmc1.doc
", "abstract": "Histidine triad nucleotide binding protein (Hint) is considered as the ancestor of the histidine triad protein superfamily and is highly conserved from bacteria to humans. Prokaryote genomes, including a wide array of both Gram-negative bacteria and Gram-positive bacteria, typically encode one Hint gene. The cellular function of Hint and the rationale for its evolutionary conservation in bacteria have remained a mystery. Despite its ubiquity and high sequence similarity to eukaryote Hint1 [Escherichia coli Hint (echinT) is 48% identical with human Hint1], prokaryote Hint has been reported in only a few studies. Here we report the first conformational information on the full-length N-terminal and C-terminal residues of Hint from the E. coli complex with GMP. Structural analysis of the echinT\u2013GMP complex reveals that it crystallizes in the monoclinic space group P2\u2081 with four homodimers in the asymmetric unit. Analysis of electron density for both the N-terminal residues and the C-terminal residues of the echinT\u2013GMP complex indicates that the loops in some monomers can adopt more than one conformation. The observation of conformational flexibility in terminal loop regions could explain the presence of multiple homodimers in the asymmetric unit of this structure. To explore the impact of the echinT C-terminus on protein structure and catalysis, we conducted a series of catalytic radiolabeling and kinetic experiments on the C-terminal deletion mutants of echinT. In this study, we show that sequential deletion of the C-terminus likely has no effect on homodimerization and a modest effect on the secondary structure of echinT. However, we observed a significant impact on the folding structure, as reflected by a significant lowering of the Tm value. Kinetic analysis reveals that the C-terminal deletion mutants are within an order of magnitude less efficient in catalysis compared to wild type, while the overall kinetic mechanism that proceeds through a fast step, followed by a rate-limiting hydrolysis step, was conserved. Nevertheless, the ability of the C-terminal deletion mutants to hydrolyze lysyl-AMP generated by LysU was greatly impaired. Taken together, our results highlight the emerging role of the C-terminus in governing the catalytic function of Hints.", "date": "2010-12-10", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "404", "number": "4", "publisher": "Elsevier", "pagerange": "627-638", "id_number": "CaltechAUTHORS:20220323-565930000", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565930000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Minnesota" } ] }, "doi": "10.1016/j.jmb.2010.09.066", "primary_object": { "basename": "1-s2.0-S0022283610010843-mmc1.doc", "url": "https://authors.library.caltech.edu/records/w5cpc-hkm93/files/1-s2.0-S0022283610010843-mmc1.doc" }, "resource_type": "article", "pub_year": "2010", "author_list": "Bardaweel, Sanaa; Pace, James; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/4vz6h-fzk74", "eprint_id": 33246, "eprint_status": "archive", "datestamp": "2023-08-19 04:36:54", "lastmod": "2023-10-18 18:54:59", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "T." }, "orcid": "0000-0003-2410-2186" }, { "id": "Deshaies-R-J", "name": { "family": "Deshaies", "given": "R." }, "orcid": "0000-0002-3671-9354" } ] }, "title": "Development of p97 inhibitors as potential anti-cancer therapeutics", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2012 American Chemical Society.", "abstract": "P97/VCP is an important AAA ATPase not only due to its intriguing diverse cellular functions but also because it has\nbeen implicated in mediating turnover of many proteins involved in tumorigenesis. Specific small mol. inhibitors of\np97/VCP are important tools to investigate diverse functions of this essential AAA ATPase and to evaluate its potential to\nbe a therapeutic target. To quant. assay specificity of p97/VCP inhibitors, we develop three cell- based reporter assays\nwith distinct dependences on p97/VCP for their stability based on changes of steady-state levels and half-lives by\nknocking down p97/VCP or expression of dominant-neg. p97/VCP. We apply these assays to screen against 160 cellpermeable\nkinase inhibitors to identify an irreversible p97/VCP inhibitor with IC50 of 1.7 \u00d7M. Biochem. characterization\ndemonstrates a cysteine within the second ATP binding pocket is responsible for the obsd. inactivation. Furthermore, we\ndemonstrate the utility of these reporters on assessing effect of various kinase inhibitors in the ubiquitin proteasome\npathway and provide insight into functions of kinases in the ubiquitin proteasome system. Most importantly, we can now\napply the system to address specificity issue at an earlier stage to develop specific p97 inhibitors.", "date": "2010-12", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20120816-071903890", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120816-071903890", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "conference_item", "pub_year": "2010", "author_list": "Chou, T. and Deshaies, R." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m9b8z-34108", "eprint_id": 114057, "eprint_status": "archive", "datestamp": "2023-08-21 22:42:43", "lastmod": "2023-10-23 23:20:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cheng-Jilin", "name": { "family": "Cheng", "given": "Jilin" } }, { "id": "Zhou-Xin", "name": { "family": "Zhou", "given": "Xin" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Ghosh-Brahma", "name": { "family": "Ghosh", "given": "Brahma" } }, { "id": "Liu-Baoling", "name": { "family": "Liu", "given": "Baoling" } }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." } } ] }, "title": "Identification of the amino acid-AZT-phosphoramidase by affinity T7 phage display selection", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Pronucleotide; AZT; Prodrug; Hint1; Phosphoramidate; Organic Chemistry; Clinical Biochemistry; Drug Discovery; Pharmaceutical Science; Molecular Biology; Molecular Medicine; Biochemistry", "note": "\u00a9 2009 Published by Elsevier. \n\nReceived 25 July 2009, Revised 17 September 2009, Accepted 17 September 2009, Available online 22 September 2009. \n\nThis work was partially supported by Grant CA-61909 and the University of Minnesota Graduate School (C.R.W).", "abstract": "A CEM cell cDNA T7 phage display library was prepared and used to screen for activating enzymes of phosphoramidate prodrugs of AZT monophosphate. Although, inefficient compared to ribonucleotide based phosphoramidates, hHint 1 was identified as the likely intracellular pronucleotide activating enzyme.", "date": "2009-11-15", "date_type": "published", "publication": "Bioorganic and Medicinal Chemistry Letters", "volume": "19", "number": "22", "publisher": "Elsevier", "pagerange": "6379-6381", "id_number": "CaltechAUTHORS:20220323-565985000", "issn": "0960-894X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565985000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Minnesota" } ] }, "doi": "10.1016/j.bmcl.2009.09.067", "resource_type": "article", "pub_year": "2009", "author_list": "Cheng, Jilin; Zhou, Xin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7jpy4-ejn19", "eprint_id": 114034, "eprint_status": "archive", "datestamp": "2023-08-22 13:55:52", "lastmod": "2023-10-23 23:19:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "So-Christopher", "name": { "family": "So", "given": "Christopher" }, "orcid": "0000-0002-1393-0333" }, { "id": "White-Brian-R", "name": { "family": "White", "given": "Brian R." } }, { "id": "Carlson-Jonathan-C-T", "name": { "family": "Carlson", "given": "Jonathan C. T." }, "orcid": "0000-0003-4139-9057" }, { "id": "Sarikaya-Mehmet", "name": { "family": "Sarikaya", "given": "Mehmet" }, "orcid": "0000-0003-3856-6360" }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Enzyme Nanorings", "ispublished": "pub", "full_text_status": "public", "keywords": "Peptides and proteins, Monomers, Cyclization, Oligomers, Macrocycles; General Physics and Astronomy; General Engineering; General Materials Science", "note": "\u00a9 2008 American Chemical Society. \n\nReceived 14 September 2008. Accepted 22 November 2008. Published online 9 December 2008. Published in issue 23 December 2008. \n\nWe thank Dr. Terry W. Steele for his assistance with the SLS experiments, and Dr. R. A. Siegel for the use of the SLS instrument. We wish to thank the University of Minnesota Nanobiotechnology Initiative (C.R.W.), NIH-NCI (CA120116, C.R.W.), the Leukemia Research Foundation, and NSF-MRSEC (C.S. and M.S.) for partial support of this study (DMR-0520567).\n\nAccepted Version - nihms91468.pdf
Supplemental Material - nn800577h_si_001.pdf
", "abstract": "We have demonstrated that nanostructures, and in particular nanorings incorporating a homodimeric enzyme, can be prepared by chemically induced self-assembly of dihydrofolate reductase (DHFR)-histidine triad nucleotide binding 1 (Hint1) fusion proteins. The dimensions of the nanorings were found by static light scattering and atomic force microscopy studies to be dependent on the length and composition of the peptide linking the fusion proteins, ranging in size from 10 to 70 nm in diameter and 64 to 740 kDa. The catalytic efficiency of the nanorings was found to be dependent on ring size, thus suggesting that the arrangement of supermolecular assemblies of enzymes may be used to control their catalytic parameters.", "date": "2008-12-23", "date_type": "published", "publication": "ACS Nano", "volume": "2", "number": "12", "publisher": "American Chemical Society", "pagerange": "2519-2525", "id_number": "CaltechAUTHORS:20220323-565456000", "issn": "1936-0851", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565456000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Minnesota" }, { "agency": "NIH", "grant_number": "CA120116" }, { "agency": "Leukemia Research Foundation" }, { "agency": "NSF", "grant_number": "DMR-0520567" } ] }, "doi": "10.1021/nn800577h", "pmcid": "PMC2682639", "primary_object": { "basename": "nihms91468.pdf", "url": "https://authors.library.caltech.edu/records/7jpy4-ejn19/files/nihms91468.pdf" }, "related_objects": [ { "basename": "nn800577h_si_001.pdf", "url": "https://authors.library.caltech.edu/records/7jpy4-ejn19/files/nn800577h_si_001.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Chou, Tsui-Fen; So, Christopher; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/j68z0-dpg75", "eprint_id": 114051, "eprint_status": "archive", "datestamp": "2023-08-22 12:39:25", "lastmod": "2023-10-23 23:20:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ghosh-Phalguni", "name": { "family": "Ghosh", "given": "Phalguni" } }, { "id": "Cheng-Jilin", "name": { "family": "Cheng", "given": "Jilin" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Jia-Yan", "name": { "family": "Jia", "given": "Yan" } }, { "id": "Avdulov-Svetlana", "name": { "family": "Avdulov", "given": "Svetlana" } }, { "id": "Bitterman-Peter-B", "name": { "family": "Bitterman", "given": "Peter B." }, "orcid": "0000-0002-7995-7117" }, { "id": "Polunovsky-Vitaly-A", "name": { "family": "Polunovsky", "given": "Vitaly A." } }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Expression, purification and characterization of recombinant mouse translation initiation factor eIF4E as a dihydrofolate reductase (DHFR) fusion protein", "ispublished": "pub", "full_text_status": "public", "keywords": "Translational initiation factor; eIF4E; Fluorescence quenching; DHFR; Biotechnology", "note": "\u00a9 2008 Elsevier. \n\nReceived 13 December 2007, Revised 14 March 2008, Available online 31 March 2008. \n\nThis work was partially supported by Grants from NIH-HL076779 (PBB), HL073719 (PBB), NCI U01-CA091220 (VAP) and an AHC Faculty Development Award (CRW) Technical assistance by Cindy Choy is gratefully acknowledged.\n\nAccepted Version - nihms61420.pdf
Supplemental Material - 1-s2.0-S1046592808000764-fx5.jpg
Supplemental Material - 1-s2.0-S1046592808000764-fx6.jpg
Supplemental Material - 1-s2.0-S1046592808000764-fx7.jpg
", "abstract": "One of the earliest steps in translation initiation is recognition of the mRNA cap structure (m7GpppX) by the initiation factor eIF4E. Studies of interactions between purified eIF4E and its binding partners provide important information for understanding mechanisms underlying translational control in normal and cancer cells. Numerous impediments of the available methods used for eIF4E purification led us to develop a novel methodology for obtaining fractions of eIF4E free from undesired by-products. Herein we report methods for bacterial expression of eIF4E tagged with mutant dihydrofolate reductase (DHFR) followed by isolation and purification of the DHFR\u2013eIF4E protein by using affinity and anion exchange chromatography. Fluorescence quenching experiments indicated the cap-analog, 7MeGTP, bound to DHFR\u2013eIF4E and eIF4E with a dissociation constant (K_d) of 6 \u00b1 5 and 10 \u00b1 3 nM, respectively. Recombinant eIF4E and DHFR\u2013eIF4E were both shown to significantly enhance in vitro translation in dose dependent manner by 75% at 0.5 \u03bcM. Nevertheless increased concentrations of eIF4E and DHFR\u2013eIF4E significantly inhibited translation in a dose dependent manner by a maximum at 2 \u03bcM of 60% and 90%, respectively. Thus, we have demonstrated that we have developed an expression system for fully functional recombinant eIF4E. We have also shown that the fusion protein DHFR\u2013eIF4E is functional and thus may be useful for cell based affinity tag studies with fluorescently labeled trimethoprim analogs.", "date": "2008-08", "date_type": "published", "publication": "Protein Expression and Purification", "volume": "60", "number": "2", "publisher": "Elsevier", "pagerange": "132-139", "id_number": "CaltechAUTHORS:20220323-565905000", "issn": "1046-5928", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565905000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HL076779" }, { "agency": "NIH", "grant_number": "HL073719" }, { "agency": "NIH", "grant_number": "U01-CA091220" }, { "agency": "University of Minnesota" } ] }, "doi": "10.1016/j.pep.2008.03.024", "pmcid": "PMC2617730", "primary_object": { "basename": "1-s2.0-S1046592808000764-fx5.jpg", "url": "https://authors.library.caltech.edu/records/j68z0-dpg75/files/1-s2.0-S1046592808000764-fx5.jpg" }, "related_objects": [ { "basename": "1-s2.0-S1046592808000764-fx6.jpg", "url": "https://authors.library.caltech.edu/records/j68z0-dpg75/files/1-s2.0-S1046592808000764-fx6.jpg" }, { "basename": "1-s2.0-S1046592808000764-fx7.jpg", "url": "https://authors.library.caltech.edu/records/j68z0-dpg75/files/1-s2.0-S1046592808000764-fx7.jpg" }, { "basename": "nihms61420.pdf", "url": "https://authors.library.caltech.edu/records/j68z0-dpg75/files/nihms61420.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Ghosh, Phalguni; Cheng, Jilin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1c29e-td782", "eprint_id": 114041, "eprint_status": "archive", "datestamp": "2023-08-22 10:27:01", "lastmod": "2023-10-23 23:20:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Sham-Yuk-Y", "name": { "family": "Sham", "given": "Yuk Y." }, "orcid": "0000-0003-2601-8930" }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Impact of the C-Terminal Loop of Histidine Triad Nucleotide Binding Protein1 (Hint1) on Substrate Specificity", "ispublished": "pub", "full_text_status": "public", "keywords": "Peptides and proteins, Monomers, Adenine, Chemical specificity, Guanine; Biochemistry", "note": "\u00a9 2007 American Chemical Society. \n\nReceived 24 June 2007. Revised 1 September 2007. Published online 16 October 2007. Published in issue 1 November 2007.\n\nSupplemental Material - bi701244h_si_002.pdf
", "abstract": "Although highly sequence similar, human histidine triad nucleotide binding protein (hHint1) and E. coli hinT (echinT) exhibit significant differences in their phosphoramidase substrate specificity and lysyl-adenylate hydrolytic activity. Observing that the C termini of each enzyme are highly dissimilar, we created two chimeric Hint's:\u2009 one in which the C terminus of hHint1 was replaced with the C terminus of echinT (Hs/ec) and the other in which the C terminus of echinT was replaced with the C terminus of hHint1 (ec/Hs). The Hs/ec chimera exhibited nearly identical specificity constants (k_(cat)/K_m) to those found for echinT, whereas the specificity constants of the ec/Hs chimera were found to approximate those for hHint1. In particular, as observed for echinT, the Hs/ec chimera does not exhibit a preference for phosphoramidates containing d- or l- tryptophan, while the ec/Hs chimera adopts the human enzyme preference for the l configuration. In addition, the studies with each chimera revealed that differences in the ability of hHint1 and echinT to hydrolyze lysyl-AMP generated by either E. coli or human lysyl-tRNA synthetase were partially transferable by C-terminal loop exchange. Hence, our results support the critical role of the C-terminal loop of human and E. coli Hint1 on governing substrate specificity.", "date": "2007-11-13", "date_type": "published", "publication": "Biochemistry", "volume": "46", "number": "45", "publisher": "American Chemical Society", "pagerange": "13074-13079", "id_number": "CaltechAUTHORS:20220323-565562000", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565562000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1021/bi701244h", "primary_object": { "basename": "bi701244h_si_002.pdf", "url": "https://authors.library.caltech.edu/records/1c29e-td782/files/bi701244h_si_002.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Chou, Tsui-Fen; Sham, Yuk Y.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ra9j3-62a53", "eprint_id": 114054, "eprint_status": "archive", "datestamp": "2023-08-22 10:24:13", "lastmod": "2023-10-23 23:20:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Cheng-Jilin", "name": { "family": "Cheng", "given": "Jilin" } }, { "id": "Tikh-Ilya-B", "name": { "family": "Tikh", "given": "Ilya B." } }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Evidence that Human Histidine Triad Nucleotide Binding Protein 3 (Hint3) is a Distinct Branch of the Histidine Triad (HIT) Superfamily", "ispublished": "pub", "full_text_status": "public", "keywords": "human Hint1; human Hint3-1; human Hint3-2; lysyl-tRNA synthetase; phosphoramidase; Molecular Biology; Structural Biology", "note": "\u00a9 2007 Elsevier. \n\nReceived 20 June 2007, Revised 3 August 2007, Accepted 10 August 2007, Available online 21 August 2007. \n\nWe thank Xiaodan Liu (University of Minnesota) for help with the HPLC-ESI+ MS experiments, Dr. Karin Musier-Forsyth (The Ohio State University) for providing us the expression plasmid for hLysRS, and John Oja and Jerry Sedgewick (Biomedical Image Processing Laboratory, University of Minnesota) for assistance with confocal experiments.\n\nSupplemental Material - 1-s2.0-S0022283607010959-mmc1.pdf
", "abstract": "Human Hint3 (hHint3) has been classified as a member of the histidine triad nucleotide (Hint) binding protein subfamily. While Hint1 is ubiquitously expressed by both eukaryotes and prokaryotes, Hint3 is found only in eukaryotes. Previously, our laboratory has characterized and compared the aminoacyl-adenylate and nucleoside phosphoramidate hydrolase activity of hHint1 and Escherichia coli hinT. In this study, hHint3-1(Ala36) and its single nucleotide polymorphism, hHint3-2 (A36G variant), were cloned, overexpressed, and purified. Steady-state kinetic studies with a synthetic fluorogenic indolepropinoic acyl-adenylate (AIPA) and with a series of fluorogenic tryptamine nucleoside phosphoramidates revealed that hHint3-1 and hHint3-2 are adenylate and phosphoramidate hydrolases with apparent second-order rate constants (k_(cat)/K_m) ranging from 10\u00b2 to 10\u2076 s\u207b\u00b9 M\u207b\u00b9. Unlike hHint1, hHint3-1 and hHint3-2 prefer AIPA over tryptamine adenosine phosphoramidate by factors of 33- and 16-fold, respectively. In general, hHint3s hydrolyze phosphoramidate 370- to 2000-fold less efficiently than hHint1. Substitution of the potential active-site nucleophile, His145, by Ala was shown to abolish the adenylate and phosphoramidate hydrolase activity for hHint3-1. However, 0.2\u20130.4% residual activity was observed for the H145A mutant of hHint3-2. Both hHint3-1 and hHint3-2 were found to hydrolyze lysyl-adenylate generated by human lysyl-tRNA synthetase (hLysRS) by proceeding through an adenylated protein intermediate. hLysRS-dependent labeling of hHint3-1 and hHint3-2 was found to depend on His145, which aligns with the His112 of the Hint1 active site. The extent of active-site His145-AMP labeling was shown to be similar to His112-AMP labeling of hHint1. In contrast to all previously characterized members of the histidine triad superfamily, which have been shown to exist exclusively as homodimers, wild type and the H145A of hHint3-1 were found to exist across a range of multimeric states, from dimers to octamers and even larger oligomers, while wild type and the H145A of hHint3-2 exist predominantly in a monomeric state. The differences in oligomeric state may be important in vivo, because unlike tetracysteine-tagged Hint1, which was found along linear arrays exclusively in the cytoplasm in transfected HeLa cells, tagged Hint3-1 and Hint3-2 were found as aggregates both in the cytosol and in the nucleus. Taken together, these results imply that while Hint3 and Hint1 prefer aminoacyl-adenylates as substrates and catalytically interact with aminoacyl-tRNA synthetases, the significant differences in phosphoramidase activity, oligomeric state, and cellular localization suggest that Hint3s should be placed in a distinct branch of the histidine triad superfamily.", "date": "2007-11-02", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "373", "number": "4", "publisher": "Elsevier", "pagerange": "978-989", "id_number": "CaltechAUTHORS:20220323-565944000", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565944000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.jmb.2007.08.023", "primary_object": { "basename": "1-s2.0-S0022283607010959-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/ra9j3-62a53/files/1-s2.0-S0022283607010959-mmc1.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Chou, Tsui-Fen; Cheng, Jilin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8x2vr-yss96", "eprint_id": 114055, "eprint_status": "archive", "datestamp": "2023-08-22 09:05:20", "lastmod": "2023-10-23 16:52:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Tikh-Ilya-B", "name": { "family": "Tikh", "given": "Ilya B." } }, { "id": "Horta-Bruno-A-C", "name": { "family": "Horta", "given": "Bruno A. C." } }, { "id": "Ghosh-Brahma", "name": { "family": "Ghosh", "given": "Brahma" } }, { "id": "De-Alencastro-Ricardo-B", "name": { "family": "De Alencastro", "given": "Ricardo B." } }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." } } ] }, "title": "Engineered Monomeric Human Histidine Triad Nucleotide-binding Protein 1 Hydrolyzes Fluorogenic Acyl-adenylate and Lysyl-tRNA Synthetase-generated Lysyl-adenylate", "ispublished": "pub", "full_text_status": "public", "keywords": "Cell Biology; Molecular Biology; Biochemistry", "note": "\u00a9 2007 ASBMB. Attribution 4.0 International (CC BY 4.0).\n\nReceived 21 July 2006, Revised 20 February 2007, Available online 2 March 2007. \n\nWe thank Dr. Jonathan C. T. Carlson for preparing the dimerizer, Bis-MTX-C\u2089, Dr. Terry W. Steele for assistance with the static light scattering experiments, and Dr. Yuk S. Sham for assisting with molecular graphics. We thank Dr. R. A. Siegel for the use of the static light scattering instrument and Dr. Alexey Wolfson (University of Colorado, Department of Chemistry and Biochemistry) for sharing the procedure for aminoacyl-adenylate synthesis. We thank Dr. Karin Musier-Forsyth (The Ohio State University) for providing the expression plasmid for human LysRS. \n\nThis work was supported in part by a University of Minnesota Faculty Academic Health Center Development Grant and a grant from the National Institutes of Health. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.\n\nPublished - 1-s2.0-S0021925820636705-main.pdf
Supplemental Material - 1-s2.0-S0021925820636705-mmc1.pdf
", "abstract": "Hint1 is a homodimeric protein and member of the ubiquitous HIT superfamily. Hint1 catalyzes the hydrolysis of purine phosphoramidates and lysyl-adenylate generated by lysyl-tRNA synthetase (LysRS). To determine the importance of homodimerization on the biological and catalytic activity of Hint1, the dimer interface of human Hint1 (hHint1) was destabilized by replacement of Val97 of hHint1 with Asp, Glu, or Arg. The mutants were shown to exist as monomers in solution by a combination of size exclusion chromatograph, static light scattering, and chemically induced dimerization studies. Circular dichroism studies revealed little difference between the stability of the V97D, V97E, and wild-type hHint1. Relative to wild-type and the V97E mutant, however, significant perturbation of the V97D mutant structure was observed. hHint1 was shown to prefer 3-indolepropionic acyl-adenylate (AIPA) over tryptamine adenosine phosphoramidate monoester (TpAd). Wild-type hHint1 was found to be 277- and 1000-fold more efficient (k_(cat)/K_m values) than the V97E and V97D mutants, respectively. Adenylation of wild-type, V97D, and V97E hHint1 by human LysRS was shown to correlate with the mutant k_(cat)/K_m values using 3-indolepropionic acyl-adenylate as a substrate, but not tryptamine adenosine phosphoramidate monoester. Significant perturbations of the active site residues were not detected by molecular dynamics simulations of the hHint1s. Taken together, these results demonstrate that for hHint1; 1) the efficiency (k_(cat)/K_m) of acylated AMP hydrolysis, but not maximal catalytic turnover (k_(cat)), is dependent on homodimerization and 2) the hydrolysis of lysyl-AMP generated by LysRS is not dependent on homodimerization if the monomer structure is similar to the wild-type structure.", "date": "2007-05-18", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "282", "number": "20", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "15137-15147", "id_number": "CaltechAUTHORS:20220323-565961000", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565961000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Minnesota" }, { "agency": "NIH" } ] }, "doi": "10.1074/jbc.m606972200", "primary_object": { "basename": "1-s2.0-S0021925820636705-main.pdf", "url": "https://authors.library.caltech.edu/records/8x2vr-yss96/files/1-s2.0-S0021925820636705-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0021925820636705-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/8x2vr-yss96/files/1-s2.0-S0021925820636705-mmc1.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Chou, Tsui-Fen; Tikh, Ilya B.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6yswn-yvx73", "eprint_id": 114036, "eprint_status": "archive", "datestamp": "2023-08-22 08:51:04", "lastmod": "2023-10-23 23:19:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Baraniak-Janina", "name": { "family": "Baraniak", "given": "Janina" } }, { "id": "Kaczmarek-Renata", "name": { "family": "Kaczmarek", "given": "Renata" }, "orcid": "0000-0002-3869-1068" }, { "id": "Zhou-Xin", "name": { "family": "Zhou", "given": "Xin" } }, { "id": "Cheng-Jilin", "name": { "family": "Cheng", "given": "Jilin" } }, { "id": "Ghosh-Brahma", "name": { "family": "Ghosh", "given": "Brahma" }, "orcid": "0000-0003-2288-8293" }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Phosphoramidate Pronucleotides:\u2009 A Comparison of the Phosphoramidase Substrate Specificity of Human and Escherichia coli Histidine Triad Nucleotide Binding Proteins", "ispublished": "pub", "full_text_status": "public", "keywords": "Histidine triad nucleotide binding proteins (Hints); phosphoramidase; human Hint1; Escherichia coli hinT; fluorogenic phosphoramidates; Drug Discovery; Pharmaceutical Science; Molecular Medicine", "note": "\u00a9 2007 American Chemical Society. \n\nReceived 23 June 2006. Accepted 26 October 2006. Revised 19 October 2006. Published online 12 January 2007. Published in issue 1 April 2007. \n\nWe thank Dr. Phalguni Ghosh for technical assistance and for providing a sample of 7-benzylguanosine monophosphate. We thank Dr. W. Stec (Polish Academy of Sciences) for stimulating discussions. We gratefully acknowledge the National Institutes of Health (HL073719 and HL076779) and the University of Minnesota Academic Health Center for partial support of this research.\n\nSupplemental Material - mp060070y_si_001.pdf
", "abstract": "To facilitate the delivery of nucleotide-based therapeutics to cells and tissues, a variety of pronucleotide approaches have been developed. Our laboratory and others have demonstrated that nucleoside phosphoramidates can be activated intracellularly to the corresponding 5'-monophosphate nucleotide and that histidine triad nucleotide binding proteins (Hints) are potentially responsible for their bioactivation. Hints are conserved and ubiquitous enzymes that hydrolyze phosphoramidate bonds between nucleoside 5'-monophosphate and an amine leaving group. On the basis of the ability of nucleosides to quench the fluorescence of covalently linked amines containing indole, a sensitive, continuous fluorescence-based assay was developed. A series of substrates linking the naturally fluorogenic indole derivatives to nucleoside 5'-monophosphates were synthesized, and their steady state kinetic parameters of hydrolysis by human Hint1 and Escherichia coli hinT were evaluated. To characterize the elemental and stereochemical effect on the reaction, two P-diastereoisomers of adenosine or guanosine phosphoramidothioates were synthesized and studied to reveal a 15\u2212200-fold decrease in the specificity constant (k_(cat)/K_m) when the phosphoryl oxygen is replaced with sulfur. While a stereochemical preference was not observed for E. coli hinT, hHint1 exhibited a 300-fold preference for d-tryptophan phosphoramidates over l-isomers. The most efficient substrates evaluated to date are those that contain the less sterically hindering amine leaving group, tryptamine, with k_(cat) and K_m values comparable to those found for adenosine kinase. The apparent second-order rate constants (k_(cat)/K_m) for adenosine tryptamine phosphoramidate monoester were found to be 10\u2077 M\u207b\u00b9 s\u207b\u00b9 for hHint1 and 10\u2076 M\u207b\u00b9 s\u207b\u00b9 for E. coli hinT. Both the human and E. coli enzymes preferred purine over pyrimidine analogues. Consistent with observed hydrogen bonding between the 2'-OH group of adenosine monophosphate and the active site residue, Asp43, the second-order rate constant (k_(cat)/K_m) for thymidine tryptamine phosphoramidate was found to be 3\u22124 orders of magnitude smaller than that for uridine tryptamine phosphoramidate for hHint1 and 2 orders of magnitude smaller than that for E. coli hinT. Ara-A tryptamine phosphoramidate was, however, shown to be a good substrate with a specificity constant (k_(cat)/K_m) only 10-fold lower than the value for adenosine tryptamine phosphoramidate. Consequently, nucleoside phosphoramidates containing unhindered primary amines and either an \u03b1 or \u03b2 2'-OH group should be easily bioactivated by Hints with efficiencies rivaling those for the 5'-monophosphorylation of nucleosides by nucleoside kinases. The differential substrate specificity observed for human and E. coli enzymes represents a potential therapeutic rationale for the development of selective antibiotic phosphoramidate pronucleotides.", "date": "2007-04-01", "date_type": "published", "publication": "Molecular Pharmaceutics", "volume": "4", "number": "2", "publisher": "American Chemical Society", "pagerange": "208-217", "id_number": "CaltechAUTHORS:20220323-565477000", "issn": "1543-8384", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565477000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HL073719" }, { "agency": "NIH", "grant_number": "HL076779" }, { "agency": "University of Minnesota" } ] }, "doi": "10.1021/mp060070y", "primary_object": { "basename": "mp060070y_si_001.pdf", "url": "https://authors.library.caltech.edu/records/6yswn-yvx73/files/mp060070y_si_001.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Chou, Tsui-Fen; Baraniak, Janina; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/vx4rq-8x886", "eprint_id": 114056, "eprint_status": "archive", "datestamp": "2023-08-22 08:33:13", "lastmod": "2023-10-23 19:32:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." } } ] }, "title": "Lysyl-tRNA Synthetase-generated Lysyl-Adenylate Is a Substrate for Histidine Triad Nucleotide Binding Proteins", "ispublished": "pub", "full_text_status": "public", "keywords": "Cell Biology; Molecular Biology; Biochemistry", "note": "\u00a9 2007 The American Society for Biochemistry and Molecular Biology. Attribution 4.0 International (CC BY 4.0).\n\nReceived 13 November 2006, Revised 8 December 2006, Available online 8 December 2006. \n\nWe thank Dr. Karin Musier-Forsyth and Dr. Robert Kennedy (University of Minnesota) for kindly providing us the expression plasmid for human LysRS and helpful discussions. We thank Dr. Paul Schimmel (The Scripps Research Institute) for providing ecLysU expression plasmid. \n\nThe costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.\n\nPublished - 1-s2.0-S002192582065044X-main.pdf
", "abstract": "Histidine triad nucleotide binding proteins (Hints) are the most ancient members of the histidine triad protein superfamily of nucleotidyltransferases and hydrolyases. Protein-protein interaction studies have found that complexes of the transcription factors MITF or USF2 and lysyl-tRNA synthetase (LysRS) are associated with human Hint1. Therefore, we hypothesized that lysyl-AMP or the LysRS\u00b7lysyl-AMP may be a native substrate for Hints. To explore the biochemical relationship between Hint1 and LysRS, a series of catalytic radiolabeling, mutagenesis, and kinetic experiments was conducted with purified LysRSs and Hints from human and Escherichia coli. After incubation of the E. coli or human LysRS with Hints and [\u03b1-\u00b3\u00b2P]ATP, but not [\u03b1-\u00b3\u00b2P]GTP, \u00b3\u00b2P-labeled Hints were observed. By varying time and the concentrations of lysine, Mg\u00b2\u207a, or LysRS, the adenylation of Hint was found to be dependent on the formation of lysyl-AMP. Site-directed mutagenesis studies of the active site histidine triad revealed that Hint labeling could be abolished by substitution of either His-101 of E. coli hinT or His-112 of human Hint1 by either alanine or glycine. Ap\u2084A, believed to be synthesized by LysRS in vivo, and Zn\u00b2\u207a were shown to inhibit the formation of Hint-AMP with an IC\u2085\u2080 value in the low micromolar range. Consistent with pyrophosphate being an inhibitor for aminoacyl-tRNA synthetase, incubations in the presence of pyrophosphatase resulted in enhanced formation of Hint-AMP. These results demonstrate that the lysyl-AMP intermediate formed by LysRS is a natural substrate for Hints and suggests a potential highly conserved regulatory role for Hints on LysRS and possibly other aminoacyl-tRNA synthetases.", "date": "2007-02-16", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "282", "number": "7", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "4719-4727", "id_number": "CaltechAUTHORS:20220323-565970000", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565970000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1074/jbc.m610530200", "primary_object": { "basename": "1-s2.0-S002192582065044X-main.pdf", "url": "https://authors.library.caltech.edu/records/vx4rq-8x886/files/1-s2.0-S002192582065044X-main.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Chou, Tsui-Fen and Wagner, Carston R." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bc3zr-tg780", "eprint_id": 114037, "eprint_status": "archive", "datestamp": "2023-08-22 05:53:55", "lastmod": "2023-10-23 23:19:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Carlson-Jonathan-C-T", "name": { "family": "Carlson", "given": "Jonathan C. T." }, "orcid": "0000-0003-4139-9057" }, { "id": "Jena-Sidhartha-S", "name": { "family": "Jena", "given": "Sidhartha S." }, "orcid": "0000-0002-9221-7455" }, { "id": "Flenniken-Michelle", "name": { "family": "Flenniken", "given": "Michelle" }, "orcid": "0000-0003-0356-3370" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Siegel-Ronald-A", "name": { "family": "Siegel", "given": "Ronald A." }, "orcid": "0000-0002-9591-1282" }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Chemically Controlled Self-Assembly of Protein Nanorings", "ispublished": "pub", "full_text_status": "public", "keywords": "Nanostructures, Supramolecular structures and assemblies, Monomers, Oligomers, Conformation; Colloid and Surface Chemistry; Biochemistry; General Chemistry; Catalysis", "note": "\u00a9 2006 American Chemical Society. \n\nReceived 4 February 2006. Published online 17 May 2006. Published in issue 1 June 2006. \n\nWe would like to thank the Division of Medicinal Chemistry\u2212American Chemical Society for a Pre-doctoral Fellowship to J.C.T.C. This research was supported by a Ziagen Faculty Development Grant (C.R.W.) from the University of Minnesota, Department of Medicinal Chemistry, and an AHC Seed-grant (C.R.W.) from the University of Minnesota Academic Health Center. We would also like to thank Dr. Trevor Douglas for access to the electron microscopy facilities at Montana State University.\n\nSupplemental Material - ja060631e_si_001.pdf
", "abstract": "The exploitation of biological macromolecules, such as nucleic acids, for the fabrication of advanced materials is a promising area of research. Although a greater variety of structural and functional uses can be envisioned for protein-based materials, systematic approaches for their construction have yet to emerge. Consistent with theoretical models of polymer macrocyclization, we have demonstrated that, in the presence of dimeric methotrexate (bisMTX), wild-type Escherichia coli dihydrofolate reductase (DHFR) molecules tethered together by a flexible peptide linker (ecDHFR2) are capable of spontaneously forming highly stable cyclic structures with diameters ranging from 8 to 20 nm. The nanoring size is dependent on the length and composition of the peptide linker, on the affinity and conformational state of the dimerizer, and on induced protein\u2212protein interactions. Delineation of these and other rules for the control of protein oligomer assembly by chemical induction provides an avenue to the future design of protein-based materials and nanostructures.", "date": "2006-06-14", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "128", "number": "23", "publisher": "American Chemical Society", "pagerange": "7630-7638", "id_number": "CaltechAUTHORS:20220323-565490000", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565490000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "American Chemical Society Division of Medicinal Chemistry" }, { "agency": "University of Minnesota" } ] }, "doi": "10.1021/ja060631e", "primary_object": { "basename": "ja060631e_si_001.pdf", "url": "https://authors.library.caltech.edu/records/bc3zr-tg780/files/ja060631e_si_001.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Carlson, Jonathan C. T.; Jena, Sidhartha S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n9vaa-jmb15", "eprint_id": 114035, "eprint_status": "archive", "datestamp": "2023-08-22 01:41:09", "lastmod": "2023-10-23 23:19:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kim-Jisook", "name": { "family": "Kim", "given": "Jisook" } }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Griesgraber-George-W", "name": { "family": "Griesgraber", "given": "George W." } }, { "id": "Wagner-Carston-R", "name": { "family": "Wagner", "given": "Carston R." }, "orcid": "0000-0001-7927-719X" } ] }, "title": "Direct Measurement of Nucleoside Monophosphate Delivery from a Phosphoramidate Pronucleotide by Stable Isotope Labeling and LC\u2212ESI\u207b-MS/MS", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Prodrugs; antiviral agent; AZT; phosphoramidate; Drug Discovery; Pharmaceutical Science; Molecular Medicine", "note": "\u00a9 2004 American Chemical Society. \n\nReceived 24 December 2003. Published online 3 February 2004. Published in issue 1 March 2004. \n\nWe thank Dr. Balfour's group in ACTU in the Department of Laboratory Medicine and Pathology at the University of Minnesota for providing PBMCs. Also, we thank Dr. Natalia Y. Tretyakova at the University of Minnesota for her assistance in LC\u2212MS. We are grateful to the Unversity of Minnesota Cancer Center for access to the capillary HPLC\u2212ESI-MS instrument. This research is supported by NIH-NCI Grant CA 89615.", "abstract": "Amino acid phosphoramidates of nucleosides have been shown to be potent antiviral and anticancer agents with the potential to act as nucleoside monophosphate prodrugs. To access their ability to deliver 3'-azido-3'-deoxythymidine (AZT) 5'-monophosphate to cells, the decomposition pathway of an \u00b9\u2078O-labeled AZT amino acid phosphoramidate was investigated by capillary reverse-phase high-performance liquid chromatography interfaced with negative ion electrospray ionization mass spectrometry (LC\u2212ESI--MS/MS). \u00b9\u2078O-labeled l-AZT tryptophan phosphoramidate methyl ester ([\u00b9\u2078O]2) was synthesized with an \u00b9\u2078O/\u00b9\u2076O relative ratio of 1.22 \u00b1 0.18. For CEM cells, a human T-lymphoblast leukemia cell line, incubated with [18O]2, values of 1.55 \u00b1 0.37, 0.34, and 0.13 were found for the \u00b9\u2078O/\u00b9\u2076O relative ratio of intracellular AZT-MP for time intervals of 0.5, 4, and 20 h, respectively. The decrease in the level of labeled AZT-MP in CEM cells corresponded to a rapid increase in the amount of intracellular AZT presumably by dephosphorylation of AZT-MP. In contrast, for peripheral blood mononuclear cells (PBMCs), the \u00b9\u2078O/\u00b9\u2076O relative ratio values of intracellular AZT-MP were 1.43, 1.06, and 0.61 for time intervals of 0.5, 4, and 20 h, respectively. Intracellular AZT in PBMCs was nearly undetectable for each time interval. Taken together, these results are consistent with the detection of direct P\u2212N bond cleavage by CEM cells and PBMCs. However, AZT phosphoramidates are able to more effectively deliver AZT-MP to PBMCs than to CEM cells. Differential expression of 5'-nucleotidase in CEM cells relative to PBMCs is likely the reason for this discrepancy. Although applied to a phosphoramidate pronucleotide, the judicious use of \u00b9\u2078O labeling and LC\u2212MS is a general approach that could be applied to the investigation of the intracellular fate of other pronucleotides.", "date": "2004-03-01", "date_type": "published", "publication": "Molecular Pharmaceutics", "volume": "1", "number": "2", "publisher": "American Chemical Society", "pagerange": "102-111", "id_number": "CaltechAUTHORS:20220323-565463000", "issn": "1543-8384", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220323-565463000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "CA 89615" } ] }, "doi": "10.1021/mp0340338", "resource_type": "article", "pub_year": "2004", "author_list": "Kim, Jisook; Chou, Tsui-fen; et el." } ]