[ { "id": "https://authors.library.caltech.edu/records/f08sq-jmm29", "eprint_status": "archive", "datestamp": "2024-03-06 20:52:37", "lastmod": "2024-03-06 20:52:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Haloi-Nandan", "name": { "family": "Haloi", "given": "Nandan" }, "orcid": "0000-0003-3542-333X" }, { "id": "Huang-Shan", "name": { "family": "Huang", "given": "Shan" } }, { "id": "Nichols-Aaron-L", "name": { "family": "Nichols", "given": "Aaron L." }, "orcid": "0000-0001-9341-0049" }, { "id": "Fine-Eve-J", "name": { "family": "Fine", "given": "Eve J." }, "orcid": "0000-0001-7404-897X" }, { "id": "Friesenhahn-Nicholas-J", "name": { "family": "Friesenhahn", "given": "Nicholas J." }, "orcid": "0000-0002-8129-0171" }, { "id": "Marotta-Christopher-B", "name": { "family": "Marotta", "given": "Christopher B." } }, { "id": "Dougherty-D-A", "name": { "family": "Dougherty", "given": "Dennis A." }, "orcid": "0000-0003-1464-2461" }, { "id": "Lindahl-Erik", "name": { "family": "Lindahl", "given": "Erik" }, "orcid": "0000-0002-2734-2794" }, { "id": "Howard-Rebecca-J", "name": { "family": "Howard", "given": "Rebecca J." }, "orcid": "0000-0003-2049-3378" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" } ] }, "title": "Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids", "ispublished": "pub", "full_text_status": "public", "keywords": "Molecular Biology; Biochemistry; Bioengineering; Biotechnology", "note": "
© The Author(s) 2024. Published by Oxford University Press. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/pages/standard-publication-reuse-rights)
", "abstract": "We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for \u2206F/F0vs [nicotine] (δ-slope, 2.7 μM−1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the ‘candle snuffer’ mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.
\n\n", "date": "2024-01-29", "date_type": "published", "publication": "Protein Engineering, Design and Selection", "volume": "37", "publisher": "Oxford University Press", "pagerange": "gzae003", "issn": "1741-0126", "official_url": "https://authors.library.caltech.edu/records/f08sq-jmm29", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Swedish e-Science Research Centre", "grant_number": "EU-823830" }, { "agency": "Knut and Alice Wallenberg Foundation", "grant_number": "2021-05806" }, { "agency": "Knut and Alice Wallenberg Foundation", "grant_number": "2019-02433" }, { "agency": "European Research Council", "grant_number": "101107036" }, { "agency": "Swedish National Infrastructure for Computing", "grant_number": "SNIC2022/3-40" }, { "agency": "Karolina through EuroHPC", "grant_number": "EHPC-REG-2021R0074" }, { "agency": "National Institutes of Health", "grant_number": "T29IR0455" }, { "agency": "National Institutes of Health", "grant_number": "GM-123582" }, { "agency": "National Institutes of Health", "grant_number": "DA049140" }, { "agency": "California TRDRP", "grant_number": "27IP-0057" }, { "agency": "California Tobacco-Related Disease Research Program", "grant_number": "27FT-0022" } ] }, "collection": "CaltechAUTHORS", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering", "value": "Division of Biology and Biological Engineering" } ] }, "doi": "10.1093/protein/gzae003", "resource_type": "article", "pub_year": "2024", "author_list": "Haloi, Nandan; Huang, Shan; et el." }, { "id": "https://authors.library.caltech.edu/records/r9rth-vbb77", "eprint_id": 120567, "eprint_status": "archive", "datestamp": "2023-08-22 20:24:25", "lastmod": "2024-01-18 22:50:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Huang-Shan", "name": { "family": "Huang", "given": "Shan" }, "orcid": "0000-0002-4436-3327" }, { "id": "Wang-Kaihang", "name": { "family": "Wang", "given": "Kaihang" }, "orcid": "0000-0001-7657-8755" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Genome manipulation by guide-directed Argonaute cleavage", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics", "note": "\u00a9 The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. 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\nWe thank Dr Alexei A. Aravin, Dr Andrey Kulbachinskiy, Dr Daria Esyunina and Dr David R. F. Leach for helpful discussions. We thank Rochelle A. Diamond and Jamie Tijerina for their help in flow cytometry experiments. \n\nAuthor contributions: S.H. designed and carried out experiments, with K.W. and S.L.M. providing guidance. S.H., K.W. and S.L.M. wrote the manuscript. \n\nFUNDING. Caltech Rosen Bioengineering Center Award; Shurl and Kay Curci Foundation Award. Funding for open access charge: Caltech Rosen Bioengineering Center Award. \n\nDATA AVAILABILITY. Additional notes and data are available in the Supplemental materials. \n\nConflict of interest statement. None declared.\n\nPublished - gkad188.pdf
Supplemental Material - gkad188_supplemental_file.pdf
", "abstract": "Many prokaryotic argonautes (pAgos) mediate DNA interference by using small DNA guides to cleave target DNA. A recent study shows that CbAgo, a pAgo from Clostridium butyricum, induces DNA interference between homologous sequences and generates double-stranded breaks (DSBs) in target DNAs. This mechanism enables the host to defend against invading DNAs such as plasmids and viruses. However, whether such a CbAgo-mediated DNA cleavage is mutagenic remains unexplored. Here we demonstrate that CbAgo, directed by plasmid-encoded guide sequences, can cleave genome target sites and induce chromosome recombination between downstream homologous sequences in Escherichia coli. The recombination rate correlates well with pAgo DNA cleavage activity and the mechanistic study suggests the recombination involves DSBs and RecBCD processing. In RecA-deficient E. coli strain, guide-directed CbAgo cleavage on chromosomes severely impairs cell growth, which can be utilized as counter-selection to assist Lambda-Red recombineering. These findings demonstrate the guide-directed cleavage of pAgo on the host genome is mutagenic and can lead to different outcomes according to the function of the host DNA repair machinery. We anticipate this novel DNA-guided interference to be useful in broader genetic manipulation. Our study also provides an in vivo assay to characterize or engineer pAgo DNA cleavage activity.", "date": "2023-05-08", "date_type": "published", "publication": "Nucleic Acids Research", "volume": "51", "number": "8", "publisher": "Oxford University Press", "pagerange": "4078-4085", "id_number": "CaltechAUTHORS:20230328-708572000.64", "issn": "0305-1048", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230328-708572000.64", "funders": { "items": [ { "agency": "Donna and Benjamin M. Rosen Bioengineering Center" }, { "agency": "Shurl and Kay Curci Foundation" } ] }, "local_group": { "items": [ { "id": "Rosen-Bioengineering-Center" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/nar/gkad188", "pmcid": "PMC10164581", "primary_object": { "basename": "gkad188.pdf", "url": "https://authors.library.caltech.edu/records/r9rth-vbb77/files/gkad188.pdf" }, "related_objects": [ { "basename": "gkad188_supplemental_file.pdf", "url": "https://authors.library.caltech.edu/records/r9rth-vbb77/files/gkad188_supplemental_file.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Huang, Shan; Wang, Kaihang; et el." }, { "id": "https://authors.library.caltech.edu/records/wpph8-10s29", "eprint_id": 111928, "eprint_status": "archive", "datestamp": "2023-08-20 05:25:28", "lastmod": "2023-12-22 23:15:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Breunig-Stephanie-L", "name": { "family": "Breunig", "given": "Stephanie" } }, { "id": "Chapman-Alex", "name": { "family": "Chapman", "given": "Alex" } }, { "id": "Aceves-Aiden", "name": { "family": "Aceves", "given": "Aiden" } }, { "id": "LeBon-Jeanne-M", "name": { "family": "LeBon", "given": "Jeanne" } }, { "id": "Quijano-Janine-C", "name": { "family": "Quijano", "given": "Janine" } }, { "id": "Ku-Hsun-Teresa", "name": { "family": "Ku", "given": "Hsun Teresa" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Steven" }, "orcid": "0000-0002-9785-5018" }, { "id": "Tirrell-D-A", "name": { "family": "Tirrell", "given": "David" }, "orcid": "0000-0003-3175-4596" } ] }, "title": "Modification of Insulin Lispro by Incorporation of Non-canonical Proline Residues", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 The Protein Society. \n\nIssue Online: 27 October 2021.", "abstract": "[no abstract]", "date": "2021-10", "date_type": "published", "publication": "Protein Science", "volume": "30", "number": "S1", "publisher": "Wiley", "pagerange": "89", "id_number": "CaltechAUTHORS:20211117-181926510", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211117-181926510", "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": "10.1002/pro.4191", "resource_type": "article", "pub_year": "2021", "author_list": "Breunig, Stephanie; Chapman, Alex; et el." }, { "id": "https://authors.library.caltech.edu/records/jb5pk-e5h83", "eprint_id": 107449, "eprint_status": "archive", "datestamp": "2023-08-20 01:20:35", "lastmod": "2023-12-22 23:08:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "LaPelusa-Michael", "name": { "family": "LaPelusa", "given": "Michael" } }, { "id": "Donoviel-Dorit", "name": { "family": "Donoviel", "given": "Dorit" } }, { "id": "Branzini-Sergio-E", "name": { "family": "Branzini", "given": "Sergio E." } }, { "id": "Carlson-Paul-E-Jr", "name": { "family": "Carlson", "given": "Paul E., Jr." }, "orcid": "0000-0002-7900-7154" }, { "id": "Culler-Stephanie-J", "name": { "family": "Culler", "given": "Stephanie" } }, { "id": "Cheema-Amrita-K", "name": { "family": "Cheema", "given": "Amrita K." }, "orcid": "0000-0003-4877-7583" }, { "id": "Kaddurah-Daouk-Rima", "name": { "family": "Kaddurah-Daouk", "given": "Rima" }, "orcid": "0000-0003-1858-5732" }, { "id": "Kelly-Denise", "name": { "family": "Kelly", "given": "Denise" } }, { "id": "de-Cremoux-Isabelle", "name": { "family": "de Cremoux", "given": "Isabelle" } }, { "id": "Knight-Rob", "name": { "family": "Knight", "given": "Rob" }, "orcid": "0000-0002-0975-9019" }, { "id": "Krajmalnik-Brown-Rosa", "name": { "family": "Krajmalnik-Brown", "given": "Rosa" }, "orcid": "0000-0001-6064-3524" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Mazmanian-S-K", "name": { "family": "Mazmanian", "given": "Sarkis K." }, "orcid": "0000-0003-2713-1513" }, { "id": "Mayer-Emeran-A", "name": { "family": "Mayer", "given": "Emeran A." }, "orcid": "0000-0003-3923-3349" }, { "id": "Petrosino-Joseph-F", "name": { "family": "Petrosino", "given": "Joseph F." }, "orcid": "0000-0002-4046-6898" }, { "id": "Garrison-Keith", "name": { "family": "Garrison", "given": "Keith" }, "orcid": "0000-0002-7966-8833" } ] }, "title": "Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020", "ispublished": "pub", "full_text_status": "public", "keywords": "Microbiome, Spaceflight, Radiation, Multiple sclerosis, Behavior, Gut-brain axis, Metabolome, Sequencing,\nAutism spectrum disorder, Fecal microbiota transplants, Live biotherapeutic products", "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/. 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\nReceived 19 October 2020. Accepted 06 December 2020. Published 04 January 2021. \n\nSLM and DD would like to thank Rachael Dempsey (Baylor College of Medicine) for her creative and effective outreach efforts and materials. SKM and SLM would like to thank Lauren Breeyear for the administrative support, Leslie Maxfield and the Caltech Academic Media Technologies and Communications team for hosting the webinar, and members of the Mazmanian laboratory (Reem Abdel-Haq, Joseph Boktor, Jessica Griffiths, and Henry Schreiber) for moderating questions. \n\nSupport for the conference was provided by the Translational Research Institute for Space Health (TRISH) through NASA Cooperative Agreement NNX16AO69A. Additional support was provided by Caltech. \n\nMichael LaPelusa and Keith Garrison contributed equally to this work. \n\nAuthor Contributions. KG and ML wrote the manuscript. DD, SKM, and SLM organized the meeting. RK, SEB, SKM, EAM, JFP, RKB, RKD, AKC, DK, SC, and PEC were speakers. All authors read, edited, and approved the final manuscript. \n\nEthics approval and consent to participate: Not applicable. \n\nConsent for publication: Not applicable. \n\nCompeting interests. SC declares financial interests in Persephone Biosciences, Inc. DK and IC declare financial interests in Seventure Partners. RKB received research funding from Crestovo/Finch Therapeutics. SKM declares financial interests in Axial Biotherapeutics, Inc. EAM is a scientific advisory board member of Danone, Axial Biotherapeutics, Viome, Amare, Mahana Therapeutics, Pendulum, Bloom Biosciences, and APC Microbiome Ireland. The remaining authors declare that they have no competing interests.\n\nPublished - s40168-020-00951-5.pdf
", "abstract": "The inaugural \"Microbiome for Mars\" virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and how this growing field could broadly impact human health and space exploration. This report summarizes each speaker's presentation in the order presented at the workshop.", "date": "2021-01-04", "date_type": "published", "publication": "Microbiome", "volume": "9", "publisher": "BioMed Central", "pagerange": "Art. No. 2", "id_number": "CaltechAUTHORS:20210112-151232385", "issn": "2049-2618", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210112-151232385", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NASA", "grant_number": "NNX16AO69A" }, { "agency": "Caltech" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1186/s40168-020-00951-5", "pmcid": "PMC7781430", "primary_object": { "basename": "s40168-020-00951-5.pdf", "url": "https://authors.library.caltech.edu/records/jb5pk-e5h83/files/s40168-020-00951-5.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "LaPelusa, Michael; Donoviel, Dorit; et el." }, { "id": "https://authors.library.caltech.edu/records/d72qh-1qm54", "eprint_id": 91558, "eprint_status": "archive", "datestamp": "2023-08-22 02:16:09", "lastmod": "2023-10-23 17:00:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nisthal-Alex", "name": { "family": "Nisthal", "given": "Alex" } }, { "id": "Wang-Connie-Y", "name": { "family": "Wang", "given": "Connie Y." }, "orcid": "0000-0003-2971-3971" }, { "id": "Ary-Marie-L", "name": { "family": "Ary", "given": "Marie L." }, "orcid": "0000-0002-0756-1746" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis", "ispublished": "pub", "full_text_status": "public", "keywords": "thermodynamic stability; mutagenesis; protein engineering; protein stability prediction; protein G", "note": "\u00a9 2019 National Academy of Sciences. Published under the PNAS license. \n\nContributed by Stephen L. Mayo, July 3, 2019 (sent for review March 6, 2019; reviewed by Elizabeth M. Meiering and Timothy Whitehead). \n\nA.N. thanks Jost Vielmetter for advice and feedback on the automated platform. S.L.M. acknowledges grants from the National Security Science and Engineering Faculty Fellowship program and the Defense Advanced Research Projects Agency Protein Design Processes program. \n\nAuthor contributions: A.N. and S.L.M. designed research; A.N. performed research; A.N. and C.Y.W. contributed new reagents/analytic tools; A.N., C.Y.W., and M.L.A. analyzed data; and A.N., C.Y.W., M.L.A., and S.L.M. wrote the paper. \n\nReviewers: E.M.M., University of Waterloo; and T.W., University of Colorado Boulder. \n\nThe authors declare no conflict of interest. \n\nData deposition: The data reported in this paper have been deposited in Protabank, https://www.protabank.org/ (ID no. gwoS2haU3). \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1903888116/-/DCSupplemental.\n\nPublished - 16367.full.pdf
Supplemental Material - pnas.1903888116.sapp.pdf
", "abstract": "The accurate prediction of protein stability upon sequence mutation is an important but unsolved challenge in protein engineering. Large mutational datasets are required to train computational predictors, but traditional methods for collecting stability data are either low-throughput or measure protein stability indirectly. Here, we develop an automated method to generate thermodynamic stability data for nearly every single mutant in a small 56-residue protein. Analysis reveals that most single mutants have a neutral effect on stability, mutational sensitivity is largely governed by residue burial, and unexpectedly, hydrophobics are the best tolerated amino acid type. Correlating the output of various stability-prediction algorithms against our data shows that nearly all perform better on boundary and surface positions than for those in the core and are better at predicting large-to-small mutations than small-to-large ones. We show that the most stable variants in the single-mutant landscape are better identified using combinations of 2 prediction algorithms and including more algorithms can provide diminishing returns. In most cases, poor in silico predictions were tied to compositional differences between the data being analyzed and the datasets used to train the algorithm. Finally, we find that strategies to extract stabilities from high-throughput fitness data such as deep mutational scanning are promising and that data produced by these methods may be applicable toward training future stability-prediction tools.", "date": "2019-08-13", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "116", "number": "33", "publisher": "National Academy of Sciences", "pagerange": "16367-16377", "id_number": "CaltechAUTHORS:20181207-083716880", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181207-083716880", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Security Science and Engineering Faculty Fellowship" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "doi": "10.1073/pnas.1903888116", "pmcid": "PMC6697890", "primary_object": { "basename": "16367.full.pdf", "url": "https://authors.library.caltech.edu/records/d72qh-1qm54/files/16367.full.pdf" }, "related_objects": [ { "basename": "pnas.1903888116.sapp.pdf", "url": "https://authors.library.caltech.edu/records/d72qh-1qm54/files/pnas.1903888116.sapp.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Nisthal, Alex; Wang, Connie Y.; et el." }, { "id": "https://authors.library.caltech.edu/records/w2t7y-t3w24", "eprint_id": 100445, "eprint_status": "archive", "datestamp": "2023-08-19 16:08:18", "lastmod": "2023-10-18 20:33:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oki-Kenji", "name": { "family": "Oki", "given": "Kenji" } }, { "id": "Lee-Frederick-S", "name": { "family": "Lee", "given": "Frederick S." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Attempts to develop an enzyme converting DHIV to KIV", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 The Author(s). Published by Oxford University Press.\nThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived: 23 August 2019; Revision requested: 21 September 2019; Accepted: 01 October 2019; Published: 23 December 2019.", "abstract": "Dihydroxy-acid dehydratase (DHAD) catalyzes the dehydration of R-2,3-dihydroxyisovalerate (DHIV) to 2-ketoisovalerate (KIV) using an Fe-S cluster as a cofactor, which is sensitive to oxidation and expensive to synthesize. In contrast, sugar acid dehydratases catalyze the same chemical reactions using a magnesium ion. Here, we attempted to substitute the high-cost DHAD with a cost-efficient engineered sugar acid dehydratase using computational protein design (CPD). First, we tried without success to modify the binding pocket of a sugar acid dehydratase to accommodate the smaller, more hydrophobic DHIV. Then, we used a chemically activated substrate analog to react with sugar acid dehydratases or other enolase superfamily enzymes. Mandelate racemase from Pseudomonas putida (PpManR) and the putative sugar acid dehydratase from Salmonella typhimurium (StPutD) showed beta-elimination activity towards chlorolactate (CLD). CPD combined with medium-throughput selection improved the PpManR kcat/KM for CLD by four-fold. However, these enzyme variants did not show dehydration activity towards DHIV. Lastly, assuming phosphorylation could also be a good activation mechanism, we found that mevalonate-3-kinase (M3K) from Picrophilus torridus (PtM3K) exhibited adenosine triphosphate (ATP) hydrolysis activity when mixed with DHIV, indicating phosphorylation activity towards DHIV. Engineering PpManR or StPutD to accept 3-phospho-DHIV as a substrate was performed, but no variants with the desired activity were obtained.", "date": "2019-06", "date_type": "published", "publication": "Protein Engineering, Design and Selection", "volume": "32", "number": "6", "publisher": "Oxford University Press", "pagerange": "261-270", "id_number": "CaltechAUTHORS:20200102-092224643", "issn": "1741-0126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200102-092224643", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-SC0011396" }, { "agency": "Mitsubishi Chemical Corporation" } ] }, "doi": "10.1093/protein/gzz042", "resource_type": "article", "pub_year": "2019", "author_list": "Oki, Kenji; Lee, Frederick S.; et el." }, { "id": "https://authors.library.caltech.edu/records/q3eqc-ajr77", "eprint_id": 95384, "eprint_status": "archive", "datestamp": "2023-08-19 15:50:12", "lastmod": "2023-10-20 20:11:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ross-Matthew-O", "name": { "family": "Ross", "given": "Matthew O." } }, { "id": "MacMillan-Fraser", "name": { "family": "MacMillan", "given": "Fraser" } }, { "id": "Wang-Jingzhou", "name": { "family": "Wang", "given": "Jingzhou" } }, { "id": "Nisthal-Alex", "name": { "family": "Nisthal", "given": "Alex" } }, { "id": "Lawton-Thomas-J", "name": { "family": "Lawton", "given": "Thomas J." } }, { "id": "Olafson-Barry-D", "name": { "family": "Olafson", "given": "Barry D." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Rosenzweig-Amy-C", "name": { "family": "Rosenzweig", "given": "Amy C." } }, { "id": "Hoffman-Brian-M", "name": { "family": "Hoffman", "given": "Brian M." }, "orcid": "0000-0002-3100-0746" } ] }, "title": "Particulate methane monooxygenase contains only mononuclear copper centers", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 American Association for the Advancement of Science. This is an article distributed under the terms of the Science Journals Default License. \n\nReceived 29 August 2018; accepted 15 April 2019. \n\nWe thank G. E. Cutsail III, M. A. Culpepper, and H. W. Pinkett for helpful discussions as well as an anonymous reviewer for the expert analysis of the Gaussian fitting and providing above and beyond effort. \n\nThis work was supported by NIH grants GM118035 (A.C.R.), GM111097 (B.M.H.), and 5T32GM008382 (M.O.R.) and NSF grant 1534743 (S.L.M., B.D.O., and A.C.R.). F.M. was supported by a Royal Society Wolfson Research Merit Award. \n\nAuthor contributions: M.O.R, F.M., A.N., T.J.L., B.D.O, S.L.M., A.C.R., and B.M.H. designed experiments. M.O.R., F.M., J.W., and A.N. carried out experiments. M.O.R, A.C.R., and B.M.H. wrote the manuscript. \n\nCompeting interests: A patent related to this work has been issued: A. C. Rosenzweig, T. J. Lawton, A. Nisthal, J. S. Kostecki, H. K. Privett, F. Lee, B. Olafson, A. D. Dousis, \"Engineered recombinant enzymes for methane oxidation\" U.S. patent US9896700B2. B.D.O. is a cofounder and the CEO of Protabit, a for-profit company that develops and markets software for protein engineering and computational protein design. S.L.M. is a cofounder of Protabit. \nData and materials availability: All data are available in the manuscript or the supplementary materials.\n\nAccepted Version - nihms-1043022.pdf
Supplemental Material - aav2572-Ross-SM.pdf
", "abstract": "Bacteria that oxidize methane to methanol are central to mitigating emissions of methane, a potent greenhouse gas. The nature of the copper active site in the primary metabolic enzyme of these bacteria, particulate methane monooxygenase (pMMO), has been controversial owing to seemingly contradictory biochemical, spectroscopic, and crystallographic results. We present biochemical and electron paramagnetic resonance spectroscopic characterization most consistent with two monocopper sites within pMMO: one in the soluble PmoB subunit at the previously assigned active site (Cu_B) and one ~2 nanometers away in the membrane-bound PmoC subunit (Cu_C). On the basis of these results, we propose that a monocopper site is able to catalyze methane oxidation in pMMO.", "date": "2019-05-10", "date_type": "published", "publication": "Science", "volume": "364", "number": "6440", "publisher": "American Association for the Advancement of Science", "pagerange": "566-570", "id_number": "CaltechAUTHORS:20190509-152916236", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190509-152916236", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM118035" }, { "agency": "NIH", "grant_number": "GM111097" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32GM008382" }, { "agency": "NSF", "grant_number": "IIP-1534743" }, { "agency": "Royal Society" } ] }, "doi": "10.1126/science.aav2572", "pmcid": "PMC6664434", "primary_object": { "basename": "aav2572-Ross-SM.pdf", "url": "https://authors.library.caltech.edu/records/q3eqc-ajr77/files/aav2572-Ross-SM.pdf" }, "related_objects": [ { "basename": "nihms-1043022.pdf", "url": "https://authors.library.caltech.edu/records/q3eqc-ajr77/files/nihms-1043022.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Ross, Matthew O.; MacMillan, Fraser; et el." }, { "id": "https://authors.library.caltech.edu/records/ma97j-g6022", "eprint_id": 84127, "eprint_status": "archive", "datestamp": "2023-08-22 00:20:46", "lastmod": "2023-10-18 15:12:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wannier-Timothy-M", "name": { "family": "Wannier", "given": "Timothy M." } }, { "id": "Gillespie-Sarah-K", "name": { "family": "Gillespie", "given": "Sarah K." } }, { "id": "Hutchins-Nicholas", "name": { "family": "Hutchins", "given": "Nicholas" } }, { "id": "McIsaac-R-Scott", "name": { "family": "McIsaac", "given": "R. Scott" }, "orcid": "0000-0002-5339-6032" }, { "id": "Wu-Sheng-Yi", "name": { "family": "Wu", "given": "Sheng-Yi" } }, { "id": "Shen-Yi", "name": { "family": "Shen", "given": "Yi" } }, { "id": "Campbell-Robert-E", "name": { "family": "Campbell", "given": "Robert E." } }, { "id": "Brown-Kevin-S", "name": { "family": "Brown", "given": "Kevin S." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Monomerization of Far-Red Fluorescent Proteins", "ispublished": "pub", "full_text_status": "public", "keywords": "fluorescent protein; red fluorescent protein; protein engineering; computational protein design; RFP", "note": "\u00a9 2018 National Academy of Sciences. Published under the PNAS license. \n\nContributed by Stephen L. Mayo, October 12, 2018 (sent for review June 13, 2018; reviewed by Amy E. Palmer and Vladislav V. Verkhusha). PNAS published ahead of print November 13, 2018. \n\nWe thank Yun Mou, Matthew Moore, and Roberto Chica for many helpful conversations. We would also like to thank Prof. Frances Arnold for her advice and support. Jens Kaiser and Pavle Nikolovski were generous with their time and advice in troubleshooting protein crystallography. The authors are grateful for the use of the beamline 12-2 at the Stanford Synchrotron Radiation Lightsource and to the Gordon and Betty Moore Foundation for support of the Molecular Observatory at the California Institute of Technology. We also acknowledge the funding and support of the National Institute of Biomedical Imaging and Bioengineering (Grant R21EB018579). \n\nAuthor contributions: T.M.W., R.S.M., R.E.C., K.S.B., and S.L.M. designed research; T.M.W., S.K.G., N.H., S.-Y.W., and Y.S. performed research; T.M.W., Y.S., and K.S.B. analyzed data; and T.M.W. and S.L.M. wrote the paper. \n\nReviewers: A.E.P., University of Colorado; and V.V.V., Albert Einstein College of Medicine. \n\nThe authors declare no conflict of interest. \n\nData deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.wwpdb.org (PDB ID code: 6DEJ). GenBank IDs [accession nos. MK040729 (mGinger), MK040730 (mGinger2), MK040731 (mKelly1), and MK040732 (mKelly2)]. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1807449115/-/DCSupplemental.\n\nPublished - E11294.full.pdf
Submitted - 162842.full.pdf
Supplemental Material - pnas.1807449115.sapp.pdf
", "abstract": "Anthozoa-class red fluorescent proteins (RFPs) are frequently used as biological markers, with far-red (\u03bb_(em) \u223c 600\u2013700 nm) emitting variants sought for whole-animal imaging because biological tissues are more permeable to light in this range. A barrier to the use of naturally occurring RFP variants as molecular markers is that all are tetrameric, which is not ideal for cell biological applications. Efforts to engineer monomeric RFPs have typically produced dimmer and blue-shifted variants because the chromophore is sensitive to small structural perturbations. In fact, despite much effort, only four native RFPs have been successfully monomerized, leaving the majority of RFP biodiversity untapped in biomarker development. Here we report the generation of monomeric variants of HcRed and mCardinal, both far-red dimers, and describe a comprehensive methodology for the monomerization of red-shifted oligomeric RFPs. Among the resultant variants is mKelly1 (emission maximum, \u03bb_(em) = 656 nm), which, along with the recently reported mGarnet2 [Matela G, et al. (2017) Chem Commun (Camb) 53:979\u2013982], forms a class of bright, monomeric, far-red FPs.", "date": "2018-11-27", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "115", "number": "48", "publisher": "National Academy of Sciences", "pagerange": "E11294-E11301", "id_number": "CaltechAUTHORS:20180105-112949227", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180105-112949227", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "NIH", "grant_number": "R21EB018579" } ] }, "doi": "10.1101/162842", "pmcid": "PMC6275547", "primary_object": { "basename": "E11294.full.pdf", "url": "https://authors.library.caltech.edu/records/ma97j-g6022/files/E11294.full.pdf" }, "related_objects": [ { "basename": "pnas.1807449115.sapp.pdf", "url": "https://authors.library.caltech.edu/records/ma97j-g6022/files/pnas.1807449115.sapp.pdf" }, { "basename": "162842.full.pdf", "url": "https://authors.library.caltech.edu/records/ma97j-g6022/files/162842.full.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Wannier, Timothy M.; Gillespie, Sarah K.; et el." }, { "id": "https://authors.library.caltech.edu/records/8fsyh-2xc44", "eprint_id": 91531, "eprint_status": "archive", "datestamp": "2023-08-19 12:28:07", "lastmod": "2023-10-19 23:10:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Connie-Y", "name": { "family": "Wang", "given": "Connie" }, "orcid": "0000-0003-2971-3971" }, { "id": "Chang-Paul-M", "name": { "family": "Chang", "given": "Paul" } }, { "id": "Ary-Marie-L", "name": { "family": "Ary", "given": "Marie L." }, "orcid": "0000-0002-0756-1746" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen" }, "orcid": "0000-0002-9785-5018" }, { "id": "Olafson-Barry-D", "name": { "family": "Olafson", "given": "Barry" } } ] }, "title": "Protabank: A Repository for Protein Design and Engineering Data", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 The Protein Society. \n\nFirst published: 21 November 2018.", "abstract": "[no abstract]", "date": "2018-11", "date_type": "published", "publication": "Protein Science", "volume": "27", "number": "S1", "publisher": "Wiley", "pagerange": "115", "id_number": "CaltechAUTHORS:20181206-080139767", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181206-080139767", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1002/pro.3513", "resource_type": "article", "pub_year": "2018", "author_list": "Wang, Connie; Chang, Paul; et el." }, { "id": "https://authors.library.caltech.edu/records/vd5e8-0ft43", "eprint_id": 85553, "eprint_status": "archive", "datestamp": "2023-08-21 23:25:30", "lastmod": "2023-10-23 15:54:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Connie-Y", "name": { "family": "Wang", "given": "Connie Y." }, "orcid": "0000-0003-2971-3971" }, { "id": "Chang-Paul-M", "name": { "family": "Chang", "given": "Paul M." } }, { "id": "Ary-Marie-L", "name": { "family": "Ary", "given": "Marie L." }, "orcid": "0000-0002-0756-1746" }, { "id": "Allen-Benjamin-D", "name": { "family": "Allen", "given": "Benjamin D." }, "orcid": "0000-0001-6914-5572" }, { "id": "Chica-Roberto-A", "name": { "family": "Chica", "given": "Roberto A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Olafson-Barry-D", "name": { "family": "Olafson", "given": "Barry D." } } ] }, "title": "ProtaBank: A repository for protein design and engineering data", "ispublished": "pub", "full_text_status": "public", "keywords": "protein engineering; protein design; relational database; protein mutants; data resource; protein stability; data sets", "note": "\u00a9 2018 The Authors. Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society. This is an open access article under the terms of the Creative Commons Attribution\u2010NonCommercial\u2010NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non\u2010commercial and no modifications or adaptations are made. \n\nIssue Online 28 May 2018; Version of Record online: 30 April 2018; Accepted manuscript online: 25 March 2018; Manuscript accepted: 21 March 2018; Manuscript revised: 13 March 2018; Manuscript received: 15 February 2018. \n\nThe content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. \n\nConflict of Interest: None declared.\n\nThe authors declare the following competing financial interest(s): BDA, SLM and BDO are co\u2010founders/owners of Protabit LLC, a limited liability company. CYW and PMC are employees of Protabit LLC and have ownership interests in Protabit LLC. MLA is an independent contractor and receives compensation from Protabit LLC. RAC declares no competing financial interests. Protabit LLC owns the rights to the ProtaBank Database and associated tools and technologies.\n\nCurrent address: Protabit LLC, 1010 E Union Street, Suite 110, Pasadena, CA 91106.\n\nData accessibility statement: All data stored in the ProtaBank Database are free and accessible to all users. Data from individual study pages may be downloaded to the user's device in Excel or csv formats, or be copied to the users clipboard.\n\nProtabit LLC may develop and commercialize certain aspects of the ProtaBank technology, including providing separate databases and tools for commercial entities that have a desire to store proprietary data.\n\nPublished - Wang_et_al-2018-Protein_Science.pdf
Submitted - 272211.full.pdf
Supplemental Material - pro3406-sup-0001-suppinfo01.docx
Erratum - Wang_et_al-2019-Protein_Science.pdf
", "abstract": "We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user\u2010friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org.", "date": "2018-06", "date_type": "published", "publication": "Protein Science", "volume": "27", "number": "6", "publisher": "Wiley", "pagerange": "1113-1124", "id_number": "CaltechAUTHORS:20180402-082750705", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180402-082750705", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R44GM117961" } ] }, "doi": "10.1002/pro.3406", "pmcid": "PMC5980626", "primary_object": { "basename": "272211.full.pdf", "url": "https://authors.library.caltech.edu/records/vd5e8-0ft43/files/272211.full.pdf" }, "related_objects": [ { "basename": "Wang_et_al-2018-Protein_Science.pdf", "url": "https://authors.library.caltech.edu/records/vd5e8-0ft43/files/Wang_et_al-2018-Protein_Science.pdf" }, { "basename": "Wang_et_al-2019-Protein_Science.pdf", "url": "https://authors.library.caltech.edu/records/vd5e8-0ft43/files/Wang_et_al-2019-Protein_Science.pdf" }, { "basename": "pro3406-sup-0001-suppinfo01.docx", "url": "https://authors.library.caltech.edu/records/vd5e8-0ft43/files/pro3406-sup-0001-suppinfo01.docx" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Wang, Connie Y.; Chang, Paul M.; et el." }, { "id": "https://authors.library.caltech.edu/records/3rjwa-na587", "eprint_id": 86578, "eprint_status": "archive", "datestamp": "2023-08-19 07:44:23", "lastmod": "2023-10-18 19:44:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Connie-Y", "name": { "family": "Wang", "given": "Connie" }, "orcid": "0000-0003-2971-3971" }, { "id": "Chang-Paul-M", "name": { "family": "Chang", "given": "Paul" } }, { "id": "Ary-Marie-L", "name": { "family": "Ary", "given": "Marie L." }, "orcid": "0000-0002-0756-1746" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen" }, "orcid": "0000-0002-9785-5018" }, { "id": "Olafson-Barry-D", "name": { "family": "Olafson", "given": "Barry" } } ] }, "title": "PEBank: A Comprehensive Database for Protein Engineering and Design", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2018 Biophysical Society. \n\nAvailable online 6 February 2018.", "abstract": "Recent advances in gene synthesis, microfluidics, deep sequencing, and microarray techniques have made it possible to construct and assay large libraries of variant protein sequences. This rapid generation of large sets of mutational data has significantly enhanced researchers' ability to study how proteins function and to engineer proteins with new and improved properties. Although many groups around the world are currently generating large amounts of protein engineering data, there is no standardized format to report this data and no simple mechanism for groups to share the data that they generate.\n\nWe have developed PEBank (Protein Engineering data Bank), a comprehensive database for protein engineering data where users can store their data as well as query and analyze data submitted by themselves and others. PEBank stores the data in a relational database using a standardized schema that requires full protein sequence information and detailed assay descriptions. These features allow for accurate comparison of measurements made across different proteins and by different groups. PEBank is comprehensive in that it accepts data for several different protein properties, including those related to stability, folding, activity, and binding. PEBank thus provides a central repository for data that is often scattered across many different specialized databases. PEBank features a web interface and REST API that streamlines data deposition and allows for batch input and queries. A suite of analysis tools are provided to allow for discovery and analysis of relationships between mutated sequences. We demonstrate the importance of a standardized format for reporting protein engineering data that allows for accurate comparisons between different data sets and enables future data mining and machine learning approaches to be applied.", "date": "2018-02-02", "date_type": "published", "publication": "Biophysical Journal", "volume": "114", "number": "3", "publisher": "Biophysical Society", "pagerange": "411A", "id_number": "CaltechAUTHORS:20180523-151803691", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180523-151803691", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2017.11.2279", "resource_type": "article", "pub_year": "2018", "author_list": "Wang, Connie; Chang, Paul; et el." }, { "id": "https://authors.library.caltech.edu/records/36aza-saz71", "eprint_id": 71018, "eprint_status": "archive", "datestamp": "2023-08-19 01:34:21", "lastmod": "2023-10-23 15:16:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cahn-Jackson-K-B", "name": { "family": "Cahn", "given": "Jackson K. B." }, "orcid": "0000-0001-8849-4516" }, { "id": "Werlang-Caroline-A", "name": { "family": "Werlang", "given": "Caroline A." }, "orcid": "0000-0001-7554-8431" }, { "id": "Baumschlager-Armin", "name": { "family": "Baumschlager", "given": "Armin" }, "orcid": "0000-0002-2546-9038" }, { "id": "Brinkmann-Chen-Sabine", "name": { "family": "Brinkmann-Chen", "given": "Sabine" }, "orcid": "0000-0002-5419-4192" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" } ] }, "title": "A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases", "ispublished": "pub", "full_text_status": "public", "keywords": "cofactor specificity, oxidoreductases, protein engineering, library design, semirational engineering", "note": "\u00a9 2017 American Chemical Society. \n\nReceived: July 7, 2016; Published: September 20, 2016. \n\nThis work was supported by the Gordon and Betty Moore Foundation through Grant No. GBMF2809 to the Caltech Programmable Molecular Technology Initiative and by American Recovery and Reinvestment Act (ARRA) funds through the National Institutes of Health Shared Instrumentation Grant Program, Grant No. S10RR027203, to F.H.A. J.K.B.C. acknowledges the support of the Resnick Sustainability Institute (Caltech). The authors thank Ruchi Jahagirdar and Lisa Mears for experimental assistance and Tilman Flock for providing the list of nonredundant PDBs used for CSR-SALAD testing and validation. They also thank numerous former and current members of the Arnold and Mayo laboratories for invaluable suggestions and discussions. \n\nAccession Codes: PDB: 4XDY, PDB: 4TSK, PDB: 3DOJ, PDB: 1PIW, PDB: 1K8C, PDB: 1VHD, PDB: 3PEF \n\nAuthor Contributions: This project was conceived by J.K.B.C., S.B-C., S.L.M., and F.H.A. J.K.B.C. designed and programmed CSR-SALAD, which was implemented online by C.A.W. J.K.B.C. performed the validation experiments with assistance from A.B., and produced the figures and tables. J.K.B.C., S.B-C., and F.H.A. wrote the manuscript with input from all authors. \n\nThe authors declare no competing financial interest.\n\nAccepted Version - nihms-1754172.pdf
Supplemental Material - sb6b00188_si_001.pdf
", "abstract": "The ability to control enzymatic nicotinamide cofactor utilization is critical for engineering efficient metabolic pathways. However, the complex interactions that determine cofactor-binding preference render this engineering particularly challenging. Physics-based models have been insufficiently accurate and blind directed evolution methods too inefficient to be widely adopted. Building on a comprehensive survey of previous studies and our own prior engineering successes, we present a structure-guided, semirational strategy for reversing enzymatic nicotinamide cofactor specificity. This heuristic-based approach leverages the diversity and sensitivity of catalytically productive cofactor binding geometries to limit the problem to an experimentally tractable scale. We demonstrate the efficacy of this strategy by inverting the cofactor specificity of four structurally diverse NADP-dependent enzymes: glyoxylate reductase, cinnamyl alcohol dehydrogenase, xylose reductase, and iron-containing alcohol dehydrogenase. The analytical components of this approach have been fully automated and are available in the form of an easy-to-use web tool: Cofactor Specificity Reversal\u2013Structural Analysis and Library Design (CSR-SALAD).", "date": "2017-02-17", "date_type": "published", "publication": "ACS Synthetic Biology", "volume": "6", "number": "2", "publisher": "American Chemical Society", "pagerange": "326-333", "id_number": "CaltechAUTHORS:20161012-112258970", "issn": "2161-5063", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161012-112258970", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "NIH", "grant_number": "S10RR027203" }, { "agency": "Resnick Sustainability Institute" } ] }, "collection": "CaltechAUTHORS", "local_group": { "items": [ { "id": "Resnick-Sustainability-Institute", "value": "Resnick Sustainability Institute" } ] }, "doi": "10.1021/acssynbio.6b00188", "pmcid": "PMC8611728", "primary_object": { "basename": "nihms-1754172.pdf", "url": "https://authors.library.caltech.edu/records/36aza-saz71/files/nihms-1754172.pdf" }, "related_objects": [ { "basename": "sb6b00188_si_001.pdf", "url": "https://authors.library.caltech.edu/records/36aza-saz71/files/sb6b00188_si_001.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Cahn, Jackson K. B.; Werlang, Caroline A.; et el." }, { "id": "https://authors.library.caltech.edu/records/rs15w-xt215", "eprint_id": 55478, "eprint_status": "archive", "datestamp": "2023-08-20 11:17:27", "lastmod": "2023-10-23 15:25:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "de-los-Santos-E-L-C", "name": { "family": "de los Santos", "given": "Emmanuel L. C." } }, { "id": "Meyerowitz-J-T", "name": { "family": "Meyerowitz", "given": "Joseph T." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Murray-R-M", "name": { "family": "Murray", "given": "Richard M." }, "orcid": "0000-0002-5785-7481" } ] }, "title": "Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor", "ispublished": "pub", "full_text_status": "public", "keywords": "synthetic biology, cell-free systems, in vitro biological circuit prototyping, computational protein design, protein engineering, TX-TL", "note": "\u00a9 2015 American Chemical Society.\n\nReceived: May 6, 2015; Publication Date (Web): August 19, 2015.\n\nThe authors thank Jongmin Kim and Jackson Cahn for reading the manuscript. This research was conducted with support from the Institute for Collaborative Biotechnologies through Grant W911NF-09-0001 from the U.S. Army Research Office. Additional support was granted in part by the Benjamin M. Rosen Bioengineering Center, the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative, and DARPA through the Living Foundries Program. \n\nThe authors declare no competing financial interest.\n\nSubmitted - 015438.full.pdf
Supplemental Material - sb5b00090_si_001.pdf
Supplemental Material - sb5b00090_si_002.zip
", "abstract": "The pursuit of circuits and metabolic pathways of increasing complexity and robustness in synthetic biology will require engineering new regulatory tools. Feedback control based on relevant molecules, including toxic intermediates and environmental signals, would enable genetic circuits to react appropriately to changing conditions. In this work, variants of qacR, a tetR family repressor, were generated by computational protein design and screened in a cell-free transcription\u2013translation (TX-TL) system for responsiveness to a new targeted effector. The modified repressors target vanillin, a growth-inhibiting small molecule found in lignocellulosic hydrolysates and other industrial processes. Promising candidates from the in vitro screen were further characterized in vitro and in vivo in a gene circuit. The screen yielded two qacR mutants that respond to vanillin both in vitro and in vivo. While the mutants exhibit some toxicity to cells, presumably due to off-target effects, they are prime starting points for directed evolution toward vanillin sensors with the specifications required for use in a dynamic control loop. We believe this process, a combination of the generation of variants coupled with in vitro screening, can serve as a framework for designing new sensors for other target compounds.", "date": "2016-04-15", "date_type": "published", "publication": "ACS Synthetic Biology", "volume": "5", "number": "4", "publisher": "American Chemical Society", "pagerange": "287-295", "id_number": "CaltechAUTHORS:20150303-123633257", "issn": "2161-5063", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150303-123633257", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-09-0001" }, { "agency": "Benjamin M. Rosen Bioengineering Center" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "doi": "10.1021/acssynbio.5b00090", "primary_object": { "basename": "015438.full.pdf", "url": "https://authors.library.caltech.edu/records/rs15w-xt215/files/015438.full.pdf" }, "related_objects": [ { "basename": "sb5b00090_si_001.pdf", "url": "https://authors.library.caltech.edu/records/rs15w-xt215/files/sb5b00090_si_001.pdf" }, { "basename": "sb5b00090_si_002.zip", "url": "https://authors.library.caltech.edu/records/rs15w-xt215/files/sb5b00090_si_002.zip" } ], "resource_type": "article", "pub_year": "2016", "author_list": "de los Santos, Emmanuel L. C.; Meyerowitz, Joseph T.; et el." }, { "id": "https://authors.library.caltech.edu/records/f2zmb-qya96", "eprint_id": 60411, "eprint_status": "archive", "datestamp": "2023-08-22 17:17:08", "lastmod": "2023-10-24 16:31:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Jian", "name": { "family": "Li", "given": "Jian" }, "orcid": "0000-0003-0297-6528" }, { "id": "Lawton-T-J", "name": { "family": "Lawton", "given": "Thomas J." } }, { "id": "Kostecki-J-S", "name": { "family": "Kostecki", "given": "Jan S." } }, { "id": "Nisthal-A", "name": { "family": "Nisthal", "given": "Alex" } }, { "id": "Fang-Jia", "name": { "family": "Fang", "given": "Jia" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Rosenzweig-A-C", "name": { "family": "Rosenzweig", "given": "Amy C." } }, { "id": "Jewett-M-C", "name": { "family": "Jewett", "given": "Michael C." } } ] }, "title": "Cell-free protein synthesis enables high yielding synthesis of an active multicopper oxidase", "ispublished": "pub", "full_text_status": "public", "keywords": "Cell-free protein synthesis; Metalloprotein; Multicopper oxidase; Transcription and translation", "note": "\u00a9 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. \n\nReceived 22 April 2015; Revised 26 June 2015; Accepted 31 July 2015; Accepted: article online 03 August 2015. \n\nThis work was supported by the Advanced Research Projects Agency-Energy (ARPA-E) REMOTE program (DE-AR0000435). \n\nThe authors declare no financial or commercial conflict of interest.\n\nIn Press - Li_2015.pdf
", "abstract": "Multicopper oxidases (MCOs) are broadly distributed in all kingdoms of life and perform a variety of important oxidative reactions. These enzymes have potential biotechnological applications; however, the applications are impeded by low expression yields in traditional recombinant hosts, solubility issues, and poor copper cofactor assembly. As an alternative to traditional recombinant protein expression, we show the ability to use cell-free protein synthesis (CFPS) to produce complex MCO proteins with high soluble titers. Specifically, we report the production of MCOs in an Escherichia coli-based cell-free transcription-translation system. Total yields as high as 1.2 mg mL-1 were observed after a 20-h batch reaction. More than 95% of the protein was soluble and activity was obtained by simple post-CFPS addition of copper ions in the form of CuSO4. Scale-up reactions were achieved from 15 to 100 \u03bcL without a decrease in productivity and solubility. CFPS titers were higher than in vivo expression titers and more soluble, avoiding the formation of inclusion bodies. Our work extends the utility of the cell-free platform to the production of active proteins containing copper cofactors and demonstrates a simple method for producing MCOs.", "date": "2016-02", "date_type": "published", "publication": "Biotechnology Journal", "volume": "11", "number": "2", "publisher": "Wiley", "pagerange": "212-218", "id_number": "CaltechAUTHORS:20150922-111505818", "issn": "1860-7314", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150922-111505818", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Advanced Research Projects Agency-Energy (ARPA-E)", "grant_number": "DE-AR0000435" } ] }, "doi": "10.1002/biot.201500030", "primary_object": { "basename": "Li_2015.pdf", "url": "https://authors.library.caltech.edu/records/f2zmb-qya96/files/Li_2015.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Li, Jian; Lawton, Thomas J.; et el." }, { "id": "https://authors.library.caltech.edu/records/xzma1-83664", "eprint_id": 57891, "eprint_status": "archive", "datestamp": "2023-08-20 08:10:00", "lastmod": "2023-10-23 15:24:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mou-Yun", "name": { "family": "Mou", "given": "Yun" } }, { "id": "Yu-Jiun-Yann", "name": { "family": "Yu", "given": "Jiun-Yann" } }, { "id": "Wannier-T-M", "name": { "family": "Wannier", "given": "Timothy M." } }, { "id": "Guo-Chin-Lin", "name": { "family": "Guo", "given": "Chin-Lin" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computational design of co-assembling protein\u2013DNA nanowires", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Macmillan Publishers Limited. \n\nReceived 15 March 2015. Accepted 30 June 2015. Published online 2 September 2015. \n\nThis study was supported by the Defense Advanced Research Projects Agency Protein Design Processes Program, a National Security Science and Engineering Faculty Fellowship (NSSEFF N00244-09-1-0011, N00244-09-1-0082), and the Gordon and Betty Moore Foundation through grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative. We would like to acknowledge the Gordon and Betty Moore Foundation for support of the Molecular Observatory at Caltech, and the Department of Energy and National Institutes of Health for supporting the Stanford Synchrotron Radiation Lightsource. We thank J. Kaiser, J. Hoy and P. Nikolovski at the Caltech Molecular Observatory for assistance in crystal screening and crystallographic data collection. Y.M. thanks L.-C. Ho for her encouragement and literature research in the crystallographic work. Y.M. thanks T. J. Zwang for assistance with AFM measurements. Y.M. thanks X. Zhang and S. Yan for the useful discussion. We are grateful to J. Kostecki and M. Ary for assistance with the manuscript. \n\nContributions: Y.M. designed and performed the experiments. Y.M. and J.-Y.Y. performed the optical microscope experiments. All authors wrote the manuscript. \n\nThe authors declare no competing financial interests.\n\nSupplemental Material - nature14874-s1.pdf
Supplemental Material - nature14874-sf1.jpg
Supplemental Material - nature14874-sf2.jpg
Supplemental Material - nature14874-sf3.jpg
Supplemental Material - nature14874-sf4.jpg
Supplemental Material - nature14874-sf5.jpg
Supplemental Material - nature14874-sf6.jpg
Supplemental Material - nature14874-sf7.jpg
Supplemental Material - nature14874-st1.jpg
Supplemental Material - nature14874-st2.jpg
", "abstract": "Biomolecular self-assemblies are of great interest to nanotechnologists because of their functional versatility and their biocompatibility. Over the past decade, sophisticated single-component nanostructures composed exclusively of nucleic acids, peptides and proteins have been reported, and these nanostructures have been used in a wide range of applications, from drug delivery to molecular computing. Despite these successes, the development of hybrid co-assemblies of nucleic acids and proteins has remained elusive. Here we use computational protein design to create a protein\u2013DNA co-assembling nanomaterial whose assembly is driven via non-covalent interactions. To achieve this, a homodimerization interface is engineered onto the Drosophila Engrailed homeodomain (ENH), allowing the dimerized protein complex to bind to two double-stranded DNA (dsDNA) molecules. By varying the arrangement of protein-binding sites on the dsDNA, an irregular bulk nanoparticle or a nanowire with single-molecule width can be spontaneously formed by mixing the protein and dsDNA building blocks. We characterize the protein\u2013DNA nanowire using fluorescence microscopy, atomic force microscopy and X-ray crystallography, confirming that the nanowire is formed via the proposed mechanism. This work lays the foundation for the development of new classes of protein\u2013DNA hybrid materials. Further applications can be explored by incorporating DNA origami, DNA aptamers and/or peptide epitopes into the protein\u2013DNA framework presented here.", "date": "2015-09-10", "date_type": "published", "publication": "Nature", "volume": "525", "number": "7568", "publisher": "Nature Publishing Group", "pagerange": "230-233", "id_number": "CaltechAUTHORS:20150528-195712684", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150528-195712684", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "National Security Science and Engineering Faculty Fellowship (NSSEFF)", "grant_number": "N00244-09-1-0011" }, { "agency": "National Security Science and Engineering Faculty Fellowship (NSSEFF)", "grant_number": "N00244-09-1-0082" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH" } ] }, "doi": "10.1038/nature14874", "primary_object": { "basename": "nature14874-s1.pdf", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-s1.pdf" }, "related_objects": [ { "basename": "nature14874-sf3.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-sf3.jpg" }, { "basename": "nature14874-sf5.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-sf5.jpg" }, { "basename": "nature14874-sf6.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-sf6.jpg" }, { "basename": "nature14874-sf7.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-sf7.jpg" }, { "basename": "nature14874-st1.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-st1.jpg" }, { "basename": "nature14874-st2.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-st2.jpg" }, { "basename": "nature14874-sf1.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-sf1.jpg" }, { "basename": "nature14874-sf2.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-sf2.jpg" }, { "basename": "nature14874-sf4.jpg", "url": "https://authors.library.caltech.edu/records/xzma1-83664/files/nature14874-sf4.jpg" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Mou, Yun; Yu, Jiun-Yann; et el." }, { "id": "https://authors.library.caltech.edu/records/re8pz-j2s72", "eprint_id": 59769, "eprint_status": "archive", "datestamp": "2023-08-22 16:12:02", "lastmod": "2023-10-23 22:41:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mou-Yun", "name": { "family": "Mou", "given": "Yun" } }, { "id": "Huang-Po-Ssu", "name": { "family": "Huang", "given": "Po-Ssu" } }, { "id": "Hsu-Fang-Ciao", "name": { "family": "Hsu", "given": "Fang-Ciao" } }, { "id": "Huang-Shing-Jong", "name": { "family": "Huang", "given": "Shing-Jong" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computational design and experimental verification of a symmetric protein homodimer", "ispublished": "pub", "full_text_status": "public", "keywords": "computational protein design; homodimer; docking; nuclear magnetic resonance", "note": "\u00a9 2015 National Academy of Sciences. Freely available online through the PNAS open access option. \n\nContributed by Stephen L. Mayo, May 18, 2015 (sent for review December 1, 2014). Published ahead of print August 12, 2015.\n\nWe thank Justin Chartron for useful discussion about solution NMR structural determination and Marie Ary for assistance with the manuscript. NMR measurements were carried out at Instrumentation Center of National Taiwan University, Taiwan (NSC 102-2731-M-002-002-MY2). This work was supported by the Defense Advanced Research Projects Agency Protein Design Processes Program, a National Security Science and Engineering Faculty Fellowship (NSSEFF N00244-09-1-0011, N00244-09-1-0082), and the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative. \n\nAuthor contributions: Y.M., P.-S.H., and S.L.M. designed research; Y.M., P.-S.H., F.-C.H., and S.-J.H. performed research; Y.M., P.-S.H., F.-C.H., S.-J.H., and S.L.M. analyzed data; and Y.M., P.-S.H., S.-J.H., and S.L.M. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nData deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2MG4 and 4NDL).\n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1505072112/-/DCSupplemental.\n\nPublished - PNAS-2015-Mou-10714-9.pdf
Supplemental Material - pnas.201505072SI.pdf
", "abstract": "Homodimers are the most common type of protein assembly in nature and have distinct features compared with heterodimers and higher order oligomers. Understanding homodimer interactions at the atomic level is critical both for elucidating their biological mechanisms of action and for accurate modeling of complexes of unknown structure. Computation-based design of novel protein\u2013protein interfaces can serve as a bottom-up method to further our understanding of protein interactions. Previous studies have demonstrated that the de novo design of homodimers can be achieved to atomic-level accuracy by \u03b2-strand assembly or through metal-mediated interactions. Here, we report the design and experimental characterization of a \u03b1-helix\u2013mediated homodimer with C2 symmetry based on a monomeric Drosophila engrailed homeodomain scaffold. A solution NMR structure shows that the homodimer exhibits parallel helical packing similar to the design model. Because the mutations leading to dimer formation resulted in poor thermostability of the system, design success was facilitated by the introduction of independent thermostabilizing mutations into the scaffold. This two-step design approach, function and stabilization, is likely to be generally applicable, especially if the desired scaffold is of low thermostability.", "date": "2015-08-25", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences", "volume": "112", "number": "34", "publisher": "National Academy of Sciences", "pagerange": "10714-10719", "id_number": "CaltechAUTHORS:20150819-123344330", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150819-123344330", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Taiwan University", "grant_number": "NSC 102-2731-M-002-002-MY2" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "National Security Science and Engineering Faculty Fellowship (NSSEFF)", "grant_number": "N00244-09-1-0011" }, { "agency": "National Security Science and Engineering Faculty Fellowship (NSSEFF)", "grant_number": "N00244-09-1-0082" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" } ] }, "doi": "10.1073/pnas.1505072112", "pmcid": "PMC4553821", "primary_object": { "basename": "PNAS-2015-Mou-10714-9.pdf", "url": "https://authors.library.caltech.edu/records/re8pz-j2s72/files/PNAS-2015-Mou-10714-9.pdf" }, "related_objects": [ { "basename": "pnas.201505072SI.pdf", "url": "https://authors.library.caltech.edu/records/re8pz-j2s72/files/pnas.201505072SI.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Mou, Yun; Huang, Po-Ssu; et el." }, { "id": "https://authors.library.caltech.edu/records/7psmm-38h44", "eprint_id": 58621, "eprint_status": "archive", "datestamp": "2023-08-22 16:10:51", "lastmod": "2023-10-23 19:32:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mou-Yun", "name": { "family": "Mou", "given": "Yun" } }, { "id": "Huang-Po-Ssu", "name": { "family": "Huang", "given": "Po-Ssu" } }, { "id": "Thomas-L-M", "name": { "family": "Thomas", "given": "Leonard M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Using molecular dynamics simulations as an aid in the prediction of domain swapping of computationally designed protein variants", "ispublished": "pub", "full_text_status": "restricted", "keywords": "molecular dynamics; computational protein design; in silico screening; homodimer; domain-swapped dimer", "note": "\u00a9 2015 Elsevier Ltd. \n\nReceived 11 March 2015, Revised 11 June 2015, Accepted 16 June 2015, Available online 21 June 2015. \n\nThe authors are grateful for the use of beamline 12-2 at the Stanford Synchrotron Radiation Lightsource (SSRL) in Menlo Park, CA, operated by Stanford University and supported by the Department of Energy and the National Institutes of Health. We also thank Jens Kaiser and Pavle Nikolovski at the California Institute of Technology for their advice on crystallography. We thank the Gordon and Betty Moore Foundation for support of the Molecular Observatory at the California Institute of Technology. This work was supported by the Defense Advanced Research Projects Agency Protein Design Processes Program, a National Security Science and Engineering Faculty Fellowship (NSSEFF N00244-09-1-0011, N00244-09-1-0082) and the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative. We are grateful to Marie Ary for assistance with the manuscript.", "abstract": "In standard implementations of computational protein design, a positive-design approach is used to predict sequences that will be stable on a given backbone structure. Possible competing states are typically not considered, primarily because appropriate structural models are not available. One potential competing state, the domain-swapped dimer, is especially compelling because it is often nearly identical to its monomeric counterpart, differing by just a few mutations in a hinge region. Molecular dynamics (MD) simulations provide a computational method to sample different conformational states of a structure. Here, we tested whether MD simulations could be used as a post-design screening tool to identify sequence mutations leading to domain-swapped dimers. We hypothesized that a successful computationally-designed sequence would have backbone structure and dynamics characteristics similar to that of the input structure, and that in contrast, domain-swapped dimers would exhibit increased backbone flexibility and/or altered structure in the hinge-loop region to accommodate the large conformational change required for domain swapping. While attempting to engineer a homodimer from a 51 amino acid fragment of the monomeric protein engrailed homeodomain (ENH), we had instead generated a domain-swapped dimer (ENH_DsD). MD simulations on these proteins showed increased MD simulation derived B factors in the hinge loop of the ENH_DsD domain-swapped dimer relative to monomeric ENH. Two point mutants of ENH_DsD designed to recover the monomeric fold were then tested with an MD simulation protocol. The MD simulations suggested that one of these mutants would adopt the target monomeric structure, which was subsequently confirmed by X-ray crystallography.", "date": "2015-08-14", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "427", "number": "16", "publisher": "Elsevier", "pagerange": "2697-2706", "id_number": "CaltechAUTHORS:20150625-151326038", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150625-151326038", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)" }, { "agency": "NIH" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "National Security Science and Engineering Faculty Fellowship (NSSEFF)", "grant_number": "N00244-09-1-0011" }, { "agency": "National Security Science and Engineering Faculty Fellowship (NSSEFF)", "grant_number": "N00244-09-1-0082" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" } ] }, "doi": "10.1016/j.jmb.2015.06.006", "resource_type": "article", "pub_year": "2015", "author_list": "Mou, Yun; Huang, Po-Ssu; et el." }, { "id": "https://authors.library.caltech.edu/records/955a2-jzj23", "eprint_id": 58449, "eprint_status": "archive", "datestamp": "2023-08-20 06:54:19", "lastmod": "2023-10-23 19:21:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wannier-T-M", "name": { "family": "Wannier", "given": "Timothy M." } }, { "id": "Moore-M-M", "name": { "family": "Moore", "given": "Matthew M." } }, { "id": "Mou-Yun", "name": { "family": "Mou", "given": "Yun" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computational Design of the \u03b2-Sheet Surface of a Red Fluorescent Protein Allows Control of Protein Oligomerization", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Wannier 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 25, 2015; Accepted: May 21, 2015; Published: June 15, 2015. \n\nThis work was supported by the Defense Advanced Research Projects Agency Protein Design Processes Program, a National Security Science and Engineering Faculty Fellowship (NSSEFF N00244-09-1-0011, N00244-09-1-0082), the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative and a National Institute of Health grant (1R21EB018579-01). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nWe would like to acknowledge the help of Melissa Lin and Shweta Bhatia for constructing some of the variants used in this study, and Alex Nisthal and Jan Kostecki for helpful discussions. \n\nAuthor Contributions: Conceived and designed the experiments: TW MM SM. Performed the experiments: TW. Analyzed the data: TW YM MM SM. Wrote the paper: TW YM MM SM. \n\nData Availability: All relevant data are within the paper and its Supporting Information files. \n\nCompeting interests: The authors have declared that no competing interests exist.\n\nPublished - journal.pone.0130582.pdf
Supplemental Material - journal.pone.0130582.s001.TIFF
Supplemental Material - journal.pone.0130582.s002.TIFF
Supplemental Material - journal.pone.0130582.s003.TIFF
Supplemental Material - journal.pone.0130582.s004.TIFF
", "abstract": "Computational design has been used with mixed success for the design of protein surfaces, with directed evolution heretofore providing better practical solutions than explicit design. Directed evolution, however, requires a tractable high-throughput screen because the random nature of mutation does not enrich for desired traits. Here we demonstrate the successful design of the \u03b2-sheet surface of a red fluorescent protein (RFP), enabling control over its oligomerization. To isolate the problem of surface design, we created a hybrid RFP from DsRed and mCherry with a stabilized protein core that allows for monomerization without loss of fluorescence. We designed an explicit library for which 93 of 96 (97%) of the protein variants are soluble, stably fluorescent, and monomeric. RFPs are heavily used in biology, but are natively tetrameric, and creating RFP monomers has proven extremely difficult. We show that surface design and core engineering are separate problems in RFP development and that the next generation of RFP markers will depend on improved methods for core design.", "date": "2015-06-15", "date_type": "published", "publication": "PLoS ONE", "volume": "10", "number": "6", "publisher": "Public Library of Science", "pagerange": "Art. No. e0130582", "id_number": "CaltechAUTHORS:20150623-115009160", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150623-115009160", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "National Security Science and Engineering Faculty Fellowship (NSSEFF)", "grant_number": "N00244-09-1-0011" }, { "agency": "National Security Science and Engineering Faculty Fellowship (NSSEFF)", "grant_number": "N00244-09-1-0082" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "NIH", "grant_number": "1R21EB018579-01" } ] }, "doi": "10.1371/journal.pone.0130582", "pmcid": "PMC4468108", "primary_object": { "basename": "journal.pone.0130582.pdf", "url": "https://authors.library.caltech.edu/records/955a2-jzj23/files/journal.pone.0130582.pdf" }, "related_objects": [ { "basename": "journal.pone.0130582.s001.TIFF", "url": "https://authors.library.caltech.edu/records/955a2-jzj23/files/journal.pone.0130582.s001.TIFF" }, { "basename": "journal.pone.0130582.s002.TIFF", "url": "https://authors.library.caltech.edu/records/955a2-jzj23/files/journal.pone.0130582.s002.TIFF" }, { "basename": "journal.pone.0130582.s003.TIFF", "url": "https://authors.library.caltech.edu/records/955a2-jzj23/files/journal.pone.0130582.s003.TIFF" }, { "basename": "journal.pone.0130582.s004.TIFF", "url": "https://authors.library.caltech.edu/records/955a2-jzj23/files/journal.pone.0130582.s004.TIFF" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Wannier, Timothy M.; Moore, Matthew M.; et el." }, { "id": "https://authors.library.caltech.edu/records/eqrr4-9ye39", "eprint_id": 46177, "eprint_status": "archive", "datestamp": "2023-08-20 02:03:23", "lastmod": "2023-10-26 19:33:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wannier-T-M", "name": { "family": "Wannier", "given": "Timothy M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "The structure of a far-red fluorescent protein, AQ143, shows evidence in support of reported red-shifting chromophore interactions", "ispublished": "pub", "full_text_status": "public", "keywords": "Red Fluorescent Protein (RFP), Near-Infrared, Bathochromic Shift, Fluorescent Protein, Chromoprotein", "note": "\u00a9 2014 The Protein Society.\n\nReceived: Apr 04, 2014; Revised: May 28, 2014; Accepted: May 29, 2014.\nPublished online 3 June 2014 proteinscience.org\nThe authors are grateful for the use of beamline 12-2 at the Stanford Synchrotron\nRadiation Lightsource (SSRL) in Menlo Park, CA, operated by Stanford University and\nsupported by the Department of Energy and the National Institutes of Health. They\nadditionally are thankful to Jens Kaiser and Pavle Nikolovski at the California Institute of\nTechnology for helpful discussions. Finally they thank the Gordon and Betty Moore\nFoundation, the Beckman Institute, and the Sanofi-Aventis Bioengineering Research\nProgram for support of the Molecular Observatory at the California Institute of\nTechnology.\n\nAccepted Version - Wannier_2014.pdf
", "abstract": "Engineering fluorescent proteins (FPs) to emit light at longer wavelengths is a significant focus in the development of the next generation of fluorescent biomarkers, as far-red light penetrates tissue with minimal absorption, allowing better imaging inside of biological hosts. Structure-guided design and directed evolution have led to the discovery of red FPs with significant bathochromic shifts to their emission. Here, we present the crystal structure of one of the most bathochromically shifted FPs reported to date, AQ143, a nine-point mutant of aeCP597, a chromoprotein from Actinia equina. The 2.19 \u00c5 resolution structure reveals several important chromophore interactions that contribute to the protein's far-red emission and shows dual occupancy of the green and red chromophores.", "date": "2014-08", "date_type": "published", "publication": "Protein Science", "volume": "23", "number": "8", "publisher": "Wiley", "pagerange": "1148-1153", "id_number": "CaltechAUTHORS:20140610-104728713", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140610-104728713", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)" }, { "agency": "NIH" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Sanofi-Aventis Bioengineering Research Program" } ] }, "doi": "10.1002/pro.2498", "pmcid": "PMC4116662", "primary_object": { "basename": "Wannier_2014.pdf", "url": "https://authors.library.caltech.edu/records/eqrr4-9ye39/files/Wannier_2014.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Wannier, Timothy M. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/rhrbf-xk328", "eprint_id": 43121, "eprint_status": "archive", "datestamp": "2023-08-22 10:55:40", "lastmod": "2023-10-25 23:17:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Blomberg-R", "name": { "family": "Blomberg", "given": "Rebecca" } }, { "id": "Kries-H", "name": { "family": "Kries", "given": "Hajo" } }, { "id": "Pinkas-D-M", "name": { "family": "Pinkas", "given": "Daniel M." } }, { "id": "Mittl-P-R-E", "name": { "family": "Mittl", "given": "Peer R. E." } }, { "id": "Gr\u00fctter-M-G", "name": { "family": "Gr\u00fctter", "given": "Markus G." } }, { "id": "Privett-H-K", "name": { "family": "Privett", "given": "Heidi K." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Hilvert-D", "name": { "family": "Hilvert", "given": "Donald" } } ] }, "title": "Precision is essential for efficient catalysis in an\n evolved Kemp eliminase", "ispublished": "pub", "full_text_status": "public", "keywords": "X-ray crystallography; Protein design; Enzyme mechanisms", "note": "\u00a9 2013 Macmillan Publishers Limited.\n\nReceived 7 June; accepted 30 August 2013; Published online 16 October 2013.\n\nThe authors are grateful to A. Aires-Trapote and C. Mayer for experimental assistance. We also thank C. Stutz and B. Blattmann for help in protein crystallization, and the beamline staff at the Swiss Light Source for support during data collection. This work was supported by the Swiss National Science Foundation (SNSF), the National Center of Excellence in Research (NCCR) Structural Biology program of\nthe SNSF, the ETH Zurich, and the Defense Advanced Research Projects Agency (DARPA). Fellowships from the Fonds des Verbandes der chemischen Industrie (to R.B.), the Stipendienfonds der Schweizer Chemischen Industrie (to H.K.), the Studienstiftung des deutschen Volkes (to R.B. and H.K.), and the National Security Science and Engineering Faculty Fellowship (to S.L.M.) are gratefully acknowledged.\n\n\nAuthor Contributions:\nD.H., M.G.G., S.L.M., H.K.P., P.R.E.M., D.M.P., H.K. and R.B. designed the experiments. R.B. and H.K. evolved and biochemically characterized the variants; D.M.P. and P.R.E.M. crystallized the proteins and solved their structures. The manuscript and figures were prepared by R.B., H.K., D.M.P. and D.H. \n\nThe crystal structure of HG3.17 was deposited in the RCSB Protein Data Bank (PDB) under the accession number 4BS0.\n\nSupplemental Material - nature12623-s1.pdf
Supplemental Material - nature12623-s2.xlsx
", "abstract": "Linus Pauling established the conceptual framework for understanding and mimicking enzymes more than six decades ago. The notion that enzymes selectively stabilize the rate-limiting transition state of the catalysed reaction relative to the bound ground state reduces the problem of design to one of molecular recognition. Nevertheless, past attempts to capitalize on this idea, for example by using transition state analogues to elicit antibodies with catalytic activities, have generally failed to deliver true enzymatic rates. The advent of computational design approaches, combined with directed evolution, has provided an opportunity to revisit this problem. Starting from a computationally designed catalyst for the Kemp elimination\u2014a well-studied model system for proton transfer from carbon\u2014we show that an artificial enzyme can be evolved that accelerates an elementary chemical reaction 6\u2009\u00d7\u200910^8-fold, approaching the exceptional efficiency of highly optimized natural enzymes such as triosephosphate isomerase. A 1.09\u2009\u00c5 resolution crystal structure of the evolved enzyme indicates that familiar catalytic strategies such as shape complementarity and precisely placed catalytic groups can be successfully harnessed to afford such high rate accelerations, making us optimistic about the prospects of designing more sophisticated catalysts.", "date": "2013-11-21", "date_type": "published", "publication": "Nature", "volume": "503", "number": "7476", "publisher": "Nature Publishing Group", "pagerange": "418-421", "id_number": "CaltechAUTHORS:20131220-135748515", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131220-135748515", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Swiss National Science Foundation (SNSF)" }, { "agency": "ETH Zurich" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Fonds des Verbandes der chemischen Industrie" }, { "agency": "Stipendienfonds der Schweizer Chemischen Industrie" }, { "agency": "Studienstiftung des deutschen Volkes" }, { "agency": "National Security Science and Engineering Faculty Fellowship" } ] }, "doi": "10.1038/nature12623", "primary_object": { "basename": "nature12623-s1.pdf", "url": "https://authors.library.caltech.edu/records/rhrbf-xk328/files/nature12623-s1.pdf" }, "related_objects": [ { "basename": "nature12623-s2.xlsx", "url": "https://authors.library.caltech.edu/records/rhrbf-xk328/files/nature12623-s2.xlsx" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Blomberg, Rebecca; Kries, Hajo; et el." }, { "id": "https://authors.library.caltech.edu/records/fg5n4-8zh83", "eprint_id": 39030, "eprint_status": "archive", "datestamp": "2023-08-22 09:20:48", "lastmod": "2023-10-24 14:59:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jaru-Ampornpan-P", "name": { "family": "Jaru-Ampornpan", "given": "Peera" } }, { "id": "Liang-Fu-Cheng", "name": { "family": "Liang", "given": "Fu-Cheng" } }, { "id": "Nisthal-A", "name": { "family": "Nisthal", "given": "Alex" } }, { "id": "Nguyen-Thang-X", "name": { "family": "Nguyen", "given": "Thang X." } }, { "id": "Wang-Pengcheng", "name": { "family": "Wang", "given": "Pengcheng" } }, { "id": "Shen-Kuang", "name": { "family": "Shen", "given": "Kuang" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Steven L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Shan-S-O", "name": { "family": "Shan", "given": "Shu-ou" }, "orcid": "0000-0002-6526-1733" } ] }, "title": "Mechanism of an ATP-independent Protein Disaggregase. II. Distinct Molecular Interactions Drive Multiple Steps During Aggregate Disassembly", "ispublished": "pub", "full_text_status": "public", "keywords": "Enzyme Mechanisms; Kinetics; Molecular Chaperone; Mutagenesis Mechanisms; Protein Aggregation; ATP-independent Disaggregase; Membrane Proteins; Protein Biogenesis; Signal Recognition Particle.", "note": "\u00a9 2013 by The American Society for Biochemistry and Molecular Biology, Inc. \n\nReceived February 18, 2013; Revision received March 12, 2013. \n\nSupported by the Department of Defense, National Security Science and Engineering Faculty Fellowship. \n\nSupported by the David and Lucile Packard Fellowship in science and engineering, the Henry Dreyfus Teacher-Scholar Award, and the Breakthroughs in Gerontology award from the American Federation for Aging Research.\n\nWe thank Drs. W. M. Clemons, J. Chartron, and C. Suloway for the plasmids of SERP1, Sec61b_s, and cytochrome b5 and the Shan laboratory for helpful comments on the manuscript.\n\nPublished - J._Biol._Chem.-2013-Jaru-Ampornpan-13431-45.pdf
", "abstract": "The ability of molecular chaperones to overcome the misfolding and aggregation of proteins is essential for the maintenance of proper protein homeostasis in all cells. Thus far, the best studied disaggregase systems are the Clp/Hsp100 family of \"ATPases associated with various cellular activities\" (AAA^+) ATPases, which use mechanical forces powered by ATP hydrolysis to remodel protein aggregates. An alternative system to disassemble large protein aggregates is provided by the 38-kDa subunit of the chloroplast signal recognition particle (cpSRP43), which uses binding energy with its substrate proteins to drive disaggregation. The mechanism of this novel chaperone remains unclear. Here, molecular genetics and structure-activity analyses show that the action of cpSRP43 can be dissected into two steps with distinct molecular requirements: (i) initial recognition, during which cpSRP43 binds specifically to a recognition motif displayed on the surface of the aggregate; and (ii) aggregate remodeling, during which highly adaptable binding interactions of cpSRP43 with hydrophobic transmembrane domains of the substrate protein compete with the packing interactions within the aggregate. This establishes a useful framework to understand the molecular mechanism by which binding interactions from a molecular chaperone can be used to overcome protein aggregates in the absence of external energy input from ATP.", "date": "2013-05-10", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "288", "number": "19", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "13431-13445", "id_number": "CaltechAUTHORS:20130621-133910862", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130621-133910862", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Security Science and Engineering Faculty Fellowship" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Camille and Henry Dreyfus Foundation" }, { "agency": "American Federation for Aging Research" } ] }, "doi": "10.1074/jbc.M113.462861", "pmcid": "PMC3650381", "primary_object": { "basename": "J._Biol._Chem.-2013-Jaru-Ampornpan-13431-45.pdf", "url": "https://authors.library.caltech.edu/records/fg5n4-8zh83/files/J._Biol._Chem.-2013-Jaru-Ampornpan-13431-45.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Jaru-Ampornpan, Peera; Liang, Fu-Cheng; et el." }, { "id": "https://authors.library.caltech.edu/records/m5286-wkw25", "eprint_id": 37594, "eprint_status": "archive", "datestamp": "2023-08-22 08:53:06", "lastmod": "2023-10-23 17:50:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chitsaz-M", "name": { "family": "Chitsaz", "given": "Mohsen" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "GRID: A high-resolution protein structure refinement algorithm", "ispublished": "pub", "full_text_status": "restricted", "keywords": "protein structure refinement; flexible backbone; energy-based refinement; conformational search; backrub motion", "note": "\u00a9 2012 Wiley Periodicals, Inc.\nReceived: 12 April 2012;\nRevised: 31 July 2012;\nAccepted: 27 August 2012;\nPublished online on 15 October 2012.\nThe authors would like to thank Marie Ary for her comments and assistance\nin writing the manuscript.\n\nContract/grant sponsors: Defense Advanced Research Projects Agency\n(DARPA), Department of Defense National Security Science and\nEngineering Faculty Fellowship.", "abstract": "The energy-based refinement of protein structures generated by fold prediction algorithms to atomic-level accuracy remains a major challenge in structural biology. Energy-based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high-resolution refinement algorithm called GRID. It takes a three-dimensional protein structure as input and, using an all-atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side-chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high-resolution (\u2264 2.8 \u00c5) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 \u00b1 0.02 \u00c5 for GRID versus 0.14 \u00b1 0.04 \u00c5 for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms.", "date": "2013-03-05", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "34", "number": "6", "publisher": "Wliey", "pagerange": "445-450", "id_number": "CaltechAUTHORS:20130321-144912093", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130321-144912093", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Department of Defense National Security Science and Engineering Faculty Fellowship" } ] }, "doi": "10.1002/jcc.23151", "resource_type": "article", "pub_year": "2013", "author_list": "Chitsaz, Mohsen and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/q6jf5-49r48", "eprint_id": 36554, "eprint_status": "archive", "datestamp": "2023-08-19 13:53:21", "lastmod": "2023-10-20 23:17:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Moore-M-M", "name": { "family": "Moore", "given": "Matthew M." } }, { "id": "Oteng-Pabi-S-K", "name": { "family": "Oteng-Pabi", "given": "Samuel K." } }, { "id": "Pandelieva-A-T", "name": { "family": "Pandelieva", "given": "Antonia T." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Chica-R-A", "name": { "family": "Chica", "given": "Roberto A." } } ] }, "title": "Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Moore 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: September 18, 2012; Accepted: November 19, 2012; Published: December 20, 2012.\n\nThis work was supported by the Natural Sciences and Engineering Research Council of Canada (http://www.nserc-crsng.gc.ca), the University of Ottawa (http://www.uottawa.ca), and the Defense Advanced Research Projects Agency Protein Design Processes (http://www.darpa.mil). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nWe thank Marie L. Ary for help with the manuscript. We would like to acknowledge the Gordon and Betty Moore Foundation for support of the Molecular Observatory at Caltech, and the Department of Energy and National Institutes of Health for supporting the Stanford Synchrotron\nRadiation Lightsource.\n\nAuthor Contributions:\nConceived and designed the experiments: MMM SLM RAC. Performed\nthe experiments: MMM SKO ATP. Analyzed the data: MMM SKO ATP\nRAC. Wrote the paper: MMM RAC.\n\nPublished - journal.pone.0052463.pdf
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Supplemental Material - journal.pone.0052463.s005.docx
", "abstract": "Red fluorescent proteins (RFPs) derived from organisms in the class Anthozoa have found widespread application as imaging tools in biological research. For most imaging experiments, RFPs that mature quickly to the red chromophore and produce little or no green chromophore are most useful. In this study, we used rational design to convert a yellow fluorescent mPlum mutant to a red-emitting RFP without reverting any of the mutations causing the maturation deficiency and without altering the red chromophore's covalent structure. We also created an optimized mPlum mutant (mPlum-E16P) that matures almost exclusively to the red chromophore. Analysis of the structure/function relationships in these proteins revealed two structural characteristics that are important for efficient red chromophore maturation in DsRed-derived RFPs. The first is the presence of a lysine residue at position 70 that is able to interact directly with the chromophore. The second is an absence of non-bonding interactions limiting the conformational flexibility at the peptide backbone that is oxidized during red chromophore formation. Satisfying or improving these structural features in other maturation-deficient RFPs may result in RFPs with faster and more complete maturation to the red chromophore.", "date": "2012-12-20", "date_type": "published", "publication": "PLoS ONE", "volume": "7", "number": "12", "publisher": "Public Library of Science", "pagerange": "Art. No. e52463", "id_number": "CaltechAUTHORS:20130124-083857529", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130124-083857529", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "University of Ottawa" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH" } ] }, "doi": "10.1371/journal.pone.0052463", "pmcid": "PMC3527499", "primary_object": { "basename": "journal.pone.0052463.s001.tif", "url": "https://authors.library.caltech.edu/records/q6jf5-49r48/files/journal.pone.0052463.s001.tif" }, "related_objects": [ { "basename": "journal.pone.0052463.s002.tif", "url": "https://authors.library.caltech.edu/records/q6jf5-49r48/files/journal.pone.0052463.s002.tif" }, { "basename": "journal.pone.0052463.s003.tif", "url": "https://authors.library.caltech.edu/records/q6jf5-49r48/files/journal.pone.0052463.s003.tif" }, { "basename": "journal.pone.0052463.s004.tif", "url": "https://authors.library.caltech.edu/records/q6jf5-49r48/files/journal.pone.0052463.s004.tif" }, { "basename": "journal.pone.0052463.s005.docx", "url": "https://authors.library.caltech.edu/records/q6jf5-49r48/files/journal.pone.0052463.s005.docx" }, { "basename": "journal.pone.0052463.pdf", "url": "https://authors.library.caltech.edu/records/q6jf5-49r48/files/journal.pone.0052463.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Moore, Matthew M.; Oteng-Pabi, Samuel K.; et el." }, { "id": "https://authors.library.caltech.edu/records/zekp4-t7w36", "eprint_id": 33535, "eprint_status": "archive", "datestamp": "2023-08-19 11:53:14", "lastmod": "2023-10-18 20:24:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-T-M", "name": { "family": "Lee", "given": "Toni" } }, { "id": "Farrow-M-F", "name": { "family": "Farrow", "given": "Mary" } }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances" }, "orcid": "0000-0002-4027-364X" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen" }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computational Thermostable Cellulase Engineering for Enhanced Biofuel Production", "ispublished": "pub", "full_text_status": "restricted", "note": "This work was made possible through funding from the National Science Foundation.", "abstract": "Generating biofuels from cellulosic material may\nmitigate the detrimental environmental effects of\ncurrent production schemes. Common agricultural\nbyproducts and algal feedstocks are cellulosic in nature,\nproviding more biomass than grain sources while\nminimizing agricultural intensification. Employing\ncellulosic feedstocks, however, requires the use of\nrelatively expensive cellulases, enzymes capable\nof cleaving cellulose into fermentable sugars. One\nmethod of reducing cellulase cost relies on an idea\nencapsulated in the Arrhenius equation, that reaction\nrates increase as temperature increases. Employing\nthermostable cellulases would not only minimize\nprocess time, but would also reduce the amount of\nenzyme necessary per gallon of synthesized fuel.\nWe are currently computationally engineering\nhyperthermostable variants of Cel5A from the fungus\nHypocrea jecorina (Hj_ Cel5A), one of the most heavily\nemployed cellulases in the biofuels industry. To obtain a\nstarting scaffold for design purposes, we have recently\nsolved the structure of this enzyme. When compared\nto a thermostable homolog, the Hj_Cel5A structure\ndemonstrates long, solvent-exposed loops. As such, we\nare combining traditional core-repacking algorithms\nwith loop truncation software to generate thermostable\nvariants. To ensure loop truncation does not disrupt\nprotein stability, we utilize an algorithm to predict\nloop trajectories around the mutated sites, and then\nperform sequence optimization on the new structure.\nHere we present the crystal structure of H. jecorina\nCel5A to 2.1 \u00c5, data demonstrating the robustness of\nour design methodology, and preliminary designs that\nawait biochemical testing.", "date": "2012-08", "date_type": "published", "publication": "Protein Science", "volume": "21", "number": "S1", "publisher": "Wiley", "pagerange": "71-72", "id_number": "CaltechAUTHORS:20120824-161422230", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120824-161422230", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" } ] }, "resource_type": "article", "pub_year": "2012", "author_list": "Lee, Toni; Farrow, Mary; et el." }, { "id": "https://authors.library.caltech.edu/records/n1afv-aft63", "eprint_id": 33530, "eprint_status": "archive", "datestamp": "2023-08-19 11:52:59", "lastmod": "2023-10-18 20:24:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Berry-A", "name": { "family": "Berry", "given": "Alexandria" } }, { "id": "Privett-H-K", "name": { "family": "Privett", "given": "Heidi" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen" }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Designing Conformational Control of Human Tissue Transglutaminase for Applications in Huntington's Disease Research", "ispublished": "pub", "full_text_status": "restricted", "abstract": "Human type II transglutaminase (TG2) is an enzyme\nthat exists in two dramatically different conformational\nstates, each with a unique activity. In the open, extended\nform, the transglutaminase active site is exposed,\nallowing TG2 to catalyze formation of an isopeptide\nbond between the sidechain of a peptide-bound\nglutamine and a primary amine. Upon GTP binding to\na separate GTPase active site, TG2 adopts a heavily\nfavored and compact closed conformation, which\nobstructs the glutaminase active site, and only allows\nGTPase activity. TG2 has been linked to Huntington's\ndisease, as well as to many other cellular processes,\nboth physiological and pathological. However, TG2's\ntwo conformational states, each with its own activity,\nhave made it difficult to elucidate how this enzyme\nfunctions in disease progression. In addition, because\nTG2 heavily prefers the closed state, attempts to screen\nfor inhibitors that may bind the transglutanimase site\nexposed in the open conformation, and attempts to\nobtain co-crystals of the enzyme with these inhibitors\nhave proven difficult. The purpose of this study is use\ncomputational protein design to engineer TG2 variants\nlocked in either the open or closed conformation. Multistate\nand single-state design calculations were successful\nin predicting multiple active variants with 1-4 mutations\nthat preferentially stabilized the open conformation.\nClosed-locked variants are beginning to be designed.\nThese variants then will be used in Huntington's disease\nstudies to isolate the effects of each of TG2's activities\nand to assist in rational drug design.", "date": "2012-08", "date_type": "published", "publication": "Protein Science", "volume": "21", "number": "S1", "publisher": "Wiley", "pagerange": "153", "id_number": "CaltechAUTHORS:20120824-154353922", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120824-154353922", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2012", "author_list": "Berry, Alexandria; Privett, Heidi; et el." }, { "id": "https://authors.library.caltech.edu/records/tkrwd-ten06", "eprint_id": 33586, "eprint_status": "archive", "datestamp": "2023-08-19 11:54:19", "lastmod": "2023-10-18 20:26:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wannier-T-M", "name": { "family": "Wannier", "given": "Timothy" } }, { "id": "Moore-M-M", "name": { "family": "Moore", "given": "Matthew" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen" }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Engineering Monomerization of Red Fluorescent Proteins Through Computational Design", "ispublished": "pub", "full_text_status": "restricted", "abstract": "Fluorescent proteins (FPs) have, over the last\ntwo decades, revolutionized the way biology and\nbiochemistry are studied. However, the obligate\noligomerization of many naturally occurring fluorescent\nproteins has hampered their usefulness as biological\nmarkers. Oligomerization of a fusion tag can impair the\naccuracy of characterizing a target protein, artificially\naggregating its target, altering diffusion rates, and\ncausing problems in target transport and trafficking. A\nmonomeric fluorescent protein avoids these problems.\nIn this vein, DsRed, a well-studied red fluorescent\nprotein (RFP), was successfully engineered through\ndirected evolution into monomeric mCherry by Roger\nTsien and coworkers. This was the first instance of a\nmonomeric RFP and filled a void in the color spectrum\nfor monomeric molecular labels. DsRed is only one of\nhundreds of naturally occurring fluorescent proteins,\nmany diverging significantly in fluorescent properties\nsuch as absorbance and emission spectra or quantum\nyields. Repeating the directed evolution process in\nother proteins would be a long and laborious endeavor, and therefore, a new method is desired for engineering\nmonomerization into fluorescent proteins. We have\ndevised a process through which we can engineer RFP\nmonomers in silica via computational protein design\n(CPD) of surface positions at the oligomerization\ninterfaces. To validate the method, we first engineered\nDsRed that had been modified to include mutations\nmade to the core of the protein during its directed\nevolution to mCherry. CPD predicted sequence variants\nfrom which a 96-member library was constructed; a\n24-member randomly generated library was also used\nas a control. The random library allowed hydrophilic\nresidues, but weighted them based on their frequency\nof occurrence on the surface of bacterial cytoplasmic\nproteins. The design library maintained fluorescence\nin 96.8% of cases, whereas only 9.1% of the random\nlibrary did so. These results demonstrate the power\nof our design method. The designed proteins were\nconfirmed to be monomeric by gel filtration, homoFRET,\nand analytical ultracentrifugation. As expected\nfrom the mutations to the core of the protein, the mutants\nmaintained the spectroscopic properties ofmCherry and\nnot of OsRed. We hope to repeat these results in other\nfluorescent proteins that have yet to be monomerized\nsuch as HcRed and AQ143, which are both significantly\nred-shifted from DsRed.", "date": "2012-08", "date_type": "published", "publication": "Protein Science", "volume": "21", "number": "S1", "publisher": "Wiley", "pagerange": "144-145", "id_number": "CaltechAUTHORS:20120828-072233569", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120828-072233569", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2012", "author_list": "Wannier, Timothy; Moore, Matthew; et el." }, { "id": "https://authors.library.caltech.edu/records/vq3cj-mm146", "eprint_id": 33527, "eprint_status": "archive", "datestamp": "2023-08-19 11:52:37", "lastmod": "2023-10-18 20:23:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Padilla-Araujo-B-S", "name": { "family": "Padilla Araujo", "given": "Bernardo Sosa" } }, { "id": "Miller-T-F-III", "name": { "family": "Miller", "given": "Thomas" }, "orcid": "0000-0002-1882-5380" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen" }, "orcid": "0000-0002-9785-5018" } ] }, "title": "In Silico Screening of Computational Enzyme Designs", "ispublished": "pub", "full_text_status": "restricted", "abstract": "Computational enzyme design is a very promising area\nof research. However, current computational design\ntools suffer from a serious limitation: they cannot\nreliably predict active sequences and thus produce\na large number of false positives. Consequently,\ninvestigators have had to rely on screening hundreds\nof designs to find a few active ones. In addition, both\nprotein dynamics and explicit solvation are important\naspects of enzyme function and are therefore critical to\npredicting enzymatic activity. Unfortunately, protein\ndesign methodology rarely takes these factors into\naccount. Molecular dynamics (MD) simulations, on the\nother hand, can model both. In this work, we develop a\nMD protocol that provides a rei iable and computationally\nfeasible way to pre-screen enzyme designs. Preliminary\nresults have shown excellent agreement between\nexperimental data and MD predictions. We tested the\ngenerality of the methodology on a larger and more\ndiverse set of enzymes for which experimental data\nalready exist. The method is general, sensitive (0.70) and\nspecific (0.72). It also exhibits high negative predictive\nvalue (0.91) and promising computational performance,\nand wilt be useful for de novo computational enzyme\ndesign.", "date": "2012-08", "date_type": "published", "publication": "Protein Science", "volume": "21", "number": "S1", "publisher": "Wiley", "pagerange": "132", "id_number": "CaltechAUTHORS:20120824-152508878", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120824-152508878", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "National Security Science and Engineering Faculty Fellowship" } ] }, "resource_type": "article", "pub_year": "2012", "author_list": "Padilla Araujo, Bernardo Sosa; Miller, Thomas; et el." }, { "id": "https://authors.library.caltech.edu/records/ffvcz-3y466", "eprint_id": 33526, "eprint_status": "archive", "datestamp": "2023-08-19 11:52:30", "lastmod": "2023-10-18 20:23:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cahn-J", "name": { "family": "Cahn", "given": "Jackson" } }, { "id": "Padilla-Araujo-B-S", "name": { "family": "Padilla Araujo", "given": "Bernardo Sosa" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen" }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Multi-State Computational Design and Experimental Characterization of Triosephosphate Isomerase Flexible Hinges", "ispublished": "pub", "full_text_status": "restricted", "note": "This work supported by a DARPA Protein\nDesign Processes grant and a National Security Science\nand Engineering Faculty Fellowship award to S.L.M.", "abstract": "Traditional computational protein design calculations\nenable the evaluation and selection of protein sequences\nin the context of a single native structure. However many\nproteins natively require multiple distinct conformations\nfor functionality. Recently, a novel algorithm has been\ndeveloped which considers several structures in a single\noptimization calculation. This new method could be\nuseful for designing proteins that need to accommodate\nseveral conformations. We sought to test this algorithm\non triosephosphate isomerase (TIM). Loop 6 in TIM is\na lid with open and closed conformations that facilitate\nsubstrate binding, product diffusion, and catalysis. It\nuses two 3-amino acid hinges that provide the flexibility\nfor the open-closed transition. In the present work we use\nmulti-state design (MSD) methods to design the flexible\nhinges in TIM. We are in the process of assessing the\napplicability of MSD for the design of flexible protein\nhinges by exhaustive screening of computationally\ndesigned libraries. The results will suggest whether,\nby considering both conformations of the enzyme\ninstead of purely the open or closed conformations,\nour methods provide libraries enriched in catalytically\nactive TIMs.", "date": "2012-08", "date_type": "published", "publication": "Protein Science", "volume": "21", "number": "S1", "publisher": "Wiley", "pagerange": "132", "id_number": "CaltechAUTHORS:20120824-152117796", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120824-152117796", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "DARPA Protein Design Processes Grant" }, { "agency": "National Security Science and Engineering Faculty Fellowship" } ] }, "resource_type": "article", "pub_year": "2012", "author_list": "Cahn, Jackson; Padilla Araujo, Bernardo Sosa; et el." }, { "id": "https://authors.library.caltech.edu/records/ewgwx-gkr84", "eprint_id": 33531, "eprint_status": "archive", "datestamp": "2023-08-19 11:53:06", "lastmod": "2023-10-18 20:24:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chitsaz-M", "name": { "family": "Chitsaz", "given": "Mohsen" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen" }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Replica Exchange Monte Carlo GRID: A novel high-resolution refinement algorithm", "ispublished": "pub", "full_text_status": "restricted", "abstract": "The energy-based refinement of protein structures to\natomic-level accuracy remains a major challenge in\nstructural biology. Energy-based refinement is mainly\ndependent on two components: (1) sufficiently accurate\nforce fields, and (2) efficient conformational space\nsearch algorithms. Focusing on the latter, we developed\na high-resolution Replica Exchange Monte Carlo-based\nrefinement algorithm called REMC-GRID. This\nmethod takes a three-dimensional protein structure as\ninput and, employing an all-atom force field, attempts\nto improve the energy of the structure by randomly\nselecting residues and perturbing the backbone dihedral\nangles. GRID, another refinement algorithm that we had\ndeveloped previously, similarly improves the energy of\nprotein structures, but is deterministic and perturbs the\nbackbone dihedrals and conformation of all the residues\nin a sequential fashion. We applied REMC-GRID and\nGRID to 10 high-resolution (\u2264 2.8 \u00c5) crystal structures\nfrom the Protein Data Bank and measured the energy\nimprovements obtained and the computation times\nrequired to achieve them. REMC-GRID produced\nbetter energy improvements than GRID alone and\nwas only moderately more expensive in the use of\ncomputational resources. In another set of experiments,\nwe created decoy structures by randomly perturbing\nthe backbone dihedrals, and then tested the ability of\nthe two algorithms to return the structures back to the\nnative conformation. REMC-GRID resulted in better\nrecapitulation of the native conformation than GRID as\nmeasured by backbone RMSD.", "date": "2012-08", "date_type": "published", "publication": "Protein Science", "volume": "21", "number": "S1", "publisher": "Wiley", "pagerange": "139", "id_number": "CaltechAUTHORS:20120824-155438591", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120824-155438591", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "article", "pub_year": "2012", "author_list": "Chitsaz, Mohsen and Mayo, Stephen" }, { "id": "https://authors.library.caltech.edu/records/mgt51-rjy87", "eprint_id": 32372, "eprint_status": "archive", "datestamp": "2023-08-22 06:02:00", "lastmod": "2023-10-17 23:22:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Alvizo-O", "name": { "family": "Alvizo", "given": "Oscar" } }, { "id": "Mittal-S", "name": { "family": "Mittal", "given": "Seema" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Schiffer-C-A", "name": { "family": "Schiffer", "given": "Celia A." } } ] }, "title": "Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease", "ispublished": "pub", "full_text_status": "restricted", "keywords": "HIV-1 protease; positive design; substrate specificity; X-ray crystallography; isothermal titration calorimetry; substrate envelope", "note": "\u00a9 2012 The Protein Society. Published by Wiley-Blackwell. \n\nReceived 18 January 2012; Revised 23 March 2012; Accepted 10 April 2012. Article first published online: 5 Jun. 2012. \n\nGrant sponsor: National Institutes of Health; Grant numbers: R01 GM064347P01 GM66524; Grant sponsor: National Institutes of \nHealth, National Center for Research Resources; Grant number: RR007707; Grant sponsors: Office of Biological and Environmental \nResearch; Office of Basic Energy Sciences of the US Department of Energy; National Center for Research Resources of the National\nInstitutes of Health. \n\nThe authors thank Dr. Vukica Srajer at BioCARS, sector 14 Advanced Photon Source at Argonne National Laboratory for help with data collection, Dr. William E. Royer and Dr. Madhavi N. Nalam for assistance with initial refinement, and Dr. Nese Kurt Yilmaz and Ms. Marie Ary for editorial assistance. They thank Annie Heroux, beam line scientist at the Macromolecular Crystallography Research Resource (PXRR) of the Brookhaven National Laboratory, for collecting some of the data at beamline X25 of the National Synchrotron Light Source through the mail-in crystal\nprogram.", "abstract": "HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT\u2013RH over p2-NC and CA-p2. In kinetic assays, RT\u2013RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT\u2013RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease.", "date": "2012-07", "date_type": "published", "publication": "Protein Science", "volume": "21", "number": "7", "publisher": "Wiley", "pagerange": "1029-1041", "id_number": "CaltechAUTHORS:20120712-085217104", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120712-085217104", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM064347P01" }, { "agency": "NIH", "grant_number": "GM66524" }, { "agency": "NIH", "grant_number": "RR007707" }, { "agency": "Department of Energy (DOE)" } ] }, "doi": "10.1002/pro.2086", "pmcid": "PMC3403440", "resource_type": "article", "pub_year": "2012", "author_list": "Alvizo, Oscar; Mittal, Seema; et el." }, { "id": "https://authors.library.caltech.edu/records/6s9b7-fzv37", "eprint_id": 30223, "eprint_status": "archive", "datestamp": "2023-08-19 10:26:23", "lastmod": "2023-10-17 15:33:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Mike-M-Y", "name": { "family": "Chen", "given": "Mike M. Y." } }, { "id": "Snow-C-D", "name": { "family": "Snow", "given": "Christopher D." }, "orcid": "0000-0002-7690-3519" }, { "id": "Vizcarra-C-L", "name": { "family": "Vizcarra", "given": "Christina L." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" } ] }, "title": "Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes", "ispublished": "pub", "full_text_status": "public", "keywords": "alkane hydroxylation\n C\u2013H activation\n directed evolution\n P450 enzymes\n semi-rational library design", "note": "\u00a9 The Author 2012. Published by Oxford University Press. Received January 9, 2012; revised January 9, 2012; accepted January 10, 2012. This work was supported by the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Science, US Department of Energy Grant DE-FG02-06ER15762 and the DARPA Protein Design Processes Grant. C.D.S. was supported by a Jane Coffin Childs postdoctoral fellowship. The authors thank Dr Nathan Dalleska for assistance with gas chromatography.\n\nSupplemental Material - gzs004supp.doc
", "abstract": "Three semi-rational approaches, combinatorial site-saturation mutagenesis (CSSM) using a reduced amino acid set and two libraries based on Corbit and CRAM computational design algorithms targeting up to 10 active site residues, were used to engineer cytochrome P450 BM3 to demethylate dimethyl ether and hydroxylate propane and ethane. These small libraries (343\u20131028 variants) were all enriched with respect to the fraction functional and maximal activities compared with a random mutagenesis library and individual site-saturation libraries targeting the same residues. Despite high average amino acid substitution levels of 2.6, 5 and 7.5, the CSSM, Corbit and CRAM libraries had at least 75% of library members properly folded. Propane- and ethane-hydroxylating P450 BM3 variants were identified using all three mutagenesis approaches, with as few as two amino acid substitutions. The library designed using the CRAM algorithm, which sought to reduce the size of the binding pocket, produced both a higher number of active variants and variants supporting the greatest number of catalytic turnovers. The most active variant E32 supports 16 800 propane turnovers at 36% coupling, which rivals the activity of variants obtained after 10\u201312 rounds of directed evolution using random and site-saturation mutagenesis. None of the variants in this study achieved the complete re-specialization for propane hydroxylation (including 93% coupling) previously obtained via multiple rounds of mutagenesis and screening. However, these semi-rational approaches allowed for large jumps in sequence space to variants with the desired functions.", "date": "2012-04", "date_type": "published", "publication": "Protein Engineering, Design and Selection", "volume": "25", "number": "4", "publisher": "Oxford University Press", "pagerange": "171-178", "id_number": "CaltechAUTHORS:20120420-110357141", "issn": "1741-0126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120420-110357141", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-06ER15762" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Jane Coffin Childs Memorial Fund for Medical Research" } ] }, "doi": "10.1093/protein/gzs004", "primary_object": { "basename": "gzs004supp.doc", "url": "https://authors.library.caltech.edu/records/6s9b7-fzv37/files/gzs004supp.doc" }, "resource_type": "article", "pub_year": "2012", "author_list": "Chen, Mike M. Y.; Snow, Christopher D.; et el." }, { "id": "https://authors.library.caltech.edu/records/pssdy-yy487", "eprint_id": 29849, "eprint_status": "archive", "datestamp": "2023-08-22 05:09:30", "lastmod": "2023-10-24 22:30:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Privett-H-K", "name": { "family": "Privett", "given": "Heidi K." } }, { "id": "Kiss-G", "name": { "family": "Kiss", "given": "Gert" } }, { "id": "Lee-Toni-M", "name": { "family": "Lee", "given": "Toni M." } }, { "id": "Blomberg-R", "name": { "family": "Blomberg", "given": "Rebecca" } }, { "id": "Chica-R-A", "name": { "family": "Chica", "given": "Roberto A." } }, { "id": "Thomas-L-M", "name": { "family": "Thomas", "given": "Leonard M." } }, { "id": "Hilvert-D", "name": { "family": "Hilvert", "given": "Donald" } }, { "id": "Houk-K-N", "name": { "family": "Houk", "given": "Kendall N." }, "orcid": "0000-0002-8387-5261" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Iterative approach to computational enzyme design", "ispublished": "pub", "full_text_status": "public", "keywords": "computational protein design; de novo enzyme design; proton transfer", "note": "\u00a9 2011 National Academy of Sciences.\n\nContributed by Stephen L. Mayo, November 4, 2011 (sent for review September 6, 2011).\nWe thank Jens Kaiser and Pavle Nikolovski at the Caltech\nMolecular Observatory for assistance in crystal screening, crystallographic\ndata collection, and structure determination. We are grateful to\nDaniela R\u00f6thlisberger and David Baker for providing genes for the KE positive\ncontrols and to Marie Ary and Scott A. Johnson for assistance with the\nmanuscript. Data for the HG-2 and 1A53-2 structures were collected at beamline\n12-2 at the Stanford Synchrotron Radiation Lightsource (SSRL, SLAC National\nAccelerator Laboratory, Menlo Park, CA).We acknowledge the Gordon\nand Betty Moore Foundation for support of the Molecular Observatory at\nCaltech and the Department of Energy and National Institutes of Health\nfor supporting the SSRL. This work was supported by the Defense Advanced\nResearch Projects Agency, a Department of Defense National Security Science\nand Engineering Faculty Fellowship (S.L.M.), and a Lawrence Livermore National\nLaboratory Lawrence Scholars Fellowship (G.K.). Fellowship support\nfrom the Fonds des Verbandes der chemischen Industrie and the Studienstiftung\ndes deutschen Volkes (R.B.) is gratefully acknowledged.\nAuthor contributions: H.K.P., G.K., T.M.L., D.H., K.N.H., and S.L.M. designed research;\nH.K.P., G.K., T.M.L., R.B., R.A.C., and L.M.T. performed research; H.K.P., G.K., T.M.L., R.B.,\nR.A.C., L.M.T., D.H., K.N.H., and S.L.M. analyzed data; and H.K.P., G.K., T.M.L., R.B.,\nR.A.C., L.M.T., D.H., K.N.H., and S.L.M. wrote the paper. \n\nData deposition: The atomic coordinates and structure factors have been deposited in the\nProtein Data Bank, www.pdb.org (PDB ID codes 3O2L, 3NYD, 3NYZ, and 3NZ1).\n\nPublished - Privett2012p17517P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - Appendix.pdf
", "abstract": "A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes.", "date": "2012-03-06", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "109", "number": "10", "publisher": "National Academy of Sciences", "pagerange": "3790-3795", "id_number": "CaltechAUTHORS:20120326-153311623", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120326-153311623", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "National Security Science and Engineering Faculty Fellowship" }, { "agency": "Lawrence Livermore National Laboratory" }, { "agency": "Fonds des Verbandes der chemischen Industrie" }, { "agency": "Studienstiftung des deutschen Volkes" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH" } ] }, "doi": "10.1073/pnas.1118082108", "pmcid": "PMC3309769", "primary_object": { "basename": "Appendix.pdf", "url": "https://authors.library.caltech.edu/records/pssdy-yy487/files/Appendix.pdf" }, "related_objects": [ { "basename": "Privett2012p17517P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/pssdy-yy487/files/Privett2012p17517P_Natl_Acad_Sci_Usa.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Privett, Heidi K.; Kiss, Gert; et el." }, { "id": "https://authors.library.caltech.edu/records/e5zz9-ya470", "eprint_id": 27756, "eprint_status": "archive", "datestamp": "2023-08-19 08:29:15", "lastmod": "2023-10-24 17:23:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-Toni-M", "name": { "family": "Lee", "given": "Toni M." } }, { "id": "Farrow-M-F", "name": { "family": "Farrow", "given": "Mary F." } }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "A structural study of Hypocrea jecorina Cel5A", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 The Protein Society. Published by Wiley-Blackwell.\n\nReceived 2 July 2011; Revised 19 August 2011; Accepted 22 August 2011.\nPublished online 6 September 2011.\n\nGrant sponsors: DARPA Protein Design Processes, DoD\nNational Security Science and Engineering Faculty, Gordon and\nBetty Moore Foundation, and UNCF/Merck.\n\nThe authors acknowledge the use of beamline 12-2 at\nthe Stanford Synchrotron Radiation Lightsource\n(SSRL) in Menlo Park, CA operated by Stanford University\nand supported by the Department of Energy\nand National Institutes of Health. They additionally\nacknowledge Jens Kaiser and Pavle Niklovski at the\nCalifornia Institute of Technology for their advice.\nThey thank the Gordon and Betty Moore Foundation\nfor support of the Molecular Observatory at Caltech.\n\nPublished - Lee2011p16209Protein_Sci.pdf
Supplemental Material - PRO_730_sm_SuppInfo.doc
", "abstract": "Interest in generating lignocellulosic biofuels through enzymatic hydrolysis continues to\nrise as nonrenewable fossil fuels are depleted. The high cost of producing cellulases, hydrolytic\nenzymes that cleave cellulose into fermentable sugars, currently hinders economically viable\nbiofuel production. Here, we report the crystal structure of a prevalent endoglucanase in the\nbiofuels industry, Cel5A from the filamentous fungus Hypocrea jecorina. The structure reveals a\ngeneral fold resembling that of the closest homolog with a high-resolution structure, Cel5A from\nThermoascus aurantiacus. Consistent with previously described endoglucanase structures, the\nH. jecorina Cel5A active site contains a primarily hydrophobic substrate binding groove and a\nseries of hydrogen bond networks surrounding two catalytic glutamates. The reported structure,\nhowever, demonstrates stark differences between side-chain identity, loop regions, and the\nnumber of disulfides. Such structural information may aid efforts to improve the stability of this\nprotein for industrial use while maintaining enzymatic activity through revealing nonessential and\nimmutable regions.", "date": "2011-11", "date_type": "published", "publication": "Protein Science", "volume": "20", "number": "11", "publisher": "Wiley", "pagerange": "1935-1940", "id_number": "CaltechAUTHORS:20111111-135716977", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111111-135716977", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "National Security Science and Engineering Faculty" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "UNCF/Merck" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH" } ] }, "doi": "10.1002/pro.730", "pmcid": "PMC3267957", "primary_object": { "basename": "Lee2011p16209Protein_Sci.pdf", "url": "https://authors.library.caltech.edu/records/e5zz9-ya470/files/Lee2011p16209Protein_Sci.pdf" }, "related_objects": [ { "basename": "PRO_730_sm_SuppInfo.doc", "url": "https://authors.library.caltech.edu/records/e5zz9-ya470/files/PRO_730_sm_SuppInfo.doc" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Lee, Toni M.; Farrow, Mary F.; et el." }, { "id": "https://authors.library.caltech.edu/records/m9ezv-0ye63", "eprint_id": 25313, "eprint_status": "archive", "datestamp": "2023-08-22 03:28:40", "lastmod": "2023-10-24 15:46:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Keeffe-J-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "id": "Gnanapragasam-P-N-P", "name": { "family": "Gnanapragasam", "given": "Priyanthi N. P." } }, { "id": "Gillespie-S-K", "name": { "family": "Gillespie", "given": "Sarah K." } }, { "id": "Yong-John", "name": { "family": "Yong", "given": "John" } }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Designed oligomers of cyanovirin-N show enhanced HIV neutralization", "ispublished": "pub", "full_text_status": "public", "keywords": "crystal structure; domain-swapped dimer; protein engineering", "note": "\u00a9 2011 National Academy of Sciences. \n\nContributed by Stephen L. Mayo, May 31, 2011 (sent for review April 1, 2011). Published online before print July 28, 2011. \n\nWe thank Leonard Thomas, Pavle Nikolovski, and the Molecular Observatory at Caltech, which is supported by the Gordon and Betty Moore Foundation, for assistance in setting up crystal trays, collecting and processing diffraction data, and refining crystal structures. We also thank the Collaboration for AIDS Vaccine Discovery Neutralizing Antibody Core Laboratories for performing HIV neutralization assays and Marie Ary for critical review of the manuscript. This work was funded by the National Security Science and Engineering Faculty Fellowship program and the Defense Advanced Research Projects Agency Protein Design Processes program (to S.L.M.) and by the Bill and Melinda Gates Foundation Grant 38660 through the Grand Challenges in Global Health Initiative (to P.J.B.). X-ray data for CVN_2L10 were collected at the Stanford Synchrotron Radiation Lightsource (Beam Line 12-2). Operations at Stanford Synchotron Radiation Lightsource are supported by the Department of Energy and the National Institutes of Health. \n\nAuthor contributions: J.R.K., P.J.B., and S.L.M. designed research; J.R.K., P.N.P.G., S.K.G., and J.Y. performed research; J.R.K., P.N.P.G., S.K.G., J.Y., P.J.B., and S.L.M. analyzed data; and J.R.K. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nData deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 3S3Y, 3S3Z). \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1108777108/-/DCSupplemental.\n\nPublished - Keeffe_2011_Proc_Natl_Acad_Sci_USA_Designed_oligomers_of_cyanovirin-N_show.pdf
Supplemental Material - pnas.1108777108_SI.pdf
", "abstract": "Cyanovirin-N (CV-N) is a small, cyanobacterial lectin that neutralizes many enveloped viruses, including human immunodeficiency virus type I (HIV-1). This antiviral activity is attributed to two homologous carbohydrate binding sites that specifically bind high mannose glycosylation present on envelope glycoproteins such as HIV-1 gp120. We created obligate CV-N oligomers to determine whether increasing the number of binding sites has an effect on viral neutralization. A tandem repeat of two CV-N molecules (CVN_2) increased HIV-1 neutralization activity by up to 18-fold compared to wild-type CV-N. In addition, the CVN_2 variants showed extensive cross-clade reactivity and were often more potent than broadly neutralizing anti-HIV antibodies. The improvement in activity and broad cross-strain HIV neutralization exhibited by these molecules holds promise for the future therapeutic utility of these and other engineered CV-N variants.", "date": "2011-08-23", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "108", "number": "34", "publisher": "National Academy of Sciences", "pagerange": "14079-14084", "id_number": "CaltechAUTHORS:20110913-132623950", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-132623950", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "National Security Science and Engineering Faculty Fellowship" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "38660" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH" } ] }, "doi": "10.1073/pnas.1108777108", "pmcid": "PMC3161612", "primary_object": { "basename": "Keeffe_2011_Proc_Natl_Acad_Sci_USA_Designed_oligomers_of_cyanovirin-N_show.pdf", "url": "https://authors.library.caltech.edu/records/m9ezv-0ye63/files/Keeffe_2011_Proc_Natl_Acad_Sci_USA_Designed_oligomers_of_cyanovirin-N_show.pdf" }, "related_objects": [ { "basename": "pnas.1108777108_SI.pdf", "url": "https://authors.library.caltech.edu/records/m9ezv-0ye63/files/pnas.1108777108_SI.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Keeffe, Jennifer R.; Gnanapragasam, Priyanthi N. P.; et el." }, { "id": "https://authors.library.caltech.edu/records/jgha3-6rh36", "eprint_id": 23632, "eprint_status": "archive", "datestamp": "2023-08-22 02:32:47", "lastmod": "2023-10-23 19:48:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Xin", "name": { "family": "Zhang", "given": "Xin" } }, { "id": "Lam-Vinh-Q", "name": { "family": "Lam", "given": "Vinh Q." } }, { "id": "Mou-Yun", "name": { "family": "Mou", "given": "Yun" } }, { "id": "Kimura-Tetsunari", "name": { "family": "Kimura", "given": "Tetsunari" } }, { "id": "Chung-Jaeyoon", "name": { "family": "Chung", "given": "Jaeyoon" } }, { "id": "Chandrasekar-Sowmya", "name": { "family": "Chandrasekar", "given": "Sowmya" } }, { "id": "Winkler-J-R", "name": { "family": "Winkler", "given": "Jay R." }, "orcid": "0000-0002-4453-9716" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Shan-S-O", "name": { "family": "Shan", "given": "Shu-ou" }, "orcid": "0000-0002-6526-1733" } ] }, "title": "Direct visualization reveals dynamics of a transient intermediate during protein assembly", "ispublished": "pub", "full_text_status": "public", "keywords": "EPR spectroscopy; fluorescence spectroscopy; molecular recognition; protein targeting; GTPases", "note": "\u00a9 2011 National Academy of Sciences. \n\nEdited by Jos\u00e9 N. Onuchic, University of California, San Diego, La Jolla, CA, and approved February 25, 2011 (received for review December 17, 2010). Published online before print April 4, 2011. \n\nWe thank B.S.P. Araujo for modeling the effect of fluorophore linkers on distant measurements; H.B. Gray and P.E. Wright for insightful discussions; and D.C. Rees, T.F. Miller III, and members of the Shan laboratory for comments on the manuscript. This work was supported by National Institutes of Health Grants GM078024 to S.-o.S. and GM068041 to J.R.W., DARPA Protein Design Processes to S.L.M., and career awards from the Burroughs Welcome Foundation, the Henry and Camille Dreyfus Foundation, the Arnold and Mabel Beckman Foundation, and the David and Lucile Packard Foundation to S.-o.S. \n\nAuthor contributions: X.Z., V.Q.L., J.R.W., and S.-o.S. designed research; X.Z., V.Q.L., Y.M., T.K., J.C., S.C., and S.-o.S. performed research; X.Z. and V.Q.L. contributed new reagents/analytic tools; X.Z., V.Q.L., Y.M., T.K., J.R.W., S.L.M., and S.-o.S. analyzed data; and X.Z. and S.-o.S. wrote the paper.\n\nPublished - Zhang2011p13713P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - SM01.mov
Supplemental Material - pnas.1019051108_SI.pdf
", "abstract": "Interactions between proteins underlie numerous biological functions. Theoretical work suggests that protein interactions initiate with formation of transient intermediates that subsequently relax to specific, stable complexes. However, the nature and roles of these transient intermediates have remained elusive. Here, we characterized the global structure, dynamics, and stability of a transient, on-pathway intermediate during complex assembly between the Signal Recognition Particle (SRP) and its receptor. We show that this intermediate has overlapping but distinct interaction interfaces from that of the final complex, and it is stabilized by long-range electrostatic interactions. A wide distribution of conformations is explored by the intermediate; this distribution becomes more restricted in the final complex and is further regulated by the cargo of SRP. These results suggest a funnel-shaped energy landscape for protein interactions, and they provide a framework for understanding the role of transient intermediates in protein assembly and biological regulation.", "date": "2011-04-19", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "108", "number": "16", "publisher": "National Academy of Sciences", "pagerange": "6450-6455", "id_number": "CaltechAUTHORS:20110511-090620791", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110511-090620791", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM078024" }, { "agency": "NIH", "grant_number": "GM068041" }, { "agency": "Burroughs Welcome Foundation" }, { "agency": "Camille and Henry Dreyfus Foundation" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "doi": "10.1073/pnas.1019051108", "pmcid": "PMC3081034", "primary_object": { "basename": "SM01.mov", "url": "https://authors.library.caltech.edu/records/jgha3-6rh36/files/SM01.mov" }, "related_objects": [ { "basename": "Zhang2011p13713P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/jgha3-6rh36/files/Zhang2011p13713P_Natl_Acad_Sci_Usa.pdf" }, { "basename": "pnas.1019051108_SI.pdf", "url": "https://authors.library.caltech.edu/records/jgha3-6rh36/files/pnas.1019051108_SI.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Zhang, Xin; Lam, Vinh Q.; et el." }, { "id": "https://authors.library.caltech.edu/records/a6zv5-3nn52", "eprint_id": 23219, "eprint_status": "archive", "datestamp": "2023-08-19 05:54:26", "lastmod": "2023-10-23 18:04:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hemmert-A-C", "name": { "family": "Hemmert", "given": "Andrew C." } }, { "id": "Otto-T-C", "name": { "family": "Otto", "given": "Tamara C." } }, { "id": "Chica-R-A", "name": { "family": "Chica", "given": "Roberto A." } }, { "id": "Wierdl-M", "name": { "family": "Wierdl", "given": "Monika" } }, { "id": "Edwards-J-S", "name": { "family": "Edwards", "given": "Jonathan S." } }, { "id": "Lewis-S-L", "name": { "family": "Lewis", "given": "Steven L." } }, { "id": "Edwards-C-C", "name": { "family": "Edwards", "given": "Carol C." } }, { "id": "Tsurkan-L", "name": { "family": "Tsurkan", "given": "Lyudmila" } }, { "id": "Cadieux-C-L", "name": { "family": "Cadieux", "given": "C. Linn" } }, { "id": "Kasten-S-A", "name": { "family": "Kasten", "given": "Shane A." } }, { "id": "Cashman-J-R", "name": { "family": "Cashman", "given": "John R." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Potter-P-M", "name": { "family": "Potter", "given": "Philip M." } }, { "id": "Cerasoli-D-M", "name": { "family": "Cerasoli", "given": "Douglas M." } }, { "id": "Redinbo-M-R", "name": { "family": "Redinbo", "given": "Matthew R." } } ] }, "title": "Nerve Agent Hydrolysis Activity Designed into a Human Drug Metabolism Enzyme", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Hemmert et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits\nunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\n\nReceived November 16, 2010; Accepted February 2, 2011; Published March 18, 2011.\nEditor: Fernando Rodrigues-Lima, University Paris Diderot-Paris 7, France.\nFunding: This work was funded by the National Institutes of Health CounterACT Program through the National Institute of Neurological Disorders and Stroke\n(UO1 NS58089, MRR; UO1 NS058038, JRC). This work was also supported by the American Lebanese and Syrian Associated Charities (ALSAC) and St. Jude\nChildren's Research Hospital. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nThe opinions, interpretations, conclusions, and recommendations are those\nof the authors and are not necessarily endorsed by the U.S. Army or the\nDepartment of Defense.\nAuthor Contributions:\nConceived and designed the experiments: ACH RAC MRR. Performed\nthe experiments: ACH TCO RAC MW JSE SLL CCE LT CLC SAK.\nAnalyzed the data: ACH RAC JRC SLM PMP DMC MRR. Contributed\nreagents/materials/analysis tools: ACH TCO RAC MW JSE SLL CCE\nLT CLC SAK. Wrote the paper: ACH TCO RACMWJSE SLL CCE LT\nCLC SAK JRC SLM PMP DMC MRR.\n\nPublished - Hemmert2011p13293PLoS_ONE.pdf
", "abstract": "Organophosphorus (OP) nerve agents are potent suicide inhibitors of the essential neurotransmitter-regulating enzyme acetylcholinesterase. Due to their acute toxicity, there is significant interest in developing effective countermeasures to OP poisoning. Here we impart nerve agent hydrolysis activity into the human drug metabolism enzyme carboxylesterase 1. Using crystal structures of the target enzyme in complex with nerve agent as a guide, a pair of histidine and glutamic acid residues were designed proximal to the enzyme's native catalytic triad. The resultant variant protein demonstrated significantly increased rates of reactivation following exposure to sarin, soman, and cyclosarin. Importantly, the addition of these residues did not alter the high affinity binding of nerve agents to this protein. Thus, using two amino acid substitutions, a novel enzyme was created that efficiently converted a group of hemisubstrates, compounds that can start but not complete a reaction cycle, into bona fide substrates. Such approaches may lead to novel countermeasures for nerve agent poisoning.", "date": "2011-03-18", "date_type": "published", "publication": "PLoS ONE", "volume": "6", "number": "3", "publisher": "Public Library of Science", "pagerange": "Art. No. e17441", "id_number": "CaltechAUTHORS:20110404-094940641", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110404-094940641", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH National Institute of Neurological Disorders and Stroke", "grant_number": "UO1 NS58089" }, { "agency": "NIH National Institute of Neurological Disorders and Stroke", "grant_number": "UO1 NS058038" }, { "agency": "American Lebanese and Syrian Associated Charities (ALSAC)" }, { "agency": "St. Jude Children's Research Hospital" } ] }, "doi": "10.1371/journal.pone.0017441", "pmcid": "PMC3060870", "primary_object": { "basename": "Hemmert2011p13293PLoS_ONE.pdf", "url": "https://authors.library.caltech.edu/records/a6zv5-3nn52/files/Hemmert2011p13293PLoS_ONE.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Hemmert, Andrew C.; Otto, Tamara C.; et el." }, { "id": "https://authors.library.caltech.edu/records/jzfye-qpv61", "eprint_id": 21338, "eprint_status": "archive", "datestamp": "2023-08-22 01:24:31", "lastmod": "2023-10-20 23:57:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chica-R-A", "name": { "family": "Chica", "given": "Roberto A." } }, { "id": "Moore-M-M", "name": { "family": "Moore", "given": "Matthew M." } }, { "id": "Allen-B-D", "name": { "family": "Allen", "given": "Benjamin D." }, "orcid": "0000-0001-6914-5572" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries", "ispublished": "pub", "full_text_status": "public", "keywords": "bathochromic shift; computational protein design; library design; mCherry; crystal structures", "note": "\u00a9 2010 National Academy of Sciences.\n\nContributed by Stephen L. Mayo, September 16, 2010 (sent for review June 8, 2010).\nPublished online before print November 8, 2010.\n\nWe thank Marie L. Ary for help with the manuscript,\nChristina L. Vizcarra and Eric S. Zollars for help with implementation of\nthe occluded volume solvation method, Jens Kaiser for assistance in solving\ncrystal structures and collecting diffraction data, Pavle Niklovski for setting\nup crystallization screens, and Sonja Hess, Robert L.J. Graham, and Michael J.\nSweredoski at the Caltech Proteome Exploration Laboratory for providing\nassistance with the mass spectrometry analyses. This work was supported\nby Defense Advanced Research Projects Agency (DARPA) Protein Design\nProcesses. R.A.C. was supported by a fellowship from the Fonds Qu\u00e9b\u00e9cois\nde la Recherche sur la Nature et les Technologies. We would like to acknowledge\nthe Gordon and Betty Moore Foundation for support of the Molecular\nObservatory at Caltech, and the Department of Energy and National\nInstitutes of Health for supporting the Stanford Synchrotron Radiation\nLightsource.\n\nAuthor contributions: R.A.C. and S.L.M. designed research; R.A.C., M.M.M., and B.D.A.\nperformed research; B.D.A. contributed new reagents/analytic tools; R.A.C. and M.M.M.\nanalyzed data; and R.A.C. wrote the paper.\n\nPublished - Chica2010p12091P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - pnas.1013910107_SI.pdf
", "abstract": "The longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for further red-shifted and improved RFPs continues. Herein, we report a structure-based rational design approach to red-shift the fluorescence emission of RFPs. We applied a combined computational and experimental approach that uses computational protein design as an in silico prescreen to generate focused combinatorial libraries of mCherry mutants. The computational procedure helped us identify residues that could fulfill interactions hypothesized to cause red-shifts without destabilizing the protein fold. These interactions include stabilization of the excited state through H-bonding to the acylimine oxygen atom, destabilization of the ground state by hydrophobic packing around the charged phenolate, and stabilization of the excited state by a \u03c0-stacking interaction. Our methodology allowed us to identify three mCherry mutants (mRojoA, mRojoB, and mRouge) that display emission wavelengths > 630 nm, representing red-shifts of 20\u201326 nm. Moreover, our approach required the experimental screening of a total of ~5,000 clones, a number several orders of magnitude smaller than those previously used to achieve comparable red-shifts. Additionally, crystal structures of mRojoA and mRouge allowed us to verify fulfillment of the interactions hypothesized to cause red-shifts, supporting their contribution to the observed red-shifts.", "date": "2010-11-23", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "107", "number": "47", "publisher": "National Academy of Sciences", "pagerange": "20257-20262", "id_number": "CaltechAUTHORS:20101213-155449831", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101213-155449831", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Fonds Quebecois de la Recherche sur la Nature et les Technologies" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "doi": "10.1073/pnas.1013910107", "pmcid": "PMC2996648", "primary_object": { "basename": "Chica2010p12091P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/jzfye-qpv61/files/Chica2010p12091P_Natl_Acad_Sci_Usa.pdf" }, "related_objects": [ { "basename": "pnas.1013910107_SI.pdf", "url": "https://authors.library.caltech.edu/records/jzfye-qpv61/files/pnas.1013910107_SI.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Chica, Roberto A.; Moore, Matthew M.; et el." }, { "id": "https://authors.library.caltech.edu/records/rpdwy-yzp55", "eprint_id": 21335, "eprint_status": "archive", "datestamp": "2023-08-22 01:22:20", "lastmod": "2023-10-20 23:57:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Allen-B-D", "name": { "family": "Allen", "given": "Benjamin D." }, "orcid": "0000-0001-6914-5572" }, { "id": "Nisthal-A", "name": { "family": "Nisthal", "given": "Alex" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles", "ispublished": "pub", "full_text_status": "public", "keywords": "protein engineering; high-throughput stability determination; library design; molecular dynamics; NMR ensemble", "note": "\u00a9 2010 by the National Academy of Sciences.\n\nContributed by Stephen L. Mayo, September 7, 2010 (sent for review April 20, 2010).\nPublished online before print November 2, 2010.\n\nWe thank Barry Olafson for preparation of the MD\nstructural ensembles, Christina Vizcarra for the pInSALect plasmid, and Jost\nVielmetter for useful discussions. This work was supported by the Howard\nHughes Medical Institute, the Defense Advanced Research Projects Agency,\nand the National Security Science and Engineering Faculty Fellowship.\n\nAuthor contributions: B.D.A. and A.N. designed research; B.D.A. and A.N. performed\nresearch; B.D.A., A.N., and S.L.M. analyzed data; and B.D.A., A.N., and S.L.M. wrote\nthe paper.\n\nPublished - Allen2010p12095P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - pnas.1012985107_SI.pdf
", "abstract": "The stability, activity, and solubility of a protein sequence are determined by a delicate balance of molecular interactions in a variety of conformational states. Even so, most computational protein design methods model sequences in the context of a single native conformation. Simulations that model the native state as an ensemble have been mostly neglected due to the lack of sufficiently powerful optimization algorithms for multistate design. Here, we have applied our multistate design algorithm to study the potential utility of various forms of input structural data for design. To facilitate a more thorough analysis, we developed new methods for the design and high-throughput stability determination of combinatorial mutation libraries based on protein design calculations. The application of these methods to the core design of a small model system produced many variants with improved thermodynamic stability and showed that multistate design methods can be readily applied to large structural ensembles. We found that exhaustive screening of our designed libraries helped to clarify several sources of simulation error that would have otherwise been difficult to ascertain. Interestingly, the lack of correlation between our simulated and experimentally measured stability values shows clearly that a design procedure need not reproduce experimental data exactly to achieve success. This surprising result suggests potentially fruitful directions for the improvement of computational protein design technology.", "date": "2010-11-16", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "107", "number": "46", "publisher": "National Academy of Sciences", "pagerange": "19838-19843", "id_number": "CaltechAUTHORS:20101213-150517069", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101213-150517069", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "National Security Science and Engineering Faculty Fellowship" } ] }, "doi": "10.1073/pnas.1012985107", "pmcid": "PMC2993350", "primary_object": { "basename": "Allen2010p12095P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/rpdwy-yzp55/files/Allen2010p12095P_Natl_Acad_Sci_Usa.pdf" }, "related_objects": [ { "basename": "pnas.1012985107_SI.pdf", "url": "https://authors.library.caltech.edu/records/rpdwy-yzp55/files/pnas.1012985107_SI.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Allen, Benjamin D.; Nisthal, Alex; et el." }, { "id": "https://authors.library.caltech.edu/records/zsj9r-zmd85", "eprint_id": 17912, "eprint_status": "archive", "datestamp": "2023-08-21 23:45:16", "lastmod": "2023-10-20 15:24:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Allen-B-D", "name": { "family": "Allen", "given": "Benjamin D." }, "orcid": "0000-0001-6914-5572" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "An efficient algorithm for multistate protein design based on FASTER", "ispublished": "pub", "full_text_status": "restricted", "keywords": "protein design; multistate design; negative design; FASTER; Monte Carlo", "note": "\u00a9 2009 Wiley Periodicals, Inc.\nReceived 10 October 2006; Revised 27 April 2009; Accepted 7 June 2009.\nPublished online 27 July 2009.\n\nContract/grant sponsors: Howard Hughes Medical Institute, Ralph M.\nParsons Foundation, IBM Shared University Research Grant, Defense\nAdvanced Research Projects Agency.\nThe authors thank Kyle Lassila, Christina Vizcarra, Jennifer\nKeeffe, and an anonymous reviewer for their insightful comments.", "abstract": "Most of the methods that have been developed for computational protein design involve the selection of side-chain conformations in the context of a single, fixed main-chain structure. In contrast, multistate design (MSD) methods allow sequence selection to be driven by the energetic contributions of multiple structural or chemical states simultaneously. This methodology is expected to be useful when the design target is an ensemble of related states rather than a single structure, or when a protein sequence must assume several distinct conformations to function. MSD can also be used with explicit negative design to suggest sequences with altered structural, binding, or catalytic specificity. We report implementation details of an efficient multistate design optimization algorithm based on FASTER (MSD-FASTER). We subjected the algorithm to a battery of computational tests and found it to be generally applicable to various multistate design problems; designs with a large number of states and many designed positions are completely feasible. A direct comparison of MSD-FASTER and multistate design Monte Carlo indicated that MSD-FASTER discovers low-energy sequences much more consistently. MSD-FASTER likely performs better because amino acid substitutions are chosen on an energetic basis rather than randomly, and because multiple substitutions are applied together. Through its greater efficiency, MSD-FASTER should allow protein designers to test experimentally better-scoring sequences, and thus accelerate progress in the development of improved scoring functions and models for computational protein design.", "date": "2010-04-15", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "31", "number": "5", "publisher": "Wliey", "pagerange": "904-916", "id_number": "CaltechAUTHORS:20100409-095211072", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100409-095211072", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "doi": "10.1002/jcc.21375", "resource_type": "article", "pub_year": "2010", "author_list": "Allen, Benjamin D. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/nnmvt-qpd81", "eprint_id": 14235, "eprint_status": "archive", "datestamp": "2023-08-22 12:55:06", "lastmod": "2023-10-18 16:25:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Crowhurst-A-K", "name": { "family": "Crowhurst", "given": "Karin A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "NMR-detected conformational exchange observed in a computationally designed variant of protein G\u03b21", "ispublished": "pub", "full_text_status": "public", "keywords": "backbone dynamics; computational protein design; conformational exchange; ORBIT/protein G\u03b21", "note": "\u00a9 2008 Oxford University Press. PEDS Advance Access originally published online on June 26, 2008. Received May 21, 2008; revised May 21, 2008; accepted May 23, 2008 \n\nEdited by Frances H. Arnold \n\nThe authors would like to thank Drs Julie Forman-Kay, John Love and\nKevin Plaxco for insightful comments on the manuscript, as well as Drs Andrew Chong, Kevin Gardner, Lewis Kay, Dorothee Kern, Gregory Lee and Leo Spyracopoulos for advice on experiments and data analysis. We are also grateful to Dr Scott Ross for NMR assistance and Mr. Ben Allen for his\ncomputational expertise. \n\nFunding\nNatural Sciences and Engineering Research Council of\nCanada (Postdoctoral Fellowship to K.A.C.); Howard Hughes\nMedical Institute. \n\nSupplementary data, including R1, R2\u00b0 (transverse relaxation rate constant that is free of chemical/conformational exchange contributions), NOE, {eta}xy, {eta}z and Rex data are provided for wild-type protein G\u03b21 and for the {Delta}1.5 variant at two concentrations, and are available at PEDS online.\n\nSupplemental Material - gzn035supp.txt
", "abstract": "Detailed biophysical characterization of computationally designed proteins has become increasingly important in order to thoroughly understand the properties of these variants compared with wild-type and to apply this knowledge to future designs. The protein dynamics and structural properties of a computationally designed variant (\u03941.5) of the \u03b21 domain of streptococcal protein G (G\u03b21) were measured using multinuclear NMR methods. Results from relaxation, diffusion and hydrogen exchange experiments indicate that the variant weakly self-associates at NMR concentrations, with evidence for multiple binding sites. Although comparison of fast (ps\u2013ns) timescale motions shows only small differences in dynamics between \u03941.5 and wild-type, results from the measurement of intermediate (\u00b5s\u2013ms) timescale motions are very different. Significant backbone conformational exchange has been observed in the variant at positions all along the sequence, whereas the wild-type G\u03b21 shows little evidence for this type of motion. This increased conformational exchange in \u03941.5 has been attributed to core overpacking resulting from the incorporation of two large hydrophobic side chains and the loss of an aromatic T-stacking interaction. These data highlight, in detail, the potential consequences of incorporating major perturbations in the core of a protein and the need to carry out more detailed analyses of the biophysical properties of designed proteins in order to better understand and predict the effects of mutations.", "date": "2008-09", "date_type": "published", "publication": "Protein Engineering, Design and Selection", "volume": "21", "number": "9", "publisher": "Oxford University Press", "pagerange": "577-587", "id_number": "CaltechAUTHORS:20090515-095406688", "issn": "1741-0126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090515-095406688", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1093/protein/gzn035", "primary_object": { "basename": "gzn035supp.txt", "url": "https://authors.library.caltech.edu/records/nnmvt-qpd81/files/gzn035supp.txt" }, "resource_type": "article", "pub_year": "2008", "author_list": "Crowhurst, Karin A. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/vf7k3-gb859", "eprint_id": 11513, "eprint_status": "archive", "datestamp": "2023-08-22 12:47:49", "lastmod": "2023-10-17 15:06:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Alvizo-O", "name": { "family": "Alvizo", "given": "Oscar" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Evaluating and optimizing computational protein design force fields using fixed composition-based negative design", "ispublished": "pub", "full_text_status": "public", "keywords": "fixed amino acid composition; force field optimization; random energy model", "note": "\u00a9 2008 by the National Academy of Sciences. Freely available online through the PNAS open access option. \n\nContributed by Stephen L. Mayo, June 17, 2008 (received for review November 5, 2007). \n\nWe thank Marie Ary for help with the manuscript, Scott Ross and Karin Crowhurst for their assistance with NMR, and Ben Allen for preparation of the conformer library. This work was supported by the Ralph M. Parsons Foundation, the Howard Hughes Medical Institute, and the National Institutes of Health. \n\nAuthor contributions: O.A. and S.L.M. designed research; O.A. performed research; O.A. and S.L.M. analyzed data; and O.A. and S.L.M. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article contains supporting information online at www.pnas.org/cgi/content/full/0805858105/DCSupplemental.\n\nPublished - ALVpnas08.pdf
Supplemental Material - ALVpnas08supp.pdf
", "abstract": "An accurate force field is essential to computational protein design and protein fold prediction studies. Proper force field tuning is problematic, however, due in part to the incomplete modeling of the unfolded state. Here, we evaluate and optimize a protein design force field by constraining the amino acid composition of the designed sequences to that of a well behaved model protein. According to the random energy model, unfolded state energies are dependent only on amino acid composition and not the specific arrangement of amino acids. Therefore, energy discrepancies between computational predictions and experimental results, for sequences of identical composition, can be directly attributed to flaws in the force field's ability to properly account for folded state sequence energies. This aspect of fixed composition design allows for force field optimization by focusing solely on the interactions in the folded state. Several rounds of fixed composition optimization of the 56-residue \u03b21 domain of protein G yielded force field parameters with significantly greater predictive power: Optimized sequences exhibited higher wild-type sequence identity in critical regions of the structure, and the wild-type sequence showed an improved Z-score. Experimental studies revealed a designed 24-fold mutant to be stably folded with a melting temperature similar to that of the wild-type protein. Sequence designs using engrailed homeodomain as a scaffold produced similar results, suggesting the tuned force field parameters were not specific to protein G.", "date": "2008-08-26", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "105", "number": "34", "publisher": "National Academy of Sciences", "pagerange": "12242-12247", "id_number": "CaltechAUTHORS:ALVpnas08", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:ALVpnas08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF" } ] }, "doi": "10.1073/pnas.0805858105", "pmcid": "PMC2516967", "primary_object": { "basename": "ALVpnas08supp.pdf", "url": "https://authors.library.caltech.edu/records/vf7k3-gb859/files/ALVpnas08supp.pdf" }, "related_objects": [ { "basename": "ALVpnas08.pdf", "url": "https://authors.library.caltech.edu/records/vf7k3-gb859/files/ALVpnas08.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Alvizo, Oscar and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/94s3y-3rh38", "eprint_id": 24050, "eprint_status": "archive", "datestamp": "2023-08-19 22:35:36", "lastmod": "2023-10-23 20:16:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Vizcarra-C-L", "name": { "family": "Vizcarra", "given": "Christina L." } }, { "id": "Zhang-Naigong", "name": { "family": "Zhang", "given": "Naigong" } }, { "id": "Marshall-S-A", "name": { "family": "Marshall", "given": "Shannon A." } }, { "id": "Wingreen-N-S", "name": { "family": "Wingreen", "given": "Ned S." } }, { "id": "Zeng-Chen", "name": { "family": "Zeng", "given": "Chen" }, "orcid": "0000-0003-2829-5018" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Static Electricity, Reproducibility of Results, Thermodynamics, Computational Biology, Computer Simulation, Computer-Aided Design, Models: Chemical, Amino Acids, Proteins, Poisson Distribution, Poisson-Boltzmann, Protein Design, Continuum Solvation, Electrostatics", "note": "\u00a9 2007 Wiley Periodicals, Inc.\nReceived 16 December 2006; Revised 1 October 2007; Accepted 17 October 2007.\nArticle first published online: 11 Dec. 2007.", "abstract": "Our goal is to develop accurate electrostatic models that can be implemented in current computational protein design protocols. To this end, we improve upon a previously reported pairwise decomposable, finite difference Poisson-Boltzmann (FDPB) model for protein design (Marshall et al., Protein Sci 2005, 14, 1293). The improvement involves placing generic sidechains at positions with unknown amino acid identity and explicitly capturing two-body perturbations to the dielectric environment. We compare the original and improved FDPB methods to standard FDPB calculations in which the dielectric environment is completely determined by protein atoms. The generic sidechain approach yields a two to threefold increase in accuracy per residue or residue pair over the original pairwise FDPB implementation, with no additional computational cost. Distance dependent dielectric and solvent-exclusion models were also compared with standard FDPB energies. The accuracy of the new pairwise FDPB method is shown to be superior to these models, even after reparameterization of the solvent-exclusion model.", "date": "2008-05", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "29", "number": "7", "publisher": "Wliey", "pagerange": "1153-1162", "id_number": "CaltechAUTHORS:20110617-165335622", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110617-165335622", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1002/jcc.20878", "resource_type": "article", "pub_year": "2008", "author_list": "Vizcarra, Christina L.; Zhang, Naigong; et el." }, { "id": "https://authors.library.caltech.edu/records/x03xj-kgk53", "eprint_id": 25321, "eprint_status": "archive", "datestamp": "2023-08-22 10:37:18", "lastmod": "2023-10-24 15:47:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Huang-Po-Ssu", "name": { "family": "Huang", "given": "Po-Ssu" } }, { "id": "Love-John-J", "name": { "family": "Love", "given": "John J." }, "orcid": "0000-0001-7220-0923" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "A de novo designed protein-protein interface", "ispublished": "pub", "full_text_status": "public", "keywords": "de novo protein\u2013protein interface; computational protein design; geometric recognition algorithm; protein G; heterodimer; NMR; docking", "note": "\u00a9 2007 The Protein Society. Published by Cold Spring Harbor Laboratory Press. \n\nReceived July 16, 2007; Final Revision September 21, 2007; Accepted September 21, 2007. \n\nThis work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, DARPA, the Institute for Collaborative Biotechnologies through grant DAAD19-03-D-0004 from the U.S. Army Research Office, and an IBM Shared University Research Grant.\n\nPublished - Huang_2007_Protein_Sci._A_de_novo_designed_protein-protein.pdf
Supplemental Material - Huang_Supp.pdf
", "abstract": "As an approach to both explore the physical/chemical parameters that drive molecular self-assembly and to generate novel protein oligomers, we have developed a procedure to generate protein dimers from monomeric proteins using computational protein docking and amino acid sequence design. A fast Fourier transform-based docking algorithm was used to generate a model for a dimeric version of the 56-amino-acid \u03b21 domain of streptococcal protein G. Computational amino acid sequence design of 24 residues at the dimer interface resulted in a heterodimer comprised of 12-fold and eightfold variants of the wild-type protein. The designed proteins were expressed, purified, and characterized using analytical ultracentrifugation and heteronuclear NMR techniques. Although the measured dissociation constant was modest (~300 \u00b5M), 2D-[^1H,^(15)N]-HSQC NMR spectra of one of the designed proteins in the absence and presence of its binding partner showed clear evidence of specific dimer formation.", "date": "2007-12", "date_type": "published", "publication": "Protein Science", "volume": "16", "number": "12", "publisher": "Wiley", "pagerange": "2770-2774", "id_number": "CaltechAUTHORS:20110913-160000725", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-160000725", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Army Research Office (ARO)", "grant_number": "DAAD19-03-D-0004" }, { "agency": "IBM" } ] }, "doi": "10.1110/ps.073125207", "pmcid": "PMC2222823", "primary_object": { "basename": "Huang_2007_Protein_Sci._A_de_novo_designed_protein-protein.pdf", "url": "https://authors.library.caltech.edu/records/x03xj-kgk53/files/Huang_2007_Protein_Sci._A_de_novo_designed_protein-protein.pdf" }, "related_objects": [ { "basename": "Huang_Supp.pdf", "url": "https://authors.library.caltech.edu/records/x03xj-kgk53/files/Huang_Supp.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Huang, Po-Ssu; Love, John J.; et el." }, { "id": "https://authors.library.caltech.edu/records/w2t3d-npm31", "eprint_id": 25323, "eprint_status": "archive", "datestamp": "2023-08-22 09:59:00", "lastmod": "2023-10-24 15:47:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shah-P-S", "name": { "family": "Shah", "given": "Premal S." } }, { "id": "Hom-G-K", "name": { "family": "Hom", "given": "Geoffrey K" } }, { "id": "Ross-S-A", "name": { "family": "Ross", "given": "Scott A." } }, { "id": "Lassila-J-K", "name": { "family": "Lassila", "given": "Jonathan Kyle" } }, { "id": "Crowhurst-A-K", "name": { "family": "Crowhurst", "given": "Karin A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Full-sequence computational design and solution structure of a thermostable protein variant", "ispublished": "pub", "full_text_status": "restricted", "keywords": "computational protein design; NMR structure; protein stability; engrailed homeodomain; FASTER", "note": "\u00a9 2007 Elsevier Ltd. Received 20 March 2007; received in revised form 7 June 2007; accepted 11 June 2007, Available online 16 June 2007. This work was supported by the National\nInstitutes of Health (P.S.S. and G.K.H.), the Ralph\nM. Parsons Foundation, and the Howard Hughes\nMedical Institute.", "abstract": "Computational protein design procedures were applied to the redesign of the entire sequence of a 51 amino acid residue protein, Drosophila melanogaster engrailed homeodomain. Various sequence optimization algorithms were compared and two resulting designed sequences were experimentally evaluated. The two sequences differ by 11 mutations and share 22% and 24% sequence identity with the wild-type protein. Both computationally designed proteins were considerably more stable than the naturally occurring protein, with midpoints of thermal denaturation greater than 99 degrees C. The solution structure was determined for one of the two sequences using multidimensional heteronuclear NMR spectroscopy, and the structure was found to closely match the original design template scaffold.", "date": "2007-09-07", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "372", "number": "1", "publisher": "Elsevier", "pagerange": "1-6", "id_number": "CaltechAUTHORS:20110913-160001277", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-160001277", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.jmb.2007.06.032", "resource_type": "article", "pub_year": "2007", "author_list": "Shah, Premal S.; Hom, Geoffrey K; et el." }, { "id": "https://authors.library.caltech.edu/records/ep4vd-c4853", "eprint_id": 25322, "eprint_status": "archive", "datestamp": "2023-08-19 20:40:44", "lastmod": "2023-10-24 15:47:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pluckthun-A", "name": { "family": "Pl\u00fcckthun", "given": "Andreas" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "The design of evolution and the evolution of design", "ispublished": "pub", "full_text_status": "restricted", "note": "Copyright \u00a9 2007 Published by Elsevier Ltd.", "abstract": "N/A", "date": "2007-08", "date_type": "published", "publication": "Current Opinion in Structural Biology", "volume": "17", "number": "4", "publisher": "Elsevier", "pagerange": "451-453", "id_number": "CaltechAUTHORS:20110913-160001099", "issn": "0959-440X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-160001099", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.sbi.2007.08.020", "resource_type": "article", "pub_year": "2007", "author_list": "Pl\u00fcckthun, Andreas and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/xag0h-5m968", "eprint_id": 25325, "eprint_status": "archive", "datestamp": "2023-08-22 09:19:03", "lastmod": "2023-10-24 15:47:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lassila-J-K", "name": { "family": "Lassila", "given": "Jonathan Kyle" } }, { "id": "Keeffe-J-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "id": "Kast-Peter", "name": { "family": "Kast", "given": "Peter" }, "orcid": "0000-0002-0209-8975" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Exhaustive mutagenesis of six secondary active-site residues in Escherichia coli chorismate mutase shows the importance of hydrophobic side chains and a helix N-capping position for stability and catalysis", "ispublished": "pub", "full_text_status": "public", "keywords": "Amino Acid Sequence; Bacterial Proteins; Protein Conformation; Amino Acid Substitution; Models: Molecular; Catalysis; Mutagenesis: Site-Directed; Escherichia coli Proteins; Binding Sites; Chorismate Mutase; Enzyme Stability; Sequence Alignment; Escherichia coli; Recombinant Proteins", "note": "\u00a9 2007 American Chemical Society. \n\nReceived January 31, 2007; Revised Manuscript Received April 12, 2007, Published on Web 05/17/2007. \n\nThis work was supported by the Howard Hughes Medical Institute, the Defense Advanced Research Projects Agency, the Institute for Collaborative Biotechnologies (ARO), the Ralph M. Parsons foundation, and an IBM Shared University Research Grant.\n\nSupplemental Material - Mayo_Biochemistry_2007_supp.pdf
", "abstract": "Secondary active-site residues in enzymes, including hydrophobic amino acids, may contribute to catalysis through critical interactions that position the reacting molecule, organize hydrogen-bonding residues, and define the electrostatic environment of the active site. To ascertain the tolerance of an important model enzyme to mutation of active-site residues that do not directly hydrogen bond with the reacting molecule, all 19 possible amino acid substitutions were investigated in six positions of the engineered chorismate mutase domain of the Escherichia coli chorismate mutase-prephenate dehydratase. The six secondary active-site residues were selected to clarify results of a previous test of computational enzyme design procedures. Five of the positions encode hydrophobic side chains in the wild-type enzyme, and one forms a helix N-capping interaction as well as a salt bridge with a catalytically essential residue. Each mutant was evaluated for its ability to complement an auxotrophic chorismate mutase deletion strain. Kinetic parameters and thermal stabilities were measured for variants with in vivo activity. Altogether, we find that the enzyme tolerated 34% of the 114 possible substitutions, with a few mutations leading to increases in the catalytic efficiency of the enzyme. The results show the importance of secondary amino acid residues in determining enzymatic activity, and they point to strengths and weaknesses in current computational enzyme design procedures.", "date": "2007-06-12", "date_type": "published", "publication": "Biochemistry", "volume": "46", "number": "23", "publisher": "American Chemical Society", "pagerange": "6883-6891", "id_number": "CaltechAUTHORS:20110913-160001644", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-160001644", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Army Research Office (ARO)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" } ] }, "doi": "10.1021/bi700215x", "primary_object": { "basename": "Mayo_Biochemistry_2007_supp.pdf", "url": "https://authors.library.caltech.edu/records/xag0h-5m968/files/Mayo_Biochemistry_2007_supp.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Lassila, Jonathan Kyle; Keeffe, Jennifer R.; et el." }, { "id": "https://authors.library.caltech.edu/records/cnsz0-3q551", "eprint_id": 24006, "eprint_status": "archive", "datestamp": "2023-08-19 19:55:47", "lastmod": "2023-10-23 20:14:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Choi-E-J", "name": { "family": "Choi", "given": "Eun Jung" } }, { "id": "Mao-Jessica", "name": { "family": "Mao", "given": "Jessica" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Biosensing Techniques, 2-Naphthylamine, Circular Dichroism, Carrier Proteins, Models: Molecular, Zea mays, Spectrometry: Fluorescence", "note": "\u00a9 2007 The Protein Society. \nPublished by Cold Spring Harbor Laboratory Press.\nReceived October 9, 2006; Final Revision October 9, 2006; Accepted December 9, 2006. \nArticle first published online: 2 Jan. 2009.\n\n\nWe thank Marie Ary for editing the manuscript. This work was\nsupported by the Howard Hughes Medical Institute, the Ralph\nM. Parsons Foundation, the Army Research Office (Institute of Collaborative Biotechnologies), and an IBM Shared University Research Grant.", "abstract": "Lipid transfer proteins (LTPs) are a family of proteins that bind and transfer lipids. Utilizing the maize LTP,\nwe have successfully engineered fluorescent reagentless biosensors for the natural ligand of LTPs; this was\nachieved by using computational protein design to remove a disulfide bridge and attaching a thio-reactive\nfluorophore. Conformational change induced by ligand titration is thought to affect the fluorescence of the\nfluorophore, allowing detection of ligand binding. Fluorescence measurements show that our LTP variants\nhave affinity to palmitate that is consistent with wild-type LTP. These molecules have the potential to be\nutilized as scaffolds to design hydrophobic ligand biosensors or to serve as drug carriers.", "date": "2007-04", "date_type": "published", "publication": "Protein Science", "volume": "16", "number": "4", "publisher": "Wiley", "pagerange": "582-588", "id_number": "CaltechAUTHORS:20110614-141918849", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110614-141918849", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Army Research Office (ARO)" }, { "agency": "IBM" } ] }, "doi": "10.1110/ps.062607007", "pmcid": "PMC2203350", "resource_type": "article", "pub_year": "2007", "author_list": "Choi, Eun Jung; Mao, Jessica; et el." }, { "id": "https://authors.library.caltech.edu/records/dp7g9-mgq49", "eprint_id": 8632, "eprint_status": "archive", "datestamp": "2023-08-22 08:36:04", "lastmod": "2023-10-16 21:36:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zong-Chenghang", "name": { "family": "Zong", "given": "Chenghang" } }, { "id": "Wilson-C-J", "name": { "family": "Wilson", "given": "Corey J." } }, { "id": "Shen-Tongye", "name": { "family": "Shen", "given": "Tongye" } }, { "id": "Wittung-Stafshede-P", "name": { "family": "Wittung-Stafshede", "given": "Pernilla" }, "orcid": "0000-0003-1058-1964" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Wolynes-P-G", "name": { "family": "Wolynes", "given": "Peter G." } } ] }, "title": "Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin", "ispublished": "pub", "full_text_status": "public", "keywords": "curved chevron, cupredoxin, metalloproteins", "note": "\u00a9 2007 by the National Academy of Sciences. \n\nContributed by Peter G. Wolynes, December 15, 2006 (received for review December 11, 2006). Published online before print February 14, 2007, 10.1073/pnas.0611149104 \n\nWe thank Jay R. Winkler and Harry B. Gray for helpful suggestions throughout the project and critical comments on the manuscript. Support for this project was provided by National Science Foundation Grant 0610425 (to C.J.W.), Gordon E. Moore Foundation Grant P449351 (to C.J.W.), National Institutes of Health Grants GM44557 (to P.G.W.) and GM059663 (to P.W.-S.), and Robert A. Welch Foundation Grant C-1588 (to P.W.-S.). \n\nAuthor contributions: C.Z., C.J.W., T.S., P.W.-S., S.L.M., and P.G.W. designed research; C.Z., C.J.W., and T.S. performed research; C.Z. and C.J.W. analyzed data; and C.Z., C.J.W., and P.G.W. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article contains supporting information online at www.pnas.org/cgi/content/full/0611149104/DC1.\n\nPublished - ZONpnas07.pdf
Supplemental Material - ZONpnas07supfig6.pdf
Supplemental Material - ZONpnas07supfig7.pdf
Supplemental Material - ZONpnas07supfig8.pdf
", "abstract": "Understanding how the folding of proteins establishes their functional characteristics at the molecular level challenges both theorists and experimentalists. The simplest test beds for confronting this issue are provided by electron transfer proteins. The environment provided by the folded protein to the cofactor tunes the metal's electron transport capabilities as envisioned in the entatic hypothesis. To see how the entatic state is achieved one must study how the folding landscape affects and in turn is affected by the metal. Here, we develop a coarse-grained functional to explicitly model how the coordination of the metal (which results in a so-called entatic or rack-induced state) modifies the folding of the metallated Pseudomonas aeruginosa azurin. Our free-energy functional-based approach directly yields the proper nonlinear extra-thermodynamic free energy relationships for the kinetics of folding the wild type and several point-mutated variants of the metallated protein. The results agree quite well with corresponding laboratory experiments. Moreover, our modified free-energy functional provides a sufficient level of detail to explicitly model how the geometric entatic state of the metal modifies the dynamic folding nucleus of azurin.", "date": "2007-02-27", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "104", "number": "9", "publisher": "National Academy of Sciences", "pagerange": "3159-3164", "id_number": "CaltechAUTHORS:ZONpnas07", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:ZONpnas07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "0610425" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "P449351" }, { "agency": "NIH", "grant_number": "GM44557" }, { "agency": "NIH", "grant_number": "GM059663" }, { "agency": "Robert A. Welch Foundation", "grant_number": "C-1588" } ] }, "doi": "10.1073/pnas.0611149104", "pmcid": "PMC1805512", "primary_object": { "basename": "ZONpnas07.pdf", "url": "https://authors.library.caltech.edu/records/dp7g9-mgq49/files/ZONpnas07.pdf" }, "related_objects": [ { "basename": "ZONpnas07supfig6.pdf", "url": "https://authors.library.caltech.edu/records/dp7g9-mgq49/files/ZONpnas07supfig6.pdf" }, { "basename": "ZONpnas07supfig7.pdf", "url": "https://authors.library.caltech.edu/records/dp7g9-mgq49/files/ZONpnas07supfig7.pdf" }, { "basename": "ZONpnas07supfig8.pdf", "url": "https://authors.library.caltech.edu/records/dp7g9-mgq49/files/ZONpnas07supfig8.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Zong, Chenghang; Wilson, Corey J.; et el." }, { "id": "https://authors.library.caltech.edu/records/8a1gj-wyn52", "eprint_id": 8428, "eprint_status": "archive", "datestamp": "2023-08-22 08:05:37", "lastmod": "2023-10-16 21:28:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Treynor-T-P", "name": { "family": "Treynor", "given": "Thomas P." } }, { "id": "Vizcarra-C-L", "name": { "family": "Vizcarra", "given": "Christina L." } }, { "id": "Nedelcu-D", "name": { "family": "Nedelcu", "given": "Daniel" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function", "ispublished": "pub", "full_text_status": "public", "keywords": "GFP; library design; protein design; protein engineering; high-throughput screening", "note": "\u00a9 2007 by The National Academy of Sciences of the USA \n\nContributed by Stephen L. Mayo, October 31, 2006 (received for review August 11, 2006) Published online before print December 19, 2006, 10.1073/pnas.0609647103 \n\nWe thank Patrick Daugherty (University of California, Santa Barbara, CA) for providing many of the primers used to assemble GFP-S65T and a pBAD-derived vector engineered with SfiI recognition sequences; Christina Smolke for the use of her plate reader; Marco Mena, Michelle Meyer, and Frances Arnold for advice in designing this project; and Marie Ary for useful comments on the manuscript. This research was supported by the Howard Hughes Medical Institute and the Army Research Office. T.P.T. was supported by National Institutes of Health Grant F32-GM07438. C.L.V. was supported by a National Science Foundation Graduate Research Fellowship. \n\nAuthor contributions: T.P.T. and S.L.M. designed research; T.P.T., C.L.V., and D.N. performed research; T.P.T. contributed new reagents/analytic tools; T.P.T. and C.L.V. analyzed data; and T.P.T. wrote the paper.\n\nThe authors declare no conflict of interest.\n\nThis article contains supporting information online at www.pnas.org/cgi/content/full/0609647103/DC1.\n\nPublished - TREpnas07.pdf
Supplemental Material - 09647Fig5.pdf
Supplemental Material - 09647Fig6.pdf
Supplemental Material - 09647Fig7.pdf
Supplemental Material - 09647Fig8.pdf
Supplemental Material - 09647Fig9.pdf
", "abstract": "To determine which of seven library design algorithms best introduces new protein function without destroying it altogether, seven combinatorial libraries of green fluorescent protein variants were designed and synthesized. Each was evaluated by distributions of emission intensity and color compiled from measurements made in vivo. Additional comparisons were made with a library constructed by error-prone PCR. Among the designed libraries, fluorescent function was preserved for the greatest fraction of samples in a library designed by using a structure-based computational method developed and described here. A trend was observed toward greater diversity of color in designed libraries that better preserved fluorescence. Contrary to trends observed among libraries constructed by error-prone PCR, preservation of function was observed to increase with a library's average mutation level among the four libraries designed with structure-based computational methods.", "date": "2007-01-02", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "104", "number": "1", "publisher": "National Academy of Sciences", "pagerange": "48-53", "id_number": "CaltechAUTHORS:TREpnas07", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:TREpnas07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Army Research Office (ARO)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32-GM07438" }, { "agency": "NSF Graduate Research Fellowship" } ] }, "doi": "10.1073/pnas.0609647103", "pmcid": "PMC1765474", "primary_object": { "basename": "09647Fig5.pdf", "url": "https://authors.library.caltech.edu/records/8a1gj-wyn52/files/09647Fig5.pdf" }, "related_objects": [ { "basename": "09647Fig6.pdf", "url": "https://authors.library.caltech.edu/records/8a1gj-wyn52/files/09647Fig6.pdf" }, { "basename": "09647Fig7.pdf", "url": "https://authors.library.caltech.edu/records/8a1gj-wyn52/files/09647Fig7.pdf" }, { "basename": "09647Fig8.pdf", "url": "https://authors.library.caltech.edu/records/8a1gj-wyn52/files/09647Fig8.pdf" }, { "basename": "09647Fig9.pdf", "url": "https://authors.library.caltech.edu/records/8a1gj-wyn52/files/09647Fig9.pdf" }, { "basename": "TREpnas07.pdf", "url": "https://authors.library.caltech.edu/records/8a1gj-wyn52/files/TREpnas07.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Treynor, Thomas P.; Vizcarra, Christina L.; et el." }, { "id": "https://authors.library.caltech.edu/records/tv0gs-1mt95", "eprint_id": 25319, "eprint_status": "archive", "datestamp": "2023-08-22 08:01:38", "lastmod": "2023-10-24 15:47:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Alvizo-O", "name": { "family": "Alvizo", "given": "Oscar" } }, { "id": "Allen-B-D", "name": { "family": "Allen", "given": "Benjamin D." }, "orcid": "0000-0001-6914-5572" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computational protein design promises to revolutionize protein engineering", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Computer Simulation; Models, Molecular; Protein Conformation; Protein Engineering/methods", "note": "\u00a9 2007 BioTechniques. O.A. and B.D.A. contributed equally to this work.", "abstract": "Natural evolution has produced an astounding array of proteins that perform the physical and chemical functions required for life on Earth. Although proteins can be reengineered to provide altered or novel functions, the utility of this approach is limited by the difficulty of identifying protein sequences that display the desired properties. Recently, advances in the field of computational protein design (CPD) have shown that molecular simulation can help to predict sequences with new and improved functions. In the past few years, CPD has been used to design protein variants with optimized specificity of binding to DNA, small molecules, peptides, and other proteins. Initial successes in enzyme design highlight CPD's unique ability to design function de novo. The use of CPD for the engineering of potential therapeutic agents has demonstrated its strength in real-life applications.", "date": "2007-01", "date_type": "published", "publication": "BioTechniques", "volume": "42", "number": "1", "publisher": "Informa Healthcare", "pagerange": "31-39", "id_number": "CaltechAUTHORS:20110913-152351498", "issn": "0736-6205", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-152351498", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.2144/000112336", "resource_type": "article", "pub_year": "2007", "author_list": "Alvizo, Oscar; Allen, Benjamin D.; et el." }, { "id": "https://authors.library.caltech.edu/records/19jg4-dm682", "eprint_id": 24132, "eprint_status": "archive", "datestamp": "2023-08-19 18:58:14", "lastmod": "2023-10-23 20:19:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mena-M-A", "name": { "family": "Mena", "given": "Marco A." } }, { "id": "Treynor-T-P", "name": { "family": "Treynor", "given": "Thomas P." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Daugherty-P-S", "name": { "family": "Daugherty", "given": "Patrick S." } } ] }, "title": "Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Nature Publishing Group.\nReceived 5 July; accepted 11 October; published online 19 November 2006.\nThe authors thank K. Dane, A. Nguyen, P. Bessette and C. Gottstein for helpful\ndiscussions and Alexander Mikhailovsky for assistance with fluorescence lifetime\nmeasurements, and acknowledge support from National Institutes of Health\u2013National Institute of Biomedical Imaging and Bioengineering grant EB-000205.\nAuthor Contributions: M.A.M., T.P.T., S.L.M. and P.S.D. designed research, M.A.M. and T.P.T. performed\nresearch, T.P.T. and S.L.M. contributed computational tools, M.A.M.,\nT.P.T. and P.S.D. analyzed data, and M.A.M. and P.S.D. wrote the paper.\n\nSupplemental Material - Fig1.pdf
Supplemental Material - Fig2.pdf
Supplemental Material - Fig3.pdf
Supplemental Material - Fig4.pdf
Supplemental Material - Fig5.pdf
Supplemental Material - Fig6.pdf
Supplemental Material - Fig7.pdf
Supplemental Material - Fig8.pdf
Supplemental Material - Methods.pdf
Supplemental Material - Table1.pdf
Supplemental Material - Table2.pdf
", "abstract": "The utility of blue fluorescent protein (BFP) has been limited by its low quantum yield and rapid photobleaching. A library targeting residues neighboring the chromophore yielded a variant with enhanced quantum yield (0.55 versus 0.34), reduced pH sensitivity and a 40-fold increase in photobleaching half-life. This BFP, named Azurite, is well expressed in bacterial and mammalian cells and extends the palette of fluorescent proteins that can be used for imaging.", "date": "2006-12", "date_type": "published", "publication": "Nature Biotechnology", "volume": "24", "number": "12", "publisher": "Nature Publishing Group", "pagerange": "1569-1571", "id_number": "CaltechAUTHORS:20110620-160435158", "issn": "1087-0156", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160435158", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "EB-000205" } ] }, "doi": "10.1038/nbt1264", "primary_object": { "basename": "Fig1.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Fig1.pdf" }, "related_objects": [ { "basename": "Fig5.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Fig5.pdf" }, { "basename": "Fig7.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Fig7.pdf" }, { "basename": "Methods.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Methods.pdf" }, { "basename": "Fig2.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Fig2.pdf" }, { "basename": "Fig3.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Fig3.pdf" }, { "basename": "Fig4.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Fig4.pdf" }, { "basename": "Fig6.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Fig6.pdf" }, { "basename": "Fig8.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Fig8.pdf" }, { "basename": "Table1.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Table1.pdf" }, { "basename": "Table2.pdf", "url": "https://authors.library.caltech.edu/records/19jg4-dm682/files/Table2.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Mena, Marco A.; Treynor, Thomas P.; et el." }, { "id": "https://authors.library.caltech.edu/records/sqv6s-v0w54", "eprint_id": 9967, "eprint_status": "archive", "datestamp": "2023-08-22 07:11:57", "lastmod": "2023-10-16 22:35:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lassila-J-K", "name": { "family": "Lassila", "given": "Jonathan Kyle" } }, { "id": "Privett-H-K", "name": { "family": "Privett", "given": "Heidi K." } }, { "id": "Allen-B-D", "name": { "family": "Allen", "given": "Benjamin D." }, "orcid": "0000-0001-6914-5572" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Combinatorial methods for small-molecule placement in computational enzyme design", "ispublished": "pub", "full_text_status": "public", "keywords": "computational protein design; conformer library; enzyme catalysis; rotamer library", "note": "\u00a9 2006 by The National Academy of Sciences of the USA. \n\nContributed by Stephen L. Mayo, September 16, 2006. Published online on October 30, 2006, 10.1073/pnas.0607691103. \n\nThis work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, the Defense Advanced Research Projects Agency, the U.S. Army Research Office Institute for Collaborative Biotechnologies, and an IBM Shared University Research Grant. \n\nAuthor contributions: J.K.L., H.K.P., B.D.A., and S.L.M. performed research; and J.K.L. wrote the paper. \n\nThe authors declare no conflict of interest.\n\nPublished - LASpnas06.pdf
Supplemental Material - LASpnas06app.pdf
Supplemental Material - LASpnas06supp.pdf
", "abstract": "The incorporation of small-molecule transition state structures into protein design calculations poses special challenges because of the need to represent the added translational, rotational, and conformational freedoms within an already difficult optimization problem. Successful approaches to computational enzyme design have focused on catalytic side-chain contacts to guide placement of small molecules in active sites. We describe a process for modeling small molecules in enzyme design calculations that extends previously described methods, allowing favorable small-molecule positions and conformations to be explored simultaneously with sequence optimization. Because all current computational enzyme design methods rely heavily on sampling of possible active site geometries from discrete conformational states, we tested the effects of discretization parameters on calculation results. Rotational and translational step sizes as well as side-chain library types were varied in a series of computational tests designed to identify native-like binding contacts in three natural systems. We find that conformational parameters, especially the type of rotamer library used, significantly affect the ability of design calculations to recover native binding-site geometries. We describe the construction and use of a crystallographic conformer library and find that it more reliably captures active-site geometries than traditional rotamer libraries in the systems tested.", "date": "2006-11-07", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "103", "number": "45", "publisher": "National Academy of Sciences", "pagerange": "16710-16715", "id_number": "CaltechAUTHORS:LASpnas06", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:LASpnas06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1073/pnas.0607691103", "pmcid": "PMC1636520", "primary_object": { "basename": "LASpnas06.pdf", "url": "https://authors.library.caltech.edu/records/sqv6s-v0w54/files/LASpnas06.pdf" }, "related_objects": [ { "basename": "LASpnas06app.pdf", "url": "https://authors.library.caltech.edu/records/sqv6s-v0w54/files/LASpnas06app.pdf" }, { "basename": "LASpnas06supp.pdf", "url": "https://authors.library.caltech.edu/records/sqv6s-v0w54/files/LASpnas06supp.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Lassila, Jonathan Kyle; Privett, Heidi K.; et el." }, { "id": "https://authors.library.caltech.edu/records/a0hxe-tkj09", "eprint_id": 9956, "eprint_status": "archive", "datestamp": "2023-08-22 06:49:48", "lastmod": "2023-10-16 22:35:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shifpam-J-M", "name": { "family": "Shifman", "given": "Julia M." } }, { "id": "Choi-Mee-H", "name": { "family": "Choi", "given": "Mee H." } }, { "id": "Mihalas-S", "name": { "family": "Mihalas", "given": "Stefan" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Kennedy-M-B", "name": { "family": "Kennedy", "given": "Mary B." }, "orcid": "0000-0003-1369-0525" } ] }, "title": "Ca2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums", "ispublished": "pub", "full_text_status": "public", "keywords": "postsynaptic; protein design; synaptic plasticity; microdomains", "note": "Copyright \u00a9 2006 by the National Academy of Sciences. \n\nContributed by Stephen L. Mayo, July 27, 2006. \n\nWe thank K. Beckingham (Rice University, Houston, TX) for providing a plasmid encoding calmodulin, E. Winfree and laboratory for the use of their spectrofluorometer, J. Oh and E. Marcora for CaMKII, A. Ingemar for help with CaLigator, and J. Zhou for help with mass spectrometry. This work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, and an IBM Shared University research grant (to S.L.M.), the Sloan-Schwartz Foundation (to M.H.C), and U.S. Public Health Service Grants NS047300 (to M.H.C) and NS44306 (to M.B.K.). \n\nAuthor contributions: J.M.S. and M.H.C. contributed equally to this work; J.M.S., M.H.C., S.M., S.L.M., and M.B.K. designed research; J.M.S., M.H.C., and S.M. performed research; J.M.S., M.H.C., S.M., S.L.M., and M.B.K. analyzed data; and J.M.S., M.H.C., and M.B.K. wrote the paper. \n\nThe authors declare no conflict of interest.\n\nPublished - SHIpnas06b.pdf
Supplemental Material - SHIpnas06bfig6.pdf
Supplemental Material - SHIpnas06bfig7.pdf
Supplemental Material - SHIpnas06bfig8.pdf
Supplemental Material - SHIpnas06bsupp.pdf
", "abstract": "Changes in synaptic strength that underlie memory formation in the CNS are initiated by pulses of Ca2+ flowing through NMDA-type glutamate receptors into postsynaptic spines. Differences in the duration and size of the pulses determine whether a synapse is potentiated or depressed after repetitive synaptic activity. Calmodulin (CaM) is a major Ca2+ effector protein that binds up to four Ca2+ ions. CaM with bound Ca2+ can activate at least six signaling enzymes in the spine. In fluctuating cytosolic Ca2+, a large fraction of free CaM is bound to fewer than four Ca2+ ions. Binding to targets increases the affinity of CaM's remaining Ca2+-binding sites. Thus, initial binding of CaM to a target may depend on the target's affinity for CaM with only one or two bound Ca2+ ions. To study CaM-dependent signaling in the spine, we designed mutant CaMs that bind Ca2+ only at the two N-terminal or two C-terminal sites by using computationally designed mutations to stabilize the inactivated Ca2+-binding domains in the \"closed\" Ca2+-free conformation. We have measured their interactions with CaMKII, a major Ca2+/CaM target that mediates initiation of long-term potentiation. We show that CaM with two Ca2+ ions bound in its C-terminal lobe not only binds to CaMKII with low micromolar affinity but also partially activates kinase activity. Our results support the idea that competition for binding of CaM with two bound Ca2+ ions may influence significantly the outcome of local Ca2+ signaling in spines and, perhaps, in other signaling pathways.", "date": "2006-09-19", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "103", "number": "38", "publisher": "National Academy of Sciences", "pagerange": "13968-13973", "id_number": "CaltechAUTHORS:SHIpnas06b", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SHIpnas06b", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "NIH", "grant_number": "NS047300" }, { "agency": "NIH", "grant_number": "NS44306" } ] }, "doi": "10.1073/pnas.0606433103", "pmcid": "PMC1599897", "primary_object": { "basename": "SHIpnas06bfig7.pdf", "url": "https://authors.library.caltech.edu/records/a0hxe-tkj09/files/SHIpnas06bfig7.pdf" }, "related_objects": [ { "basename": "SHIpnas06bfig8.pdf", "url": "https://authors.library.caltech.edu/records/a0hxe-tkj09/files/SHIpnas06bfig8.pdf" }, { "basename": "SHIpnas06bsupp.pdf", "url": "https://authors.library.caltech.edu/records/a0hxe-tkj09/files/SHIpnas06bsupp.pdf" }, { "basename": "SHIpnas06b.pdf", "url": "https://authors.library.caltech.edu/records/a0hxe-tkj09/files/SHIpnas06b.pdf" }, { "basename": "SHIpnas06bfig6.pdf", "url": "https://authors.library.caltech.edu/records/a0hxe-tkj09/files/SHIpnas06bfig6.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Shifman, Julia M.; Choi, Mee H.; et el." }, { "id": "https://authors.library.caltech.edu/records/v805k-jdc37", "eprint_id": 24141, "eprint_status": "archive", "datestamp": "2023-08-19 18:21:09", "lastmod": "2023-10-23 20:20:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zollars-E-S", "name": { "family": "Zollars", "given": "Eric S." } }, { "id": "Marshall-S-A", "name": { "family": "Marshall", "given": "Shannon A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Simple electrostatic model improves designed protein sequences", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Protein Denaturation, Protein Engineering, Homeodomain Proteins, Animals, Static Electricity, Sequence Alignment, Molecular Sequence Data, Models: Molecular, Protein Structure: Secondary, Amino Acid Sequence, Transcription Factors", "note": "\u00a9 2006 The Protein Society. Published by Cold Spring Harbor Laboratory Press. \n\nReceived January 24, 2006; Final Revision May 12, 2006; Accepted May 15, 2006. Article first published online: 1 Jan. 2009. \n\nThis work was supported by the Howard Hughes Medical Institute and the Ralph M. Parsons Foundation. E.S.Z. would like to thank the ARCS Foundation for funding.", "abstract": "Electrostatic interactions are important for both protein stability and function, including binding and catalysis. As protein design moves into these areas, an accurate description of electrostatic energy becomes necessary. Here, we show that a simple distance-dependent Coulombic function parameterized by a comparison to Poisson-Boltzmann calculations is able to capture some of these electrostatic interactions. Specifically, all three helix N-capping interactions in the engrailed homeodomain fold are recovered using the newly parameterized model. The stability of this designed protein is similar to a protein forced by sequence restriction to have beneficial electrostatic interactions.", "date": "2006-08", "date_type": "published", "publication": "Protein Science", "volume": "15", "number": "8", "publisher": "Wiley", "pagerange": "2014-2018", "id_number": "CaltechAUTHORS:20110620-160436627", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160436627", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "ARCS Foundation" } ] }, "doi": "10.1110/ps.062105506", "pmcid": "PMC2242593", "resource_type": "article", "pub_year": "2006", "author_list": "Zollars, Eric S.; Marshall, Shannon A.; et el." }, { "id": "https://authors.library.caltech.edu/records/1bztt-x4320", "eprint_id": 25327, "eprint_status": "archive", "datestamp": "2023-08-22 06:09:39", "lastmod": "2023-10-24 15:47:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Allen-B-D", "name": { "family": "Allen", "given": "Benjamin D." }, "orcid": "0000-0001-6914-5572" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Dramatic performance enhancements for the FASTER optimization algorithm", "ispublished": "pub", "full_text_status": "restricted", "keywords": "protein design; side-chain placement; combinatorial optimization; FASTER; Monte Carlo", "note": "\u00a9 2006 Wiley Periodicals, Inc. \n\nReceived 18 November 2005; Accepted 16 January 2006; Article first published online: 9 May 2006. \n\nContract/grant sponsor: Howard Hughes Medical Institute (S.L.M.).\nContract/grant sponsor: Ralph M. Parsons Foundation (S.L.M.)\nContract/grant sponsor: IBM Shared University Research Grant (S.L.M.) \n\nWe thank Marie Ary and Christina Vizcarra for critical review of this manuscript.", "abstract": "FASTER is a combinatorial optimization algorithm useful for finding low-energy side-chain configurations in side-chain placement and protein design calculations. We present two simple enhancements to FASTER that together improve the computational efficiency of these calculations by as much as two orders of magnitude with no loss of accuracy. Our results highlight the importance of choosing appropriate initial configurations, and show that efficiency can be improved by stringently limiting the number of positions that are allowed to relax in response to a perturbation. The changes we describe improve the quality of solutions found for large-scale designs, and allow them to be found in hours rather than days. The improved FASTER algorithm finds low-energy solutions more efficiently than common optimization schemes based on the dead-end elimination theorem and Monte Carlo. These advances have prompted investigations into new methods for force field parameterization and multiple state design.", "date": "2006-07-30", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "27", "number": "10", "publisher": "Wiley", "pagerange": "1071-1075", "id_number": "CaltechAUTHORS:20110913-165232651", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-165232651", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" } ] }, "doi": "10.1002/jcc.20420", "resource_type": "article", "pub_year": "2006", "author_list": "Allen, Benjamin D. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/j7411-1hv27", "eprint_id": 25328, "eprint_status": "archive", "datestamp": "2023-08-19 17:59:35", "lastmod": "2023-10-24 15:47:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Choi-Eun-Jung", "name": { "family": "Choi", "given": "Eun Jung" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L" }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Generation and analysis of proline mutants in protein G", "ispublished": "pub", "full_text_status": "public", "keywords": "proline, protein, design, protein G, protein stability", "note": "\u00a9 The Author 2006. Published by Oxford University Press. Received February 16, 2006; accepted February 17, 2006. The authors thank I. Caglar Tanrikulu for the helpful discussions and Marie Ary for editing the manuscript. This work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation and an IBM Shared University Research Grant.\n\nPublished - Choi_2006_Protein_Eng_Des_Sel_Generation_and_analysis_of_proline.pdf
", "abstract": "The pyrrolidine ring of the amino acid proline reduces the conformational freedom of the protein backbone in its unfolded form and thus enhances protein stability. The strategy of inserting proline into regions of the protein where it does not perturb the structure has been utilized to stabilize many different proteins including enzymes. However, most of these efforts have been based on trial and error, rather than rational design. Here, we try to understand proline's effect on protein stability by introducing proline mutations into various regions of the B1 domain of Streptococcal protein G. We also applied the Optimization of Rotamers By Iterative Techniques computational protein design program, using two different solvation models, to determine the extent to which it could predict the stabilizing and destabilizing effects of prolines. Use of a surface area dependent solvation model resulted in a modest correlation between the experimental free energy of folding and computed energies; on the other hand, use of a Gaussian solvent exclusion model led to significant positive correlation. Including a backbone conformational entropy term to the computational energies increases the statistical significance of the correlation between the experimental stabilities and both solvation models.", "date": "2006-06-01", "date_type": "published", "publication": "Protein Engineering, Design and Selection", "volume": "19", "number": "6", "publisher": "Oxford University Press", "pagerange": "285-289", "id_number": "CaltechAUTHORS:20110913-165232835", "issn": "1741-0126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-165232835", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" } ] }, "doi": "10.1093/protein/gzl007", "primary_object": { "basename": "Choi_2006_Protein_Eng_Des_Sel_Generation_and_analysis_of_proline.pdf", "url": "https://authors.library.caltech.edu/records/j7411-1hv27/files/Choi_2006_Protein_Eng_Des_Sel_Generation_and_analysis_of_proline.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Choi, Eun Jung and Mayo, Stephen L" }, { "id": "https://authors.library.caltech.edu/records/w2640-xaa47", "eprint_id": 25337, "eprint_status": "archive", "datestamp": "2023-08-22 05:04:48", "lastmod": "2023-10-24 15:48:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hom-G-K", "name": { "family": "Hom", "given": "Geoffrey K." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "A search algorithm for fixed-composition protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "protein design; fixed composition; FASTER; Monte Carlo; protein G", "note": "\u00a9 2005 Wiley Periodicals, Inc. \n\nArticle first published online: 27 Dec. 2005. \n\nWe are grateful to Ben Allen for help with FASTER and to\nOscar Alvizo for sharing his results on G1 prior to publication\nand for providing the test file. We also thank them and Marie\nAry, Po-Ssu Huang, and Christina Vizcarra for assistance with\nthe manuscript.", "abstract": "We present a computational protein design algorithm for finding low-energy sequences of fixed amino acid composition. The search algorithms used in protein design typically do not restrict amino acid composition. However, the random energy model of Shakhnovich suggests that the use of fixed-composition sequences may circumvent defects in the modeling of the denatured state. Our algorithm, FC_FASTER, links fixed-composition versions of Monte Carlo and the FASTER algorithm. As proof of principle, FC_FASTER was tested on an experimentally validated, full-sequence design of the \u03b21 domain of protein G. For the wild-type composition, FC_FASTER found a lower energy sequence than the experimentally validated sequence. Also, for a different composition, FC_FASTER found the hypothetical lowest-energy sequence in 14 out of 32 trials.", "date": "2006-02", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "27", "number": "3", "publisher": "Wliey", "pagerange": "375-378", "id_number": "CaltechAUTHORS:20110913-173427297", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173427297", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1002/jcc.20346", "resource_type": "article", "pub_year": "2006", "author_list": "Hom, Geoffrey K. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/cs3kv-69c94", "eprint_id": 24116, "eprint_status": "archive", "datestamp": "2023-08-22 04:30:56", "lastmod": "2023-10-23 20:18:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Vizcarra-C-L", "name": { "family": "Vizcarra", "given": "Christina L." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Electrostatics in computational protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Computer Simulation; Models: Theoretical; Protein Conformation; Proteins; Static Electricity", "note": "\u00a9 2005 Elsevier Ltd.\nAvailable online 28 October 2005.\n\nThis work was funded by Howard Hughes Medical Institute, the Ralph M\nParsons Foundation, the Defense Advanced Research Projects Agency, the\nInstitute for Collaborative Biotechnologies (grant DAAD19-03-D-0004 from\nthe US Army Research Office) (SLM), and the National Science\nFoundation (CLV). We wish to thank Benjamin D Allen for comments on\nthe manuscript.", "abstract": "Catalytic activity and protein-protein recognition have proven to be significant challenges for computational protein design. Electrostatic interactions are crucial for these and other protein functions, and therefore accurate modeling of electrostatics is necessary for successfully advancing protein design into the realm of protein function. This review focuses on recent progress in modeling electrostatic interactions in computational protein design, with particular emphasis on continuum models.", "date": "2005-12", "date_type": "published", "publication": "Current Opinion in Chemical Biology", "volume": "9", "number": "6", "publisher": "Elsevier", "pagerange": "622-626", "id_number": "CaltechAUTHORS:20110620-160432503", "issn": "1367-5931", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160432503", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Army Research Office (ARO)", "grant_number": "DAAD19-03-D-0004" }, { "agency": "NSF" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "doi": "10.1016/j.cbpa.2005.10.014", "resource_type": "article", "pub_year": "2005", "author_list": "Vizcarra, Christina L. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/bfe4k-28f41", "eprint_id": 25535, "eprint_status": "archive", "datestamp": "2023-08-22 04:07:07", "lastmod": "2023-10-24 15:57:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Huang-Po-Ssu", "name": { "family": "Huang", "given": "Po-Ssu" } }, { "id": "Love-J-J", "name": { "family": "Love", "given": "John J." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Adaptation of a fast Fourier transform-based docking algorithm for protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Algorithms; Models: Molecular; Crystallography: X-Ray; Protein Conformation; Proteins; Fourier Analysis; protein docking; protein design; reduced side-chain representation; homodimer; FFT; de novo dimer generation", "note": "\u00a9 2005 Wiley Periodicals, Inc.\nReceived 29 January 2005; Accepted 8 April 2005.\nArticle first published online: 16 Jun. 2005.\nContract/grant sponsor: Howard Hughes Medical Institute.\nContract/grant sponsor: Defense Advanced Research Projects Agency.\nContract/grant sponsor: Ralph M. Parsons Foundation.\nContract/grant sponsor: IBM Shared University Research Grant.\nContract/grant sponsor: Army Research Office/Institute for Collaborative\nTechnologies.\n\n\nThe authors would like to thank Marie Ary, Christina L. Vizcarra,\nand Benjamin D. Allen for editing and reviewing the manuscript.", "abstract": "Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to ~70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 \u00c5 C_\u03b1 RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.", "date": "2005-09", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "26", "number": "12", "publisher": "Wliey", "pagerange": "1222-1232", "id_number": "CaltechAUTHORS:20111004-074354772", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111004-074354772", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" }, { "agency": "Army Research Office (ARO)" } ] }, "doi": "10.1002/jcc.20252", "resource_type": "article", "pub_year": "2005", "author_list": "Huang, Po-Ssu; Love, John J.; et el." }, { "id": "https://authors.library.caltech.edu/records/1gdkv-44n04", "eprint_id": 24088, "eprint_status": "archive", "datestamp": "2023-08-22 03:56:18", "lastmod": "2023-10-23 20:18:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oelschlaeger-P", "name": { "family": "Oelschlaeger", "given": "Peter" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Hydroxyl groups in the \u03b2\u03b2 sandwich of metallo-\u03b2-lactamases favor enzyme activity: a computational protein design study", "ispublished": "pub", "full_text_status": "public", "keywords": "Binding Sites; beta-Lactamases; Bacteroides fragilis; Models: Molecular; Proteins; Protein Structure: Secondary; Circular Dichroism; Protein Folding; Point Mutation; Computational Biology; Software; Substrate Specificity; Catalysis; Kinetics; Zinc; Temperature; Proteomics; metallo-\u03b2-lactamase; zinc \u03b2-lactamase; protein design; catalytic efficiency", "note": "\u00a9 2005 Elsevier Ltd.\nReceived 17 February 2005; Accepted 21 April 2005. Edited by J. Thornton. Available online 11 May 2005.\n\nWe thank Jeffrey H. Toney (formerly with Merck)\nfor providing a plasmid containing the IMP-1 gene,\nMerck for the gift of imipenem, and Marie Ary for\nassistance with the manuscript. This work was\nsupported by the Howard Hughes Medical\nInstitute, DARPA, the Ralph M. Parsons\nFoundation, an IBM Shared University Research\ngrant (to S.L.M.) and the Caltech Colvin Fellowship\n(to P.O.).\n\nSupplemental Material - mmc1.pdf
", "abstract": "Metallo-\u03b2-lactamases challenge antimicrobial therapies by their ability to hydrolyze and inactivate a broad spectrum of \u03b2-lactam antibiotics. The potential of these enzymes to acquire enhanced catalytic efficiency through mutation is of great concern. Here, we explore the potential of computational protein design to predict mutants of the imipenemase IMP-1 that modulate the catalytic efficiency of the enzyme against a range of substrates. Focusing on the four amino acid positions 69, 121, 218, and 262, we carried out a number of design calculations. Two mutant enzymes were predicted: the single mutant S262A and the double mutant F218Y-S262A. Compared to IMP-1, the single mutant (S262A) results in the loss of a hydroxyl group and the double mutant (F218Y-S262A) results in a hydroxyl transfer from position 262 to position 218. The presence of both hydroxyl groups at positions 218 and 262 was tested by examining the mutant F218Y. Kinetic constants of IMP-1, the two computationally designed mutants (S262A and F218Y-S262A), and the hydroxyl addition mutant (F218Y) were determined with seven substrates. Catalytic efficiencies are highest for the enzyme with both hydroxyl groups (F218Y) and lowest for the enzyme lacking both hydroxyl groups (S262A). The catalytic efficiencies of the two enzymes with one hydroxyl group each are intermediate, with the F218Y-S262A double mutant exhibiting enhanced hydrolysis of nitrocefin, cephalothin, and cefotaxime relative to IMP-1.", "date": "2005-07-15", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "350", "number": "3", "publisher": "Elsevier", "pagerange": "395-401", "id_number": "CaltechAUTHORS:20110620-160427419", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160427419", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" }, { "agency": "Caltech Colvin Fellowship" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" } ] }, "doi": "10.1016/j.jmb.2005.04.044", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/1gdkv-44n04/files/mmc1.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Oelschlaeger, Peter and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/exghb-hvp33", "eprint_id": 24086, "eprint_status": "archive", "datestamp": "2023-08-22 03:33:55", "lastmod": "2023-10-23 20:18:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Marshall-S-A", "name": { "family": "Marshall", "given": "Shannon A." } }, { "id": "Vizcarra-C-L", "name": { "family": "Vizcarra", "given": "Christina L." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations", "ispublished": "pub", "full_text_status": "public", "keywords": "Proteins; Poisson Distribution; Static Electricity; Thermodynamics; protein design; electrostatics; Poisson-Boltzmann; solvation; force field", "note": "\u00a9 2005 The Protein Society.\n\nReceived November 29, 2004; Final revision January 19, 2005; Accepted January 20, 2005.\nArticle first published online: 1 Jan. 2009.\n\n\n\nWe thank Barry Honig and Emil Alexov for helpful conversations.\nThis work was supported by the Howard Hughes Medical Institute,\nthe Ralph M. Parsons Foundation, an IBM Shared University Research\nGrant, DARPA, ARO/ICB (S.L.M.), an NSF graduate research\nfellowship (C.L.V.), an NIH training grant, and the Caltech\nInitiative in Computational Molecular Biology program, awarded\nby the Burroughs Wellcome Fund (S.A.M.).\n\nSupplemental Material - Marshall_Supp.pdf
", "abstract": "Successfully modeling electrostatic interactions is one of the key factors required for the computational design of proteins with desired physical, chemical, and biological properties. In this paper, we present formulations of the finite difference Poisson-Boltzmann (FDPB) model that are pairwise decomposable by side chain. These methods use reduced representations of the protein structure based on the backbone and one or two side chains in order to approximate the dielectric environment in and around the protein. For the desolvation of polar side chains, the two-body model has a 0.64 kcal/mol RMSD compared to FDPB calculations performed using the full representation of the protein structure. Screened Coulombic interaction energies between side chains are approximated with an RMSD of 0.13 kcal/mol. The methods presented here are compatible with the computational demands of protein design calculations and produce energies that are very similar to the results of traditional FDPB calculations.", "date": "2005-05", "date_type": "published", "publication": "Protein Science", "volume": "14", "number": "5", "publisher": "Wiley", "pagerange": "1293-1304", "id_number": "CaltechAUTHORS:20110620-160427069", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160427069", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Army Research Office (ARO)" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "NIH Predoctoral Fellowship" }, { "agency": "Caltech Initiative in Computational Molecular Biology" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1110/ps.041259105", "pmcid": "PMC2253281", "primary_object": { "basename": "Marshall_Supp.pdf", "url": "https://authors.library.caltech.edu/records/exghb-hvp33/files/Marshall_Supp.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Marshall, Shannon A.; Vizcarra, Christina L.; et el." }, { "id": "https://authors.library.caltech.edu/records/rj9av-k4s07", "eprint_id": 5627, "eprint_status": "archive", "datestamp": "2023-08-22 03:28:49", "lastmod": "2023-10-16 19:19:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lassila-J-K", "name": { "family": "Lassila", "given": "Jonathan Kyle" } }, { "id": "Keeffe-J-R", "name": { "family": "Keeffe", "given": "Jennifer R." }, "orcid": "0000-0002-5317-6398" }, { "id": "Oelschlaeger-P", "name": { "family": "Oelschlaeger", "given": "Peter" }, "orcid": "0000-0001-5949-9297" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computationally designed variants of Escherichia coli chorismate mutase show altered catalytic activity", "ispublished": "pub", "full_text_status": "public", "keywords": "enzyme design; chorismate mutase; protein design", "note": "\u00a9 The Author 2005. Published by Oxford University Press. \n\nReceived March 2, 2005; accepted March 4, 2005. \n\nThis work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, the Defense Advanced Research Projects Agency, the Institute for Collaborative Biotechnologies (ARO) and an IBM Shared University Research Grant.\n\nPublished - LASpeds05.pdf
", "abstract": "Computational protein design methods were used to predict five variants of monofunctional Escherichia coli chorismate mutase expected to maintain catalytic activity. The variants were tested experimentally and three active site mutants exhibited catalytic activity similar to or greater than the wild-type enzyme. One mutant, Ala32Ser, showed increased catalytic efficiency.", "date": "2005-04-08", "date_type": "published", "publication": "Protein Engineering, Design and Selection", "volume": "18", "number": "4", "publisher": "Oxford University Press", "pagerange": "161-163", "id_number": "CaltechAUTHORS:LASpeds05", "issn": "1741-0126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:LASpeds05", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "Army Research Office (ARO)" }, { "agency": "IBM" } ] }, "doi": "10.1093/protein/gzi015", "primary_object": { "basename": "LASpeds05.pdf", "url": "https://authors.library.caltech.edu/records/rj9av-k4s07/files/LASpeds05.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Lassila, Jonathan Kyle; Keeffe, Jennifer R.; et el." }, { "id": "https://authors.library.caltech.edu/records/yxa2m-tbe25", "eprint_id": 24119, "eprint_status": "archive", "datestamp": "2023-08-19 15:36:35", "lastmod": "2023-10-23 20:18:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hom-G-K", "name": { "family": "Hom", "given": "Geoffrey K." } }, { "id": "Lassila-J-K", "name": { "family": "Lassila", "given": "J. Kyle" } }, { "id": "Thomas-L-M", "name": { "family": "Thomas", "given": "Leonard M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant", "ispublished": "pub", "full_text_status": "restricted", "keywords": "protein design, dioxane, engrailed homeodomain", "note": "\u00a9 2005 The Protein Society. Received December 8, 2004; Final Revision December 16, 2004; Accepted December 20, 2004. Article first published online: 1 Jan 2009. We are grateful to Premal Shah, Rhonda Digiusto, Scott Ross, and Karin Crowhurst for assistance with NMR; Doug Rees, James Holton, and J.J. Plecs for assistance with crystallography; Po-Ssu Huang for assistance with sedimentation velocity experiments and PyMOL; and Marie Ary and Jessica Mao for assistance with the manuscript. This work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, the Defense Advanced Research Projects Agency, and an IBM Shared University\nResearch Grant. Portions of this research were carried out at the Stanford Synchrotron Radiation Laboratory (SSRL), a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, and by the NIH, National Center for Research Resources, Biomedical Technology Program, and the National Institute of General Medical Sciences. We thank the Gordon and Betty Moore Foundation for their support of the crystallographic resources of the Molecular Observatory for Structural Molecular Biology used in this study.", "abstract": "Our goal was to compute a stable, full-sequence design of the Drosophila melanogaster engrailed homeodomain. Thermal and chemical denaturation data indicated the design was significantly more stable than was the wild-type protein. The data were also nearly identical to those for a similar, later full-sequence design, which was shown by NMR to adopt the homeodomain fold: a three-helix, globular monomer. However, a 1.65 \u00c5 crystal structure of the design described here turned out to be of a completely different fold: a four-helix, rodlike tetramer. The crystallization conditions included approximately ~25% dioxane, and subsequent experiments by circular dichroism and sedimentation velocity analytical ultracentrifugation indicated that dioxane increases the helicity and oligomerization state of the designed protein. We attribute at least part of the discrepancy between the target fold and the crystal structure to the presence of a high concentration of dioxane.", "date": "2005-04-01", "date_type": "published", "publication": "Protein Science", "volume": "14", "number": "4", "publisher": "Wiley", "pagerange": "1115-1119", "id_number": "CaltechAUTHORS:20110620-160432981", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160432981", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)" }, { "agency": "IBM" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1110/ps.041277305", "pmcid": "PMC2253454", "resource_type": "article", "pub_year": "2005", "author_list": "Hom, Geoffrey K.; Lassila, J. Kyle; et el." }, { "id": "https://authors.library.caltech.edu/records/s9c14-kpt78", "eprint_id": 25338, "eprint_status": "archive", "datestamp": "2023-08-22 03:15:31", "lastmod": "2023-10-24 15:48:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oelschlaeger-P", "name": { "family": "Oelschlaeger", "given": "Peter" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Pleiss-J", "name": { "family": "Pleiss", "given": "Juergen" } } ] }, "title": "Impact of remote mutations on metallo-\u03b2-lactamase substrate specificity: implications for the evolution of antibiotic resistance", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Biological Evolution; Drug Resistance: Bacterial; Escherichia coli; Mutation; Substrate Specificity; Drug Design; Kinetics; beta-Lactamases", "note": "\u00a9 2005 The Protein Society.\nPublished by Cold Spring Harbor Laboratory Press.\nReceived September 1, 2004; Final revision October 19, 2004; Accepted November 11, 2004.\nArticle first published online: 1 Jan 2009.\nWe thank Jeffrey H. Toney (formerly with Merck) for providing a\nplasmid containing the IMP-1 gene, Merck for the gift of imipenem,\nand Marie Ary for assistance with the manuscript. This\nwork was supported by the Colvin Biology Fellowship at Caltech\n(to P.O.), the Howard Hughes Medical Institute, the Ralph M.\nParsons Foundation, and an IBM Shared University research grant\n(to S.L.M.).", "abstract": "Metallo-\u03b2-lactamases have raised concerns due to their ability to hydrolyze a broad spectrum of \u03b2-lactam antibiotics. The G262S point mutation distinguishing the metallo-\u03b2-lactamase IMP-1 from IMP-6 has no effect on the hydrolysis of the drugs cephalothin and cefotaxime, but significantly improves catalytic efficiency toward cephaloridine, ceftazidime, benzylpenicillin, ampicillin, and imipenem. This change in specificity occurs even though residue 262 is remote from the active site. We investigated the substrate specificities of five other point mutants resulting from single-nucleotide substitutions at positions near residue 262: G262A, G262V, S121G, F218Y, and F218I. The results suggest two types of substrates: type I (nitrocefin, cephalothin, and cefotaxime), which are converted equally well by IMP-6, IMP-1, and G262A, but even more efficiently by the other mutants, and type II (ceftazidime, benzylpenicillin, ampicillin, and imipenem), which are hydrolyzed much less efficiently by all the mutants. G262V, S121G, F218Y, and F218I improve conversion of type I substrates, whereas G262A and IMP-1 improve conversion of type II substrates, indicating two distinct evolutionary adaptations from IMP-6. Substrate structure may explain the catalytic efficiencies observed. Type I substrates have R2 electron donors, which may stabilize the substrate intermediate in the binding pocket. In contrast, the absence of these stabilizing interactions with type II substrates may result in poor conversion. This observation may assist future drug design. As the G262A and F218Y mutants confer effective resistance to Escherichia coli BL21(DE3) cells (high minimal inhibitory concentrations), they are likely to evolve naturally.", "date": "2005-03", "date_type": "published", "publication": "Protein Science", "volume": "14", "number": "3", "publisher": "Wiley", "pagerange": "765-774", "id_number": "CaltechAUTHORS:20110913-173427641", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173427641", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Colvin Biology Fellowship" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" } ] }, "doi": "10.1110/ps.041093405", "pmcid": "PMC2279297", "resource_type": "article", "pub_year": "2005", "author_list": "Oelschlaeger, Peter; Mayo, Stephen L.; et el." }, { "id": "https://authors.library.caltech.edu/records/j7wy9-j8b82", "eprint_id": 25332, "eprint_status": "archive", "datestamp": "2023-08-22 02:42:10", "lastmod": "2023-10-24 15:47:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shah-P-S", "name": { "family": "Shah", "given": "Premal S." } }, { "id": "Hom-G-K", "name": { "family": "Hom", "given": "Geoffrey K." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Preprocessing of rotamers for protein design calculations", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Proteins; Algorithms; Protein Conformation; protein design; side-chain placement; dead-end elimination", "note": "\u00a9 2004 Wiley Periodicals, Inc.\nReceived 23 April 2004; Accepted 12 June 2004.\nArticle first published online: 27 Aug. 2004.\n\nContract/grant sponsor: National Institutes of Health (P.S.S. and G.K.H.).\nContract/grant sponsor: Howard Hughes Medical Institute (S.L.M.).\nContract/grant sponsor: Ralph M. Parsons Foundation (S.L.M.).\nContract/grant sponsor: IBM Shared University Research Grant (S.L.M.).\n\n\nThe authors would like to thank Marie Ary for critical review of\nthe manuscript and offering valuable comments.", "abstract": "We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.", "date": "2004-11-15", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "25", "number": "14", "publisher": "Wliey", "pagerange": "1797-1800", "id_number": "CaltechAUTHORS:20110913-173425840", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173425840", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM Shared University Research Grant" } ] }, "doi": "10.1002/jcc.20097", "resource_type": "article", "pub_year": "2004", "author_list": "Shah, Premal S.; Hom, Geoffrey K.; et el." }, { "id": "https://authors.library.caltech.edu/records/7q4sq-z1z59", "eprint_id": 25329, "eprint_status": "archive", "datestamp": "2023-08-22 02:40:51", "lastmod": "2023-10-24 15:47:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shukla-U-J", "name": { "family": "Shukla", "given": "Ushma J." } }, { "id": "Marino-H", "name": { "family": "Marino", "given": "Heather" } }, { "id": "Huang-P-S", "name": { "family": "Huang", "given": "Po-Ssu" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Love-J-J", "name": { "family": "Love", "given": "John J." } } ] }, "title": "A designed protein interface that blocks fibril formation", "ispublished": "pub", "full_text_status": "public", "keywords": "Amyloid; Bacterial Proteins; Mutagenesis: Site-Directed; Protein Structure: Tertiary; Protein Engineering; Fluorescence; Thiazoles", "note": "\u00a9 2004 American Chemical Society.\nReceived July 19, 2004.\nAcknowledgment is made for support of this research to the\ndonors of the American Chemical Society Petroleum Research\nFund, the Blasker-Rose-Miah fund of the San Diego Foundation,\nand the California Metabolic Research Foundation.\n\nPublished - Shukla_2004_J_Am_Chem_Soc_A_designed_protein_interface_that.pdf
", "abstract": "Protein fibril formation is implicated in many diseases, and therefore much effort has been focused toward the development of inhibitors of this process. In a previous project, a monomeric protein was computationally engineered to bind itself and form a heterodimer complex following interfacial redesign. One of the protein monomers, termed monomer-B, was unintentionally destabilized and shown to form macroscopic fibrils. Interestingly, in the presence of the designed binding partner, fibril formation was blocked. Here we describe the complete characterization of the amyloid properties of monomer-B and the inhibition of fiber formation by the designed binding partner, monomer-A. Both proteins are mutants of the betal domain of streptococcal protein-G. The free monomer-B protein forms amyloid-type fibrils, as determined by transmission electron microscopy and the change in fluorescence of Thioflavin T, an amyloid-specific dye. Fibril formation kinetics are influenced by pH, protein concentration, and seeding with preformed fibrils. Under all conditions tested, monomer-A was able to inhibit the formation of monomer-B fibrils. This inhibition is specific to the engineered interaction, as incubation of monomer-B with wild-type protein-G (a structural homologue) did not result in inhibition under the same conditions. Thus, this de novo-designed heterodimeric complex is an excellent model system for the study of protein-based fibril formation and inhibition. This system provides additional insight into the development of pharmaceuticals for amyloid disorders, as well as the potential use of amyloid fibrils for self-assembling nanostructures.", "date": "2004-11-03", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "126", "number": "43", "publisher": "American Chemical Society", "pagerange": "13914-13915", "id_number": "CaltechAUTHORS:20110913-173424834", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173424834", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "American Chemical Society Petroleum Research Fund" }, { "agency": "Blasker-Rose-Miah fund of the San Diego Foundation" }, { "agency": "California Metabolic Research Foundation" } ] }, "doi": "10.1021/ja0456858", "primary_object": { "basename": "Shukla_2004_J_Am_Chem_Soc_A_designed_protein_interface_that.pdf", "url": "https://authors.library.caltech.edu/records/7q4sq-z1z59/files/Shukla_2004_J_Am_Chem_Soc_A_designed_protein_interface_that.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Shukla, Ushma J.; Marino, Heather; et el." }, { "id": "https://authors.library.caltech.edu/records/5nq5f-c0n42", "eprint_id": 649, "eprint_status": "archive", "datestamp": "2023-08-22 01:05:42", "lastmod": "2023-10-13 21:54:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shifman-J-M", "name": { "family": "Shifman", "given": "Julia M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Exploring the origins of binding specificity through the computational redesign of calmodulin", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2003 by The National Academy of Sciences of the USA. \n\nEdited by Peter G. Wolynes, University of California at San Diego, La Jolla, CA and approved September 10, 2003 (received for review July 9, 2003) This paper was submitted directly (Track II) to the PNAS office. \n\nWe thank K. Beckingham for providing a plasmid containing wild-type calmodulin, P. Huang for providing the program PRPCR used for primer design, P. Shah for help with construction of some of the CaM mutants, and M. Ary for assistance with the manuscript. This work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, an IBM Shared University research grant (to S.L.M.), a National Institutes of Health postdoctoral fellowship, and the Caltech Initiative in Computational Molecular Biology, awarded by the Burroughs Wellcome Fund (to J.M.S.).\n\nPublished - SHIpnas03.pdf
", "abstract": "Calmodulin (CaM) is a second messenger protein that has evolved to bind tightly to a variety of targets and, as such, exhibits low binding specificity. We redesigned CaM by using a computational protein design algorithm to improve its binding specificity for one of its targets, smooth muscle myosin light chain kinase (smMLCK). Residues in or near the CaM/smMLCK binding interface were optimized; CaM interactions with alternative targets were not directly considered in the optimization. The predicted CaM sequences were constructed and tested for binding to a set of eight targets including smMLCK. The best CaM variant, obtained from a calculation that emphasized intermolecular interactions, showed up to a 155-fold increase in binding specificity. The increase in binding specificity was not due to improved binding to smMLCK, but due to decreased binding to the alternative targets. This finding is consistent with the fact that the sequence of wild-type CaM is nearly optimal for interactions with numerous targets.", "date": "2003-11-03", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "100", "number": "23", "publisher": "National Academy of Sciences", "pagerange": "13274-13279", "id_number": "CaltechAUTHORS:SHIpnas03", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SHIpnas03", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" }, { "agency": "NIH Postdoctoral Fellowship" }, { "agency": "Caltech Initiative in Computational Molecular Biology" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1073/pnas.2234277100", "pmcid": "PMC263780", "primary_object": { "basename": "SHIpnas03.pdf", "url": "https://authors.library.caltech.edu/records/5nq5f-c0n42/files/SHIpnas03.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Shifman, Julia M. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/a8z97-76074", "eprint_id": 25333, "eprint_status": "archive", "datestamp": "2023-08-22 00:57:01", "lastmod": "2023-10-24 15:47:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mooers-B-H-M", "name": { "family": "Mooers", "given": "Blaine H. M." } }, { "id": "Datta-D", "name": { "family": "Datta", "given": "Deepshikha" } }, { "id": "Baase-W-A", "name": { "family": "Baase", "given": "Walter A." } }, { "id": "Zollars-E-S", "name": { "family": "Zollars", "given": "Eric S." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Matthews-B-W", "name": { "family": "Matthews", "given": "Brian W." } } ] }, "title": "Repacking the Core of T4 lysozyme by automated design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Crystallography: X-Ray; Solvents; Models: Molecular; Protein Conformation; Enzyme Stability; Escherichia coli; Bacteriophage T4; Thermodynamics; Mutation; Methionine; Automation; Software; Water; Muramidase; Temperature; ORBIT; single-site revertants; T4 lysozyme; repacking", "note": "\u00a9 2003 Elsevier Ltd.\n\n\nReceived 25 March 2003; revised 1 July 2003; Accepted 1 July 2003. Edited by F. E. Cohen. Available online 2 September 2003.\n\n\nWe thank Hong Xiao, Leslie Gay, and Andy\nFields for making the mutant proteins and for\ncrystallizing them, Cathy Sarisky for help with the\ncalculations, Doug Juers for collecting preliminary\nX-ray data for the mutant proteins V103I and\nCore-7, and the user support staff at SSRL and\nALS for their assistance. This work was supported\nin part by grants from the NIH (GM21967 to\nB.W.M.), the Howard Hughes Medical Institute (to\nS.L.M. & B.W.M.), the Ralph M. Parsons\nFoundation (to S.L.M.) and an IBM Shared University\nResearch grant (to S.L.M.).", "abstract": "Automated protein redesign, as implemented in the program ORBIT, was used to redesign the core of phage T4 lysozyme. A total of 26 buried or partially buried sites in the C-terminal domain were allowed to vary both their sequence and side-chain conformation while the backbone and non-selected side-chains remained fixed. A variant with seven substitutions (\"Core-7\") was identified as having the most favorable energy. The redesign experiment was repeated with a penalty for the presence of methionine residues. In this case the redesigned protein (\"Core-10\") had ten amino acid changes. The two designed proteins, as well as the constituent single mutants, and several single-site revertants were over-expressed in Escherichia coli, purified, and subjected to crystallographic and thermal analyses. The thermodynamic and structural data show that some repacking was achieved although neither redesigned protein was more stable than the wild-type protein. The use of the methionine penalty was shown to be effective. Several of the side-chain rotamers in the predicted structure of Core-10 differ from those observed. Rather than changing to new rotamers predicted by the design process, side-chains tend to maintain conformations similar to those seen in the native molecule. In contrast, parts of the backbone change by up to 2.8 \u00c5 relative to both the designed structure and wild-type. Water molecules that are present within the lysozyme molecule were removed during the design process. In the redesigned protein the resultant cavities were, to some degree, re-occupied by side-chain atoms. In the observed structure, however, water molecules were still bound at or near their original sites. This suggests that it may be preferable to leave such water molecules in place during the design procedure. The results emphasize the specificity of the packing that occurs within the core of a typical protein. While point substitutions within the core are tolerated they almost always result in a loss of stability. Likewise, combinations of substitutions may also be tolerated but usually destabilize the protein. Experience with T4 lysozyme suggests that a general core repacking methodology with retention or enhancement of stability may be difficult to achieve without provision for shifts in the backbone.", "date": "2003-09-19", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "332", "number": "3", "publisher": "Elsevier", "pagerange": "741-756", "id_number": "CaltechAUTHORS:20110913-173426073", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173426073", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM21967" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" } ] }, "doi": "10.1016/S0022-2836(03)00856-8", "resource_type": "article", "pub_year": "2003", "author_list": "Mooers, Blaine H. M.; Datta, Deepshikha; et el." }, { "id": "https://authors.library.caltech.edu/records/6rmpq-fk646", "eprint_id": 25330, "eprint_status": "archive", "datestamp": "2023-08-22 00:46:04", "lastmod": "2023-10-24 15:47:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lazar-G-A", "name": { "family": "Lazar", "given": "Greg A." } }, { "id": "Marshall-S-A", "name": { "family": "Marshall", "given": "Shannon A." } }, { "id": "Plecs-J-J", "name": { "family": "Plecs", "given": "Joseph J." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Desjarlais-J-R", "name": { "family": "Desjarlais", "given": "John R." } } ] }, "title": "Designing proteins for therapeutic applications", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Animals; Antibodies: Monoclonal; Protein Engineering; Antiviral Agents; Proteins; Humans; Cytokines", "note": "\u00a9 2003 Elsevier Ltd.\nAvailable online 19 July 2003.\n\nThis review comes from a themed issue on\nEngineering and design.\nEdited by Sophie E Jackson and Lynne Regan.", "abstract": "Protein design is becoming an increasingly useful tool for optimizing protein drugs and creating novel biotherapeutics. Recent progress includes the engineering of monoclonal antibodies, cytokines, enzymes and viral fusion inhibitors.", "date": "2003-08", "date_type": "published", "publication": "Current Opinion in Structural Biology", "volume": "13", "number": "4", "publisher": "Elsevier", "pagerange": "513-518", "id_number": "CaltechAUTHORS:20110913-173425194", "issn": "0959-440X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173425194", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/S0959-440X(03)00104-0", "resource_type": "article", "pub_year": "2003", "author_list": "Lazar, Greg A.; Marshall, Shannon A.; et el." }, { "id": "https://authors.library.caltech.edu/records/4t426-znj91", "eprint_id": 25334, "eprint_status": "archive", "datestamp": "2023-08-22 00:46:12", "lastmod": "2023-10-24 15:48:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meyer-M-M", "name": { "family": "Meyer", "given": "Michelle M." } }, { "id": "Silberg-J-J", "name": { "family": "Silberg", "given": "Jonathan J." } }, { "id": "Voigt-C-A", "name": { "family": "Voigt", "given": "Christopher A." } }, { "id": "Endelman-J-B", "name": { "family": "Endelman", "given": "Jeffrey B." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Wang-Zhen-Gang", "name": { "family": "Wang", "given": "Zhen-Gang" }, "orcid": "0000-0002-3361-6114" }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" } ] }, "title": "Library analysis of SCHEMA-guided protein recombination", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Molecular Sequence Data; Recombination: Genetic; Models: Molecular; Protein Conformation; Algorithms; Recombinant Fusion Proteins; Amino Acid Sequence; beta-Lactamases; Protein Engineering; Peptide Library; DNA: Recombinant; Structure-Activity Relationship; chimera; lactamase; PSE-4; recombination; schema; TEM-1; directed evolution", "note": "\u00a9 2003 The Protein Society. Published by Cold Spring Harbor Laboratory Press. \n\nReceived February 17, 2003; Final revision May 1, 2003; Accepted May 1, 2003. \n\nThis work was supported by the Army Research Office, NIH Fellowship F32 GM64949-01 (J.J.S.), Howard Hughes Medical Institute graduate research fellowship (M.M.M.), National Defense\nScience and Engineering Fellowship (J.B.E.), National Science\nFoundation (C.A.V.), and Burroughs-Welcome Fund (C.A.V.).\nZ.G.W. acknowledges support by the W.M. Keck Foundation.\nS.L.M. is supported by the Howard Hughes Medical Institute, the\nRalph M. Parsons Foundation, and an IBM Shared University\nResearch Grant. \n\nThe publication costs of this article were defrayed in part by\npayment of page charges. This article must therefore be hereby\nmarked \"advertisement\" in accordance with 18 USC section 1734\nsolely to indicate this fact.", "abstract": "The computational algorithm SCHEMA was developed to estimate the disruption caused when amino acid residues that interact in the three-dimensional structure of a protein are inherited from different parents upon recombination. To evaluate how well SCHEMA predicts disruption, we have shuffled the distantly-related beta-lactamases PSE-4 and TEM-1 at 13 sites to create a library of 2^(14) (16,384) chimeras and examined which ones retain lactamase function. Sequencing the genes from ampicillin-selected clones revealed that the percentage of functional clones decreased exponentially with increasing calculated disruption (E = the number of residue-residue contacts that are broken upon recombination). We also found that chimeras with low E have a higher probability of maintaining lactamase function than chimeras with the same effective level of mutation but chosen at random from the library. Thus, the simple distance metric used by SCHEMA to identify interactions and compute E allows one to predict which chimera sequences are most likely to retain their function. This approach can be used to evaluate crossover sites for recombination and to create highly mosaic, folded chimeras.", "date": "2003-08", "date_type": "published", "publication": "Protein Science", "volume": "12", "number": "8", "publisher": "Wiley", "pagerange": "1686-1693", "id_number": "CaltechAUTHORS:20110913-173426256", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173426256", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Army Research Office (ARO)" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32 GM64949-01" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "National Defense Science and Engineering Graduate (NDSEG) Fellowship" }, { "agency": "NSF" }, { "agency": "Burroughs-Welcome Fund" }, { "agency": "W. M. Keck Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" } ] }, "doi": "10.1110/ps.0306603", "pmcid": "PMC2323955", "resource_type": "article", "pub_year": "2003", "author_list": "Meyer, Michelle M.; Silberg, Jonathan J.; et el." }, { "id": "https://authors.library.caltech.edu/records/nfs1p-q4105", "eprint_id": 25335, "eprint_status": "archive", "datestamp": "2023-08-22 00:44:14", "lastmod": "2023-10-24 15:48:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gillespie-B", "name": { "family": "Gillespie", "given": "Blake" } }, { "id": "Vu-Dung-M", "name": { "family": "Vu", "given": "Dung M." } }, { "id": "Shah-P-S", "name": { "family": "Shah", "given": "Premal S." } }, { "id": "Marshall-S-A", "name": { "family": "Marshall", "given": "Shannon A." } }, { "id": "Dyer-R-B", "name": { "family": "Dyer", "given": "R. Brian" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Plaxco-K-W", "name": { "family": "Plaxco", "given": "Kevin W." } } ] }, "title": "NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Kinetics; Protein Binding; Protein Folding; Algorithms; Molecular Sequence Data; Protein Structure: Tertiary; Urea; Magnetic Resonance Spectroscopy; Dose-Response Relationship: Drug; Temperature; Escherichia coli; Time Factors; Amino Acid Sequence; Thermodynamics; Sequence Homology: Amino Acid; Software; evolution; two-state; NMR lineshape", "note": "\u00a9 2003 Elsevier Ltd. \n\nReceived 23 January 2003; revised 8 May 2003; Accepted 8 May 2003. Edited by C. R. Matthews. Available online 1 July 2003. \n\nThe authors gratefully acknowledge the assistance of Jerry Hu, Scott Ross, Dan Raleigh, and Rick Dahlquist regarding various aspects of the NMR measurements reported here. This work was supported by NIH grant R01GM62868-01A1 (KWP), BioSTAR grant s97-79 (KWP), NIH grant GM053640 (RBD) and ACS junior postdoctoral research fellowship ACS CD INC 2-5-00 (BG).", "abstract": "We address the importance of natural selection in the origin and maintenance of rapid protein folding by experimentally characterizing the folding kinetics of two de novo designed proteins, NC3-NCAP and ENH-FSM1. These 51 residue proteins, which adopt the helix-turn-helix homeodomain fold, share as few as 12 residues in common with their most closely related natural analog. Despite the replacement of up to 3/4 of their residues by a computer algorithm optimizing only thermodynamic properties, the designed proteins fold as fast or faster than the 35,000 s^(-1) observed for the closest natural analog. Thus these de novo designed proteins, which were produced in the complete absence of selective pressures or design constraints explicitly aimed at ensuring rapid folding, are among the most rapidly folding proteins reported to date.", "date": "2003-07-18", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "330", "number": "4", "publisher": "Elsevier", "pagerange": "813-819", "id_number": "CaltechAUTHORS:20110913-173426521", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173426521", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM62868-01A1" }, { "agency": "BioSTAR", "grant_number": "s97-79" }, { "agency": "NIH", "grant_number": "GM053640" }, { "agency": "American Chemical Society", "grant_number": "ACS CD INC 2-5-00" } ] }, "doi": "10.1016/S0022-2836(03)00616-8", "resource_type": "article", "pub_year": "2003", "author_list": "Gillespie, Blake; Vu, Dung M.; et el." }, { "id": "https://authors.library.caltech.edu/records/wsdsx-rsm86", "eprint_id": 24129, "eprint_status": "archive", "datestamp": "2023-08-19 11:36:30", "lastmod": "2023-10-23 20:19:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bolon-D-N", "name": { "family": "Bolon", "given": "Daniel N." } }, { "id": "Marcus-J-S", "name": { "family": "Marcus", "given": "Joshua S." } }, { "id": "Ross-S-A", "name": { "family": "Ross", "given": "Scott A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Prudent modeling of core polar residues in computational protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Protein Denaturation, Escherichia coli, Thermodynamics, Models: Molecular, Hydrogen Bonding, Nuclear Magnetic Resonance: Biomolecular, Thioredoxins, Computer Simulation, Static Electricity, Hydrophobic and Hydrophilic Interactions, Amino Acid Sequence, Molecular Sequence Data, Circular Dichroism", "note": "\u00a9 2003 Elsevier Science Ltd.\nReceived 26 February 2003; accepted 19 March 2003. Edited by M. Levitt. Available online 21 May 2003. \nWe thank P. S. Shah for aid in protein expression\nand purification, P. Strop for helpful discussions\nand M. Ary for critical comments on the manuscript.\nThis research was supported by the Howard\nHughes Medical Institute and the Ralph M. Parsons\nFoundation (S.L.M.), the Helen G. and Arthur\nMcCallum Foundation, the Evelyn Sharp Graduate\nFellowship, and grant GM07616 from the National\nInstitutes of Health (D.N.B.).", "abstract": "Hydrogen bond interactions were surveyed in a set of protein structures. Compared to surface positions, polar side-chains at core positions form a greater number of intra-molecular hydrogen bonds. Furthermore, the majority of polar side-chains at core positions form at least one hydrogen bond to main-chain atoms that are not involved in hydrogen bonds to other main-chain atoms. Based on this structural survey, hydrogen bond rules were generated for each polar amino acid for use in protein core design. In the context of protein core design, these prudent polar rules were used to eliminate from consideration polar amino acid rotamers that do not form a minimum number of hydrogen bonds. As an initial test, the core of Escherichia coli thioredoxin was selected as a design target. For this target, the prudent polar strategy resulted in a minor increase in computational complexity compared to a strategy that did not allow polar residues. Dead-end elimination was used to identify global minimum energy conformations for the prudent polar and no polar strategies. The prudent polar strategy identified a protein sequence that was thermodynamically stabilized by 2.5 kcal/mol relative to wild-type thioredoxin and 2.2 kcal/mol relative to a thioredoxin variant whose core was designed without polar residues.", "date": "2003-06-06", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "329", "number": "3", "publisher": "Elsevier", "pagerange": "611-622", "id_number": "CaltechAUTHORS:20110620-160434663", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160434663", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Helen G. and Arthur McCallum Foundation" }, { "agency": "Evelyn Sharp Graduate Fellowship" }, { "agency": "NIH", "grant_number": "GM07616" } ] }, "doi": "10.1016/S0022-2836(03)00423-6", "resource_type": "article", "pub_year": "2003", "author_list": "Bolon, Daniel N.; Marcus, Joshua S.; et el." }, { "id": "https://authors.library.caltech.edu/records/b7b45-yvv65", "eprint_id": 25331, "eprint_status": "archive", "datestamp": "2023-08-22 00:10:11", "lastmod": "2023-10-24 15:47:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gordon-D-B", "name": { "family": "Gordon", "given": "D. Benjamin" } }, { "id": "Hom-G-K", "name": { "family": "Hom", "given": "Geoffrey K." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Pierce-N-A", "name": { "family": "Pierce", "given": "Niles A." }, "orcid": "0000-0003-2367-4406" } ] }, "title": "Exact rotamer optimization for protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Protein Conformation; Computational Biology; Algorithms; Proteins; dead-end elimination; side-chain placement; protein design; combinatorial optimization; NP-hard", "note": "\u00a9 2002 Wiley Periodicals, Inc. \n\nReceived 16 December 2001; Accepted 18 March 2002. Article first published online: 19 Dec. 2002. \n\nContract/grant sponsor: Helen G. and Arthur McCallum Foundation (D.B.G.).\nContract/grant sponsor: NRSA; contract/grant number: 5T32-GM07616 (G.K.H.).\nContract/grant sponsor: Howard Hughes Medical Institute (S.L.M.).\nContract/grant sponsor: Burroughs-Wellcome Foundation (N.A.P.).\nContract/grant sponsor: Caltech Initiative in Computational Molecular Biology (N.A.P.).", "abstract": "Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10^(128) conformations, a full core/boundary design of the \u03b21 domain of protein G with 25 residues and 10^(53) conformations, and a full surface design of the \u03b21 domain of protein G with 27 residues and 10^(60) conformations. In addition, a full sequence design of the \u03b21 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.", "date": "2003-01-30", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "24", "number": "2", "publisher": "Wliey", "pagerange": "232-243", "id_number": "CaltechAUTHORS:20110913-173425474", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173425474", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Helen G. and Arthur McCallum Foundation" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32-GM07616" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Burroughs-Wellcome Foundation" }, { "agency": "Caltech Initiative in Computational Molecular Biology" } ] }, "doi": "10.1002/jcc.10121", "resource_type": "article", "pub_year": "2003", "author_list": "Gordon, D. Benjamin; Hom, Geoffrey K.; et el." }, { "id": "https://authors.library.caltech.edu/records/qe1sa-r1336", "eprint_id": 25336, "eprint_status": "archive", "datestamp": "2023-08-22 00:08:22", "lastmod": "2023-10-24 15:48:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Offredi-F", "name": { "family": "Offredi", "given": "F." } }, { "id": "Dubail-F", "name": { "family": "Dubail", "given": "F." } }, { "id": "Kischel-P", "name": { "family": "Kischel", "given": "P." } }, { "id": "Sarinski-K", "name": { "family": "Sarinski", "given": "K." } }, { "id": "Stern-A-S", "name": { "family": "Stern", "given": "A. S." } }, { "id": "Van-de-Weerdt-C", "name": { "family": "Van de Weerdt", "given": "C." } }, { "id": "Hoch-J-C", "name": { "family": "Hoch", "given": "J. C." } }, { "id": "Prosperi-C", "name": { "family": "Prosperi", "given": "C." } }, { "id": "Fran\u00e7ois-J-M", "name": { "family": "Fran\u00e7ois", "given": "J. M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "S. L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Martial-J-A", "name": { "family": "Martial", "given": "J. A." } } ] }, "title": "De novo backbone and sequence design of an idealized \u03b1/\u03b2-barrel protein: evidence of stable tertiary structure", "ispublished": "pub", "full_text_status": "public", "keywords": "Protein Denaturation; Proteins; Models: Molecular; Spectrometry: Fluorescence; Temperature; Oligodeoxyribonucleotides; Escherichia coli; Nuclear Magnetic Resonance: Biomolecular; Protein Biosynthesis; Protein Structure: Tertiary; Scattering: Radiation; Molecular Sequence Data; Spectrophotometry: Ultraviolet; Structure-Activity Relationship; Protein Engineering; Thermodynamics; Circular Dichroism; Amino Acid Sequence; Protein Structure: Secondary; protein design; backbone parameterization; side-chain modeling; fluorescence; circular dichroism", "note": "\u00a9 2002 Elsevier Science Ltd. \n\nReceived 16 May 2002; received in revised form 18 October 2002; accepted 25 October 2002. Available online 3 December 2002. \n\nEdited by J. Thornton. \n\nWe are grateful to D. Schaak and P. Osterhout of the Rowland Institute, B. Gordon and A. Street of Caltech for their very stimulating scientific interest and to A. Matagne, M. Galleni and M. Muller for critical reading of the manuscript. We thank A. Stern of the Rowland Institute for the backbone construction and N. Otthiers for peptide sequencing. F.O. is the recipient of a doctoral fellowship\nfrom the Fonds pour la Formation \u00e0 la Recherche dans l'Industrie et l'Agriculture (FRIA). This work was supported, in part, by European Space Agency grant number 12987/98/NL/VJ(IC).\n\n", "abstract": "We have designed, synthesized, and characterized a 216 amino acid residue\nsequence encoding a putative idealized \u03b1/\u03b2-barrel protein. The\ndesign was elaborated in two steps. First, the idealized backbone was\ndefined with geometric parameters representing our target fold: a central\neight parallel-stranded \u03b2-sheet surrounded by eight parallel \u03b1-helices,\nconnected together with short structural turns on both sides of the barrel.\nAn automated sequence selection algorithm, based on the dead-end elimination\ntheorem, was used to find the optimal amino acid sequence fitting\nthe target structure. A synthetic gene coding for the designed sequence\nwas constructed and the recombinant artificial protein was expressed in\nbacteria, purified and characterized. Far-UV CD spectra with prominent\nbands at 222 nm and 208 nm revealed the presence of \u03b1-helix secondary\nstructures (50%) in fairly good agreement with the model. A pronounced\nabsorption band in the near-UV CD region, arising from immobilized aromatic\nside-chains, showed that the artificial protein is folded in solution.\nChemical unfolding monitored by tryptophan fluorescence revealed a\nconformational stability (\u0394GH_2O) of 35 kJ/mol. Thermal unfolding monitored by near-UV CD revealed a cooperative transition with an apparent T_m of 65 \u00b0C. Moreover, the artificial protein did not exhibit any affinity\nfor the hydrophobic fluorescent probe 1-anilinonaphthalene-8-sulfonic\nacid (ANS), providing additional evidence that the artificial barrel is not\nin the molten globule state, contrary to previously designed artificial a/\nb-barrels. Finally, ^1H NMR spectra of the folded and unfolded proteins\nprovided evidence for specific interactions in the folded protein. Taken\ntogether, the results indicate that the de novo designed \u03b1/\u03b2-barrel protein\nadopts a stable three-dimensional structure in solution. These encouraging\nresults show that de novo design of an idealized protein structure of\nmore than 200 amino acid residues is now possible, from construction of\na particular backbone conformation to determination of an amino acid\nsequence with an automated sequence selection algorithm.", "date": "2003-01-03", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "325", "number": "1", "publisher": "Elsevier", "pagerange": "163-174", "id_number": "CaltechAUTHORS:20110913-173426926", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173426926", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Fonds pour la Formation \u00e0 la Recherche dans l'Industrie et l'Agriculture (FRIA)" }, { "agency": "European Space Agency", "grant_number": "12987/98/NL/VJ(IC)" } ] }, "doi": "10.1016/S0022-2836(02)01206-8", "primary_object": { "basename": "De_novo_Backbone_and_Sequence_Design_of_an_Idealized_alpha-beta-barrel_Protein-Evidence_of_Stable_Tertiary_Structure__Offredi_2003_.pdf", "url": "https://authors.library.caltech.edu/records/qe1sa-r1336/files/De_novo_Backbone_and_Sequence_Design_of_an_Idealized_alpha-beta-barrel_Protein-Evidence_of_Stable_Tertiary_Structure__Offredi_2003_.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Offredi, F.; Dubail, F.; et el." }, { "id": "https://authors.library.caltech.edu/records/c2nby-mgk18", "eprint_id": 25479, "eprint_status": "archive", "datestamp": "2023-08-21 23:49:37", "lastmod": "2023-10-24 15:54:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shifman-J-M", "name": { "family": "Shifman", "given": "Julia M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Modulating calmodulin binding specificity through computational protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Substrate Specificity; Peptides; Sequence Alignment; Protein Binding; Models: Molecular; Calmodulin; Amino Acid Sequence; Myosin-Light-Chain Kinase; Binding Sites; Mutation; Crystallography: X-Ray; Protein Conformation; Computer Simulation; Protein Structure: Tertiary; Molecular Sequence Data; protein design; binding affinity; binding specificity; protein\u2013ligand\tinteractions", "note": "\u00a9 2002 Elsevier Science Ltd.\n\nReceived 10 April 2002; revised 13 August 2002; Accepted 16 August 2002. Edited by J. Thornton. Available online 9 October 2002.\n\nThis work was supported by the Howard\nHughes Medical Institute, the Ralph M. Parsons\nFoundation, an IBM Shared University Research\nGrant (to S.L.M.), an NIH postdoctoral fellowship,\nand the Caltech Initiative in Computational\nMolecular Biology, awarded by the Burroughs\nWellcome Fund (to J.M.S.). We thank K. Beckingham\nfor providing a plasmid containing WT CaM and\nM. Ary for assistance with the manuscript.", "abstract": "We report the computational redesign of the protein-binding interface of calmodulin (CaM), a small, ubiquitous Ca^(2+)-binding protein that is known to bind to and regulate a variety of functionally and structurally diverse proteins. The CaM binding interface was optimized to improve binding specificity towards one of its natural targets, smooth muscle myosin light chain kinase (smMLCK). The optimization was performed using optimization of rotamers by iterative techniques (ORBIT), a protein design program that utilizes a physically based force-field and the Dead-End Elimination theorem to compute sequences that are optimal for a given protein scaffold. Starting from the structure of the CaM-smMLCK complex, the program considered 10^(22) amino acid residue sequences to obtain the lowest-energy CaM sequence. The resulting eightfold mutant, CaM_8, was constructed and tested for binding to a set of seven CaM target peptides. CaM_8 displayed high binding affinity to the smMLCK peptide (1.3nM), similar to that of the wild-type protein (1.8 nM). The affinity of CaM_8 to six other target peptides was reduced, as intended, by 1.5-fold to 86-fold. Hence, CaM_8 exhibited increased binding specificity, preferring the smMLCK peptide to the other targets. Studies of this type may increase our understanding of the origins of binding specificity in protein-ligand complexes and may provide valuable information that can be used in the design of novel protein receptors and/or ligands.", "date": "2002-10-25", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "323", "number": "3", "publisher": "Elsevier", "pagerange": "417-423", "id_number": "CaltechAUTHORS:20110928-154513858", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110928-154513858", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM Shared University Research Grant" }, { "agency": "NIH Postdoctoral Fellowship" }, { "agency": "Caltech Initiative in Computational Molecular Biology" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1016/S0022-2836(02)00881-1", "resource_type": "article", "pub_year": "2002", "author_list": "Shifman, Julia M. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/9v84p-gq779", "eprint_id": 24077, "eprint_status": "archive", "datestamp": "2023-08-21 23:38:40", "lastmod": "2023-10-23 20:17:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Datta-D", "name": { "family": "Datta", "given": "Deepshikha" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "A designed apoplastocyanin variant that shows reversible folding", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Temperature; Copper; Circular Dichroism; Escherichia coli; Apoproteins; Plant Proteins; Crystallography: X-Ray; Plastocyanin; Salts; Protein Folding; Mutagenesis: Site-Directed; Protein Conformation; Protein Structure: Secondary; Binding Sites; Protein Structure: Tertiary; Reversible folding; Copper-binding site; Protein design", "note": "\u00a9 2002 Elsevier Science.\nReceived 31 July 2002; Available online 21 August 2002.", "abstract": "Plastocyanin, like many other metalloproteins, does not undergo reversible folding, which is thought to be due to an irreversible conformational change in the copper-binding site. Moreover, apoplastocyanin's ability to adopt a native tertiary structure is highly salt-dependent, and even in high salt, it has an irreversible thermal denaturation. Here, we report a designed apoplastocyanin variant, PCV, that is well folded and has reversible folding in both high and low salt conditions. This variant provides a tractable model for understanding and designing protein \u03b2-sheets.", "date": "2002-08-30", "date_type": "published", "publication": "Biochemical and Biophysical Research Communications", "volume": "296", "number": "4", "publisher": "Elsevier", "pagerange": "988-990", "id_number": "CaltechAUTHORS:20110620-160423337", "issn": "0006-291X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160423337", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/S0006-291X(02)02037-5", "resource_type": "article", "pub_year": "2002", "author_list": "Datta, Deepshikha and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/3pctj-01x61", "eprint_id": 24071, "eprint_status": "archive", "datestamp": "2023-08-21 23:36:16", "lastmod": "2023-10-23 20:17:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Desjarlais-J-R", "name": { "family": "Desjarlais", "given": "John R." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Engineering and design computational protein design - Editorial overview", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Biochemistry; Biophysics; Structural biology; Techniques & Methods", "note": "\u00a9 2002 Elsevier Science Ltd. \nAvailable online 5 August 2002.", "abstract": "N/A", "date": "2002-08-05", "date_type": "published", "publication": "Current Opinion in Structural Biology", "volume": "12", "number": "4", "publisher": "Elsevier", "pagerange": "429-430", "id_number": "CaltechAUTHORS:20110620-160422247", "issn": "0959-440X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160422247", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/S0959-440X(02)00343-3", "resource_type": "article", "pub_year": "2002", "author_list": "Desjarlais, John R. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/d72he-90a69", "eprint_id": 25453, "eprint_status": "archive", "datestamp": "2023-08-21 23:28:41", "lastmod": "2023-10-24 15:53:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Voigt-C-A", "name": { "family": "Voigt", "given": "Christopher A." } }, { "id": "Martinez-C", "name": { "family": "Martinez", "given": "Carlos" } }, { "id": "Wang-Zhen-Gang", "name": { "family": "Wang", "given": "Zhen-Gang" }, "orcid": "0000-0002-3361-6114" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" } ] }, "title": "Protein building blocks preserved by recombination", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Beta-Lactamase; Globular-Proteins; Crystal-Structure; Evolution; Units; Resolution; Domains; Organization; Genes; Exons", "note": "\u00a9 2002 Nature Publishing Group. Published online: 3 June 2002; Corrected online: 10 June 2002. C.A.V. is supported by a National Science Foundation graduate research fellowship and the California Institute of Technology Initiative in Computational Molecular Biology, a Burroughs Wellcome funded program for science at the interface. Z.G.W. acknowledges the support by the W.M. Keck Foundation. S.L.M. is supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation and an IBM Shared University Research Grant. The PSE-4 gene and the PMON vector were provided by R.C. Levesque (Universit\u00e9 Laval, Qu\u00e9bec, Canada).", "abstract": "Borrowing concepts from the schema theory of genetic algorithms, we have developed a computational algorithm to identify the fragments of proteins, or schemas, that can be recombined without disturbing the integrity of the three-dimensional structure. When recombination leaves these schemas undisturbed, the hybrid proteins are more likely to be folded and functional. Crossovers found by screening libraries of several randomly shuffled proteins for functional hybrids strongly correlate with those predicted by this approach. Experimental results from the construction of hybrids of two beta-lactamases that share 40% amino acid identity demonstrate a threshold in the amount of schema disruption that the hybrid protein can tolerate. To the extent that introns function to promote recombination within proteins, natural selection would serve to bias their locations to schema boundaries.", "date": "2002-07", "date_type": "published", "publication": "Nature Structural Biology", "volume": "9", "number": "7", "publisher": "Nature Publishing Group", "pagerange": "553-558", "id_number": "CaltechAUTHORS:20110927-143229047", "issn": "1072-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110927-143229047", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship" }, { "agency": "Caltech Initiative in Computational Molecular Biology" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "W. M. Keck Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM" } ] }, "doi": "10.1038/nsb805", "resource_type": "article", "pub_year": "2002", "author_list": "Voigt, Christopher A.; Martinez, Carlos; et el." }, { "id": "https://authors.library.caltech.edu/records/8aex9-rkf65", "eprint_id": 24112, "eprint_status": "archive", "datestamp": "2023-08-21 23:20:35", "lastmod": "2023-10-23 20:18:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Datta-D", "name": { "family": "Datta", "given": "Deepshikha" } }, { "id": "Wang-Pin", "name": { "family": "Wang", "given": "Pin" } }, { "id": "Carrico-I-S", "name": { "family": "Carrico", "given": "Isaac S." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Tirrell-D-A", "name": { "family": "Tirrell", "given": "David A." }, "orcid": "0000-0003-3175-4596" } ] }, "title": "A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins", "ispublished": "pub", "full_text_status": "public", "keywords": "Escherichia coli; Phenylalanine; Ketones; Recombinant Proteins; Phenylalanine-tRNA Ligase; Mutagenesis", "note": "\u00a9 2002 American Chemical Society.\n\nReceived December 7, 2001.\nPublication Date (Web): April 26, 2002.\n\nThe authors thank William A. Goddard III,\nNagarajan Vaidehi, Kent Kirshenbaum, and Yi Tang for helpful\ndiscussions. This work was supported by NIH Grants R01-GM62523 and T32-GM08501, the NSF Center for the Science and\nEngineering of Materials at Caltech, the Howard Hughes Medical\nInstitute, the Ralph M. Parsons Foundation, and an IBM shared\nUniversity Research Grant.\n\nPublished - Datta_2002_J_Am_Chem_Soc_A_designed_phenylalanyl-tRNA_synthetase_variant.pdf
Supplemental Material - ja0177096_s1.pdf
", "abstract": "Incorporation of non-natural amino acids into proteins in vivo expands the scope of protein synthesis and design. p-Acetylphenylalanine was incorporated into recombinant dihydrofolate reductase (DHFR) in Escherichia coli via a computationally designed mutant form of the phenylalanyl-tRNA synthetase of the host. DHFR outfitted with ketone functionality can be chemoselectively ligated with hydrazide reagents under mild conditions.", "date": "2002-05-22", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "124", "number": "20", "publisher": "American Chemical Society", "pagerange": "5652-5653", "id_number": "CaltechAUTHORS:20110620-160431532", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160431532", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01-GM62523" }, { "agency": "NIH", "grant_number": "T32-GM08501" }, { "agency": "NSF Center for the Science and Engineering of Materials at the California Institute of Technology" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM Shared University Research Grant" } ] }, "doi": "10.1021/ja0177096", "primary_object": { "basename": "Datta_2002_J_Am_Chem_Soc_A_designed_phenylalanyl-tRNA_synthetase_variant.pdf", "url": "https://authors.library.caltech.edu/records/8aex9-rkf65/files/Datta_2002_J_Am_Chem_Soc_A_designed_phenylalanyl-tRNA_synthetase_variant.pdf" }, "related_objects": [ { "basename": "ja0177096_s1.pdf", "url": "https://authors.library.caltech.edu/records/8aex9-rkf65/files/ja0177096_s1.pdf" } ], "resource_type": "article", "pub_year": "2002", "author_list": "Datta, Deepshikha; Wang, Pin; et el." }, { "id": "https://authors.library.caltech.edu/records/g9x3b-94d23", "eprint_id": 25477, "eprint_status": "archive", "datestamp": "2023-08-21 23:10:56", "lastmod": "2023-10-24 15:54:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bolon-D-N", "name": { "family": "Bolon", "given": "Daniel N." } }, { "id": "Voigt-C-A", "name": { "family": "Voigt", "given": "Christopher A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "De novo design of biocatalysts", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Molecular Mimicry; Computer Simulation; Directed Molecular Evolution; Enzymes; Drug Design; Antibodies: Catalytic; Catalysis", "note": "\u00a9 2002 Elsevier Science Ltd. \nPublished online 7th February 2002.\nThis research was supported by the Howard Hughes Medical Institute, the\nRalph M Parsons Foundation and a Shared University Research Grant from\nIBM (SLM), the Helen G and Arthur McCallum Foundation, the Evelyn\nSharp Graduate Fellowship, and grant GM07616 from the National\nInstitutes of Health (DNB), a National Science Foundation graduate\nresearch fellowship and a California Institute of Technology Initiative in\nComputational Molecular Biology funded by Burroughs Wellcome (CAV).", "abstract": "The challenging field of de novo enzyme design is beginning to produce exciting results. The application of powerful computational methods to functional protein design has recently succeeded at engineering target activities. In addition, efforts in directed evolution continue to expand the transformations that can be accomplished by existing enzymes. The engineering of completely novel catalytic activity requires traversing inactive sequence space in a fitness landscape, a feat that is better suited to computational design. Optimizing activity, which can include subtle alterations in backbone conformation and protein motion, is better suited to directed evolution, which is highly effective at scaling fitness landscapes towards maxima. Improved rational design efforts coupled with directed evolution should dramatically improve the scope of de novo enzyme design.", "date": "2002-04", "date_type": "published", "publication": "Current Opinion in Chemical Biology", "volume": "6", "number": "2", "publisher": "Elsevier", "pagerange": "125-129", "id_number": "CaltechAUTHORS:20110928-152719152", "issn": "1367-5931", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110928-152719152", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM Shared University Research Grant" }, { "agency": "Helen G. and Arthur McCallum Foundation" }, { "agency": "Evelyn Sharp Graduate Fellowship" }, { "agency": "NIH", "grant_number": "GM07616" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "Burroughs Wellcome Fund/Caltech Initiative in Computational Molecular Biology" } ] }, "doi": "10.1016/S1367-5931(02)00303-4", "resource_type": "article", "pub_year": "2002", "author_list": "Bolon, Daniel N.; Voigt, Christopher A.; et el." }, { "id": "https://authors.library.caltech.edu/records/h2hzp-vwc12", "eprint_id": 25478, "eprint_status": "archive", "datestamp": "2023-08-21 23:05:27", "lastmod": "2023-10-24 15:54:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lassila-K-S", "name": { "family": "Lassila", "given": "Kirsten S." } }, { "id": "Datta-D", "name": { "family": "Datta", "given": "Deepshikha" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Evaluation of the energetic contribution of an ionic network to beta-sheet stability", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Nerve Tissue Proteins; Amino Acids; Thermodynamics; Ions; Protein Structure: Secondary; Static Electricity; Kinetics; Models: Molecular; Mutation; Protein Binding; Protein Structure: Tertiary; \u03b2-Sheet; protein stability; protein design; electrostatics; side chain interactions", "note": "\u00a9 2002 The Protein Society. \n\nReceived June 19, 2001; Accepted November 30, 2001. Article first published online: 13 Apr. 2009.", "abstract": "We have evaluated the interaction energy of a three-residue ionic network constructed on the \u03b2-sheet surface of protein G using double mutant cycles. Although the two individual ion pairs were each stabilizing by ~0.6 kcal/mol, the excess gain in stability for the triad was small (0.06 kcal/mol).", "date": "2002-03", "date_type": "published", "publication": "Protein Science", "volume": "11", "number": "3", "publisher": "Wiley", "pagerange": "688-690", "id_number": "CaltechAUTHORS:20110928-153816383", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110928-153816383", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1110/ps.23502", "pmcid": "PMC2373463", "resource_type": "article", "pub_year": "2002", "author_list": "Lassila, Kirsten S.; Datta, Deepshikha; et el." }, { "id": "https://authors.library.caltech.edu/records/tz5fb-dg225", "eprint_id": 25452, "eprint_status": "archive", "datestamp": "2023-08-21 23:03:09", "lastmod": "2023-10-24 15:52:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Marshall-S-A", "name": { "family": "Marshall", "given": "Shannon A." } }, { "id": "Morgan-C-S", "name": { "family": "Morgan", "given": "Chantal S." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Electrostatics significantly affect the stability of designed homeodomain variants", "ispublished": "pub", "full_text_status": "restricted", "keywords": "protein design; protein stability; electrostatics; Poisson-Boltzmann; helix dipole", "note": "\u00a9 2002 Elsevier Science Ltd. Received 8 August 2001; received in revised form 29 November 2001; accepted 3 December 2001. Available online 25 February 2002. Edited by J. Thornton. We thank Barry Honig for helpful onversations. This work was supported by the Howard Hughes Medical\nInstitute, the Ralph M. Parsons Foundation, an IBM\nShared University Research Grant (to S.L.M.), the James\nIrvine Foundation Fellowship (to C.S.M.), a National\nInstitutes of Health training grant, and the Caltech\nInitiative in Computational Molecular Biology program,\nawarded by the Burroughs Wellcome Fund (to S.A.M.).", "abstract": "The role of electrostatic interactions in determining the stability of designed proteins was studied by constructing and analyzing a set of designed variants of the Drosophila engrailed homeodomain. Computational redesign of 29 surface positions results in a 25-fold mutant with moderate stability, similar to the wild-type protein. Incorporating helix dipole and N-capping considerations into the design algorithm by restricting amino acid composition at the helix termini and N-capping positions yields a ninefold mutant of the initial design (a 23-fold mutant of wild-type) that is over 3 kcal mol^(\u22121) more stable than the protein resulting from the unbiased design. Four additional proteins were constructed and analyzed to isolate the effects of helix dipole and N-capping interactions in each helix. Based on the results of urea-denaturation experiments and calculations using the finite difference Poisson-Boltzmann method, both classes of interaction are found to increase the stability of the designed proteins significantly. The simple electrostatic model used in the optimization of rotamers by iterative techniques (ORBIT) force-field, which is similar to the electrostatic models used in other protein design force-fields, is unable to predict the experimentally determined stabilities of the designed variants. The helix dipole and N-capping restrictions provide a simple but effective method to incorporate two types of electrostatic interactions that impact protein stability significantly.", "date": "2002-02-08", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "316", "number": "1", "publisher": "Elsevier", "pagerange": "189-199", "id_number": "CaltechAUTHORS:20110927-135624170", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110927-135624170", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "IBM Shared University Research Grant" }, { "agency": "James Irvine Foundation Fellowship" }, { "agency": "NIH Training Grant" }, { "agency": "Caltech Initiative in Computational Molecular Biology Program" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1006/jmbi.2001.5326", "resource_type": "article", "pub_year": "2002", "author_list": "Marshall, Shannon A.; Morgan, Chantal S.; et el." }, { "id": "https://authors.library.caltech.edu/records/tyh8b-bc648", "eprint_id": 647, "eprint_status": "archive", "datestamp": "2023-08-21 22:47:43", "lastmod": "2023-10-13 21:54:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bolon-D-N", "name": { "family": "Bolon", "given": "Daniel N." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Enzyme-like proteins by computational design", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2001 by The National Academy of Sciences\n\nFrom the cover \n\nCommunicated by Douglas C. Rees, California Institute of Technology, Pasadena, CA, October 17, 2001 (received for review August 6, 2001) \n\nWe acknowledge F. S. Lee and D. B\u00f6kenkamp for their important early efforts and P. Strop and R. A. Olofson for helpful discussions. We thank G. Hathaway and the Protein/Peptide Micro Analytical Laboratory for mass spectra. This work was supported by the Howard Hughes Medical Institute and the Ralph M. Parsons Foundation (S.L.M.), the Helen G. and Arthur McCallum Foundation, the Evelyn Sharp Graduate Fellowship, and by a training grant from the National Institutes of Health (D.N.B.). \n\nThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. \u00a71734 solely to indicate this fact.\n\nPublished - BOLpnas01.pdf
", "abstract": "We report the development and initial experimental validation of a computational design procedure aimed at generating enzyme-like protein catalysts called \"protozymes.\" Our design approach utilizes a \"compute and build\" strategy that is based on the physical/chemical principles governing protein stability and catalytic mechanism. By using the catalytically inert 108-residue Escherichia coli thioredoxin as a scaffold, the histidine-mediated nucleophilic hydrolysis of p-nitrophenyl acetate as a model reaction, and the ORBIT protein design software to compute sequences, an active site scan identified two promising catalytic positions and surrounding active-site mutations required for substrate binding. Experimentally, both candidate protozymes demonstrated catalytic activity significantly above background. One of the proteins, PZD2, displayed \"burst\" phase kinetics at high substrate concentrations, consistent with the formation of a stable enzyme intermediate. The kinetic parameters of PZD2 are comparable to early catalytic Abs. But, unlike catalytic Ab design, our design procedure is independent of fold, suggesting a possible mechanism for examining the relationships between protein fold and the evolvability of protein function.", "date": "2001-12-04", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "98", "number": "25", "publisher": "National Academy of Sciences", "pagerange": "14274-14279", "id_number": "CaltechAUTHORS:BOLpnas01", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:BOLpnas01", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Helen G. and Arthur McCallum Foundation" }, { "agency": "Evelyn Sharp Graduate Fellowship" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "doi": "10.1073/pnas.251555398", "pmcid": "PMC64672", "primary_object": { "basename": "BOLpnas01.pdf", "url": "https://authors.library.caltech.edu/records/tyh8b-bc648/files/BOLpnas01.pdf" }, "resource_type": "article", "pub_year": "2001", "author_list": "Bolon, Daniel N. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/mghj5-rsz19", "eprint_id": 25474, "eprint_status": "archive", "datestamp": "2023-08-21 22:31:07", "lastmod": "2023-10-24 15:54:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bolon-D-N", "name": { "family": "Bolon", "given": "Daniel N." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Circular Dichroism; Mutagenesis: Site-Directed; Amino Acid Substitution; Amino Acid Sequence; Models: Molecular; Hydrogen Bonding; Escherichia coli; Thioredoxins; Nuclear Magnetic Resonance: Biomolecular; Protein Folding; Computer Simulation; Calorimetry: Differential Scanning; Protein Structure: Secondary; Recombinant Proteins; Spectrometry: Fluorescence", "note": "\u00a9 2001 American Chemical Society. Received March 1, 2001; Revised Manuscript Received June 5, 2001.\nPublication Date (Web): August 1, 2001.\n\n\nThis research was supported by the Howard Hughes Medical\nInstitute and the Ralph M. Parsons Foundation (S.L.M.), the Helen G.\nand Arthur McCallum Foundation, the Evelyn Sharp Graduate Fellowship,\nand Grant GM07616 from the National Institutes of Health\n(D.N.B.).\n\nWe thank Scott Ross for guidance and assistance with\nNMR studies as well as useful discussions, and Arthur Street\nfor compiling the data set analyzed in Figure 1.", "abstract": "Most globular proteins contain a core of hydrophobic residues that are inaccessible to solvent in the folded state. In general, polar residues in the core are thermodynamically unfavorable except when they are able to form intramolecular hydrogen bonds. Compared to hydrophobic interactions, polar interactions are more directional in character and may aid in fold specificity. In a survey of 263 globular protein structures, we found a strong positive correlation between the number of polar residues at core positions and protein size. To probe the importance of buried polar residues, we experimentally tested the effects of hydrophobic mutations at the five polar core residues in Escherichia coli thioredoxin. Proteins with single hydrophobic mutations (D26I, C32A, C35A, T66L, and T77V) all have cooperative unfolding transitions like the wild type (wt), as determined by chemical denaturation. Relative to wt, D26I is more stable while the other point mutants are less stable. The combined 5-fold mutant protein (IAALV) is less stable than wt and has an unfolding transition that is substantially less cooperative than that of wt. NMR spectra as well as amide deuterium exchange indicate that IAALV is likely sampling a number of low-energy structures in the folded state, suggesting that polar residues in the core are important for specifying a well-folded native structure.", "date": "2001-08-28", "date_type": "published", "publication": "Biochemistry", "volume": "40", "number": "34", "publisher": "American Chemical Society", "pagerange": "10047-10053", "id_number": "CaltechAUTHORS:20110928-133003644", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110928-133003644", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Helen G. and Arthur McCallum Foundation" }, { "agency": "Evelyn Sharp Graduate Fellowship" }, { "agency": "NIH", "grant_number": "GM07616" } ] }, "doi": "10.1021/bi010427y", "resource_type": "article", "pub_year": "2001", "author_list": "Bolon, Daniel N. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/gzry3-03r67", "eprint_id": 25533, "eprint_status": "archive", "datestamp": "2023-08-21 22:09:12", "lastmod": "2023-10-24 15:57:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Sarisky-C-A", "name": { "family": "Sarisky", "given": "Catherine A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "The \u03b2\u03b2\u03b1 fold: explorations in sequence space", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Software; Amino Acid Sequence; Protein Engineering; Magnetic Resonance Spectroscopy; Solutions; Transcription Factors; Thermodynamics; Zinc Fingers; Molecular Sequence Data; Algorithms; DNA-Binding Proteins; Circular Dichroism; Protein Folding; Mutation; Peptides; Computer Simulation; Models: Molecular; Rubredoxins; Hydrogen Bonding; Protein Structure: Secondary; protein design; negative design; zinc finger; ORBIT", "note": "\u00a9 2001 Academic Press.\nReceived 23 August 2000; revised 14 November 2000; Accepted 15 November 2000. Available online 26 February 2002.\n\nWe thank Scott Ross for assistance with NMR data\ncollection and helpful discussions regarding the FSD-EY\nsolution structure. Shannon Marshall, Chantal Morgan,\nBassil Dahiyat, and Alyce Su provided insights into\npeptide synthesis, purification, and characterization by\nCD. This work was supported by the Howard Hughes\nMedical Institute (S. L. M.) and the National Science\nFoundation (C. A. S.).", "abstract": "The computational redesign of the second zinc finger of Zif268 to produce a 28 residue peptide (FSD-1) that assumes a \u03b2\u03b2\u03b1 fold without metal binding was recently reported. In order to explore the tolerance of this metal-free fold towards sequence variability, six additional peptides resulting from the ORBIT computational protein design process were synthesized and characterized. The experimental stabilities of five of these peptides are strongly correlated with the energies calculated by ORBIT. However, when a peptide with a mutation in the \u03b2-turn is examined, the calculated stability does not accurately predict the experimentally determined stability. The NMR solution structure of a peptide incorporating this mutation (FSD-EY) reveals that the register between the \u03b2-strands is different from the model structure used to select and score the sequences. FSD-EY has a type I' turn instead of the target EbaaagbE turn (rubredoxin knuckle). Two additional peptides that have improved side-chain to backbone hydrogen bonding and turn propensity for the target turn were characterized. Both are of stability comparable to that of FSD-1. These results demonstrate the robustness of the ORBIT protein design methods and underscore the need for continued improvements in negative design.", "date": "2001-04-13", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "307", "number": "5", "publisher": "Elsevier", "pagerange": "1411-1418", "id_number": "CaltechAUTHORS:20111003-155045528", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111003-155045528", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF" } ] }, "doi": "10.1006/jmbi.2000.4345", "resource_type": "article", "pub_year": "2001", "author_list": "Sarisky, Catherine A. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/1jvdw-88d14", "eprint_id": 640, "eprint_status": "archive", "datestamp": "2023-08-21 22:06:23", "lastmod": "2023-10-13 21:54:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Voigt-C-A", "name": { "family": "Voigt", "given": "Christopher A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" }, { "id": "Wang-Zhen-Gang", "name": { "family": "Wang", "given": "Zhen-Gang" }, "orcid": "0000-0002-3361-6114" } ] }, "title": "Computational method to reduce the search space for directed protein evolution", "ispublished": "pub", "full_text_status": "public", "keywords": "in vitro directed evolution, computational protein design, combinatorial optimization, mean-field theory, protein tolerance", "note": "\u00a9 2001 by The National Academy of Sciences \n\nCommunicated by William A. Goddard III, California Institute of Technology, Pasadena, CA, December 22, 2000 (received for review May 26, 2000) \n\nC.A.V. is supported by a National Science Foundation graduate research fellowship and by a California Institute of Technology Initiative in Computational Molecular Biology, a Burroughs Wellcome-funded program for science at the interface. Financial support was provided by the Howard Hughes Medical Institute (S.L.M.). We thank Hue Sun Chan, Peter Kollman, Alan Fersht, John Yin, and Walter Fontana for advance readings of this manuscript and critical comments. \n\nThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. \u00a71734 solely to indicate this fact.\n\nPublished - VOIpnas01.pdf
", "abstract": "We introduce a computational method to optimize the in vitro evolution of proteins. Simulating evolution with a simple model that statistically describes the fitness landscape, we find that beneficial mutations tend to occur at amino acid positions that are tolerant to substitutions, in the limit of small libraries and low mutation rates. We transform this observation into a design strategy by applying mean-field theory to a structure-based computational model to calculate each residue's structural tolerance. Thermostabilizing and activity-increasing mutations accumulated during the experimental directed evolution of subtilisin E and T4 lysozyme are strongly directed to sites identified by using this computational approach. This method can be used to predict positions where mutations are likely to lead to improvement of specific protein properties.", "date": "2001-03-27", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "98", "number": "7", "publisher": "National Academy of Sciences", "pagerange": "3778-3783", "id_number": "CaltechAUTHORS:VOIpnas01", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:VOIpnas01", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship" }, { "agency": "Caltech Initiative in Computational Molecular Biology" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1073/pnas.051614498", "pmcid": "PMC31129", "primary_object": { "basename": "VOIpnas01.pdf", "url": "https://authors.library.caltech.edu/records/1jvdw-88d14/files/VOIpnas01.pdf" }, "resource_type": "article", "pub_year": "2001", "author_list": "Voigt, Christopher A.; Mayo, Stephen L.; et el." }, { "id": "https://authors.library.caltech.edu/records/dw7x0-j1a53", "eprint_id": 24143, "eprint_status": "archive", "datestamp": "2023-08-19 07:15:19", "lastmod": "2023-10-23 20:20:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ross-S-A", "name": { "family": "Ross", "given": "Scott A." } }, { "id": "Sarisky-C-A", "name": { "family": "Sarisky", "given": "Catherine A." } }, { "id": "Su-Alyce", "name": { "family": "Su", "given": "Alyce" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Thermodynamics, Software, Mutation, Models: Molecular, Protein Structure: Tertiary, Protein Conformation, Bacterial Proteins, Magnetic Resonance Spectroscopy", "note": "\u00a9 2001 The Protein Society.\nPublished by Cold Spring Harbor Laboratory Press.\n\nReceived August 1, 2000; Final Revision November 6, 2000; Accepted November 6, 2000.\nArticle first published online: 31 Dec. 2008.\n\nWe thank Monica Breckow for assistance with molecular biology\nprotocols. This work was supported by the Howard Hughes Medical\nInstitute (S.L.M.). C.A.S. is partially supported by an NSF\ngraduate research fellowship. Coordinates and NMR restraints\nhave been deposited in the Protein Data Bank. Accession numbers\nfor the coordinates are 1fd6 and 1fc1 for \u03940 and \u03941.5, respectively.\nThe publication costs of this article were defrayed in part by\npayment of page charges. This article must therefore be hereby\nmarked \"advertisement\" in accordance with 18 USC section 1734\nsolely to indicate this fact.", "abstract": "The solution structures of two computationally designed core variants of the \u03b21 domain of streptococcal protein G (G\u03b21) were solved by ^1H NMR methods to assess the robustness of amino acid sequence selection by the ORBIT protein design package under changes in protein backbone specification. One variant has mutations at three of 10 core positions and corresponds to minimal perturbations of the native G\u03b21 backbone. The other, with mutations at six of 10 positions, was calculated for a backbone in which the separation between G\u03b21's \u03b1-helix and \u03b2-sheet was increased by 15% relative to native G\u03b21. Exchange broadening of some resonances and the complete absence of others in spectra of the sixfold mutant bespeak conformational heterogeneity in this protein. The NMR data were sufficiently abundant, however, to generate structures of similar, moderately high quality for both variants. Both proteins adopt backbone structures similar to their target folds. Moreover, the sequence selection algorithm successfully predicted all core \u03c7(1) angles in both variants, five of six \u03c7_2 angles in the threefold mutant and four of seven \u03c7_2 angles in the sixfold mutant. We conclude that ORBIT calculates sequences that fold specifically to a geometry close to the template, even when the template is moderately perturbed relative to a naturally occurring structure. There are apparently limits to the size of acceptable perturbations: In this study, the larger perturbation led to undesired dynamic behavior.", "date": "2001-02", "date_type": "published", "publication": "Protein Science", "volume": "10", "number": "2", "publisher": "Wiley", "pagerange": "450-454", "id_number": "CaltechAUTHORS:20110621-075054655", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110621-075054655", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF" } ] }, "doi": "10.1110/ps.32501", "pmcid": "PMC2373933", "resource_type": "article", "pub_year": "2001", "author_list": "Ross, Scott A.; Sarisky, Catherine A.; et el." }, { "id": "https://authors.library.caltech.edu/records/4nrp8-eyq98", "eprint_id": 24122, "eprint_status": "archive", "datestamp": "2023-08-21 21:57:29", "lastmod": "2023-10-23 20:19:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Marshall-S-A", "name": { "family": "Marshall", "given": "Shannon A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Achieving stability and conformational specificity in designed proteins via binary patterning", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Databases as Topic; Reproducibility of Results; Protein Engineering; Magnetic Resonance Spectroscopy; Protein Denaturation; Transcription Factors; Calorimetry: Differential Scanning; Thermodynamics; Homeodomain Proteins; Light; Animals; Protein Conformation; Circular Dichroism; Recombinant Proteins; Protein Folding; Mutation; Guanidine; Scattering: Radiation; Models: Molecular; Solvents; protein design; binary patterning; conformational specificity; protein stability; random energy model", "note": "\u00a9 2001 Academic Press.\nReceived 18 August 2000; revised 13 November 2000; Accepted 13 November 2000. Available online 26 February 2002.\n\nThis work was supported by the Howard Hughes Medical Institute (S.L.M.), the National Institutes of Health, and the Caltech Initiative in Computational Molecular Biology, which is funded by a Burroughs Wellcome Fund Interfaces Award (S.A.M.).", "abstract": "We have developed a method to determine the optimal binary pattern (arrangement of hydrophobic and polar amino acids) of a target protein fold prior to amino acid sequence selection in protein design studies. A solvent accessible surface is generated for a target fold using its backbone coordinates and \"generic\" side-chains, which are constructs whose size and shape are similar to an average amino acid. Each position is classified as hydrophobic or polar according to the solvent exposure of its generic side-chain. The method was tested by analyzing a set of proteins in the Protein Data Bank and by experimentally constructing and analyzing a set of engrailed homeodomain variants whose binary patterns were systematically varied. Selection of the optimal binary pattern results in a designed protein that is monomeric, well-folded, and hyperthermophilic. Homeodomain variants with fewer hydrophobic residues are destabilized, while additional hydrophobic residues induce aggregation. Binary patterning, in conjunction with a force field that models folded state energies, appears sufficient to satisfy two basic goals of protein design: stability and conformational specificity.", "date": "2001-01-19", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "305", "number": "3", "publisher": "Elsevier", "pagerange": "619-631", "id_number": "CaltechAUTHORS:20110620-160433490", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160433490", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH" }, { "agency": "Caltech Initiative in Computational Molecular Biology" }, { "agency": "Burroughs Wellcome Fund Interfaces Award" } ] }, "doi": "10.1006/jmbi.2000.4319", "resource_type": "article", "pub_year": "2001", "author_list": "Marshall, Shannon A. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/nsd2w-cq956", "eprint_id": 25455, "eprint_status": "archive", "datestamp": "2023-08-21 21:48:27", "lastmod": "2023-10-24 15:53:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Voigt-C-A", "name": { "family": "Voigt", "given": "Christopher A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Arnold-F-H", "name": { "family": "Arnold", "given": "Frances H." }, "orcid": "0000-0002-4027-364X" }, { "id": "Wang-Zhen-Gang", "name": { "family": "Wang", "given": "Zhen-Gang" }, "orcid": "0000-0002-3361-6114" } ] }, "title": "Computationally Focusing the Directed Evolution of Proteins", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Mutagenesis; Directed Molecular Evolution; Proteins; Algorithms; Recombination: Genetic; DNA; Computational Biology; directed evolution; recombination; computational methods", "note": "\u00a9 2002 Wiley-Liss, Inc. Received 18 September 2001; Accepted 19 September 2001. Article first published online: 29 Jan 2002.", "abstract": "Directed evolution has proven to be a successful strategy for the modification of enzyme properties. To date, the preferred experimental procedure has been to apply mutations or crossovers randomly throughout the gene. With the emergence of powerful computational methods, it has become possible to develop focused combinatorial searches, guided by computer algorithms. Here, we describe several computational methods that have emerged to aid the optimization of mutant libraries, the targeting of specific residues for mutagenesis, and the design of recombination experiments.", "date": "2001", "date_type": "published", "publication": "Journal of Cellular Biochemistry", "volume": "84", "number": "S37", "publisher": "Wiley-Blackwell", "pagerange": "58-63", "id_number": "CaltechAUTHORS:20110927-154155139", "issn": "0730-2312", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110927-154155139", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1002/jcb.10066", "resource_type": "article", "pub_year": "2001", "author_list": "Voigt, Christopher A.; Mayo, Stephen L.; et el." }, { "id": "https://authors.library.caltech.edu/records/sb9hm-zzn70", "eprint_id": 24128, "eprint_status": "archive", "datestamp": "2023-08-21 21:25:44", "lastmod": "2023-10-23 20:19:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shimaoka-Motomu", "name": { "family": "Shimaoka", "given": "Motomu" } }, { "id": "Shifman-Julia-M", "name": { "family": "Shifman", "given": "Julia M." } }, { "id": "Jing-Hua", "name": { "family": "Jing", "given": "Hua" } }, { "id": "Takagi-Junichi", "name": { "family": "Takagi", "given": "Junichi" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Springer-Timothy-A", "name": { "family": "Springer", "given": "Timothy A." } } ] }, "title": "Computational design of an integrin I domain stabilized in the open high affinity conformation", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Transfection; Protein Binding; Complement C3b; Thermodynamics; Integrins; Amino Acid Substitution; Computer Simulation; Humans; Dimerization; Models: Molecular; Cell Line; Protein Engineering; Protein Structure: Tertiary; Mutation; Binding Sites; Structure-Activity Relationship; Protein Structure: Secondary; Ligands", "note": "\u00a9 2000 Nature America Inc. Received 13 April, 2000; accepted 20 June, 2000. We thank M. Ferzly for technical assistance. This work was supported by the NIH.", "abstract": "We have taken a computational approach to design mutations that stabilize a large protein domain of approximately 200 residues in two alternative conformations. Mutations in the hydrophobic core of the \u03b1M\u03b22 integrin I domain were designed to stabilize the crystallographically defined open or closed conformers. When expressed on the cell surface as part of the intact heterodimeric receptor, binding of the designed open and closed I domains to the ligand iC3b, a form of the complement component C3, was either increased or decreased, respectively, compared to wild type. Moreover, when expressed in isolation from other integrin domains using an artificial transmembrane domain, designed open I domains were active in ligand binding, whereas designed closed and wild type I domains were inactive. Comparison to a human expert designed open mutant showed that the computationally designed mutants are far more active. Thus, computational design can be used to stabilize a molecule in a desired conformation, and conformational change in the I domain is physiologically relevant to regulation of ligand binding.", "date": "2000-08", "date_type": "published", "publication": "Nature Structural Biology", "volume": "7", "number": "8", "publisher": "Nature Publishing Group", "pagerange": "674-678", "id_number": "CaltechAUTHORS:20110620-160434458", "issn": "1072-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160434458", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" } ] }, "doi": "10.1038/77978", "resource_type": "article", "pub_year": "2000", "author_list": "Shimaoka, Motomu; Shifman, Julia M.; et el." }, { "id": "https://authors.library.caltech.edu/records/mn5zg-k3887", "eprint_id": 24114, "eprint_status": "archive", "datestamp": "2023-08-21 21:25:36", "lastmod": "2023-10-23 20:18:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pierce-N-A", "name": { "family": "Pierce", "given": "Niles A." }, "orcid": "0000-0003-2367-4406" }, { "id": "Spriet-J-A", "name": { "family": "Spriet", "given": "Jan A." } }, { "id": "Desmet-J", "name": { "family": "Desmet", "given": "Johan" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Conformational splitting: a more powerful criterion for dead-end elimination", "ispublished": "pub", "full_text_status": "restricted", "keywords": "dead-end elimination; conformational splitting; global minimum\nenergy conformation; side-chain placement; protein design", "note": "\u00a9 2000 John Wiley & Sons, Inc. \n\nReceived 19 November 1999; accepted 9 March 2000. Article first published online: 21 Jun. 2000. \n\nN.A.P. thanks D. B. Gordon for many helpful discussions. J.A.S. and J.D. thank I. Lasters and M. De Maeyer for their interest and occasional help as peers in the common field. \n\nContract/grant sponsors: Burroughs-Wellcome Foundation;\nCaltech Initiative in Computational Molecular Biology; Faculty\nof Agricultural and Applied Biological Sciences; Belgian National\nFund for Scientific Research (FWO); Howard Hughes Medical\nInstitute", "abstract": "Dead-end elimination (DEE) is a powerful theorem for selecting optimal protein side-chain orientations from a large set of discrete conformations. The present work describes a new approach to dead-end elimination that effectively splits conformational space into partitions to more efficiently eliminate dead-ending rotamers. Split DEE makes it possible to complete protein design calculations that were previously intractable due to the combinatorial explosion of intermediate conformations generated during the convergence process.", "date": "2000-08", "date_type": "published", "publication": "Journal of Computational Chemistry", "volume": "21", "number": "11", "publisher": "Wliey", "pagerange": "999-1009", "id_number": "CaltechAUTHORS:20110620-160432187", "issn": "0192-8651", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160432187", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs-Wellcome Foundation" }, { "agency": "Caltech Initiative in Computational Molecular Biology" }, { "agency": "Katholieke University Leuven" }, { "agency": "Fonds Wetenschappelijk Onderzoek - Vlaanderen (FWO)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1002/1096-987X(200008)21:11<999::AID-JCC9>3.0.CO;2-A", "resource_type": "article", "pub_year": "2000", "author_list": "Pierce, Niles A.; Spriet, Jan A.; et el." }, { "id": "https://authors.library.caltech.edu/records/exc3c-ej567", "eprint_id": 24136, "eprint_status": "archive", "datestamp": "2023-08-19 05:59:16", "lastmod": "2023-10-23 20:19:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Strop-P", "name": { "family": "Strop", "given": "Pavel" } }, { "id": "Marinescu-A-M", "name": { "family": "Marinescu", "given": "Andrei M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Hydrogen Bonding, Crystallography: X-Ray, Static Electricity, Mutation, Models: Molecular, Algorithms, Protein Conformation, Protein Engineering, Nerve Tissue Proteins", "note": "\u00a9 2000 The Protein Society.\n\nReceived March 29, 2000; Final Revision May 3, 2000; Accepted May 11, 2000.\nArticle first published online: 31 Dec. 2008.\nThis work was supported by the Howard Hughes\nMedical Institute (S.L.M.) and a NSF fellowship (P.S.).", "abstract": "Six helix surface positions of protein G (G\u03b21) were redesigned using a computational protein design algorithm, resulting in the five fold mutant G\u03b21m2. G\u03b21m2 is well folded with a circular dichroism spectrum nearly identical to that of G\u03b21, and a melting temperature of 91 \u00b0C, ~6 \u00b0C higher than that of G\u03b21. The crystal structure of G\u03b21m2 was solved to 2.0 \u00c5 resolution by molecular replacement. The absence of hydrogen bond or salt bridge interactions between the designed residues in G\u03b21m2 suggests that the increased stability of G\u03b21m2 is due to increased helix propensity and more favorable helix dipole interactions.", "date": "2000-07", "date_type": "published", "publication": "Protein Science", "volume": "9", "number": "7", "publisher": "Wiley", "pagerange": "1391-1394", "id_number": "CaltechAUTHORS:20110620-160435792", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160435792", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF" } ] }, "doi": "10.1110/ps.9.7.1391", "pmcid": "PMC2144681", "resource_type": "article", "pub_year": "2000", "author_list": "Strop, Pavel; Marinescu, Andrei M.; et el." }, { "id": "https://authors.library.caltech.edu/records/vzpt0-tdq09", "eprint_id": 24123, "eprint_status": "archive", "datestamp": "2023-08-21 21:16:56", "lastmod": "2023-10-23 20:19:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Voigt-C-A", "name": { "family": "Voigt", "given": "Christopher A." } }, { "id": "Gordon-D-B", "name": { "family": "Gordon", "given": "D. Benjamin" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Stochastic Processes; Protein Engineering; Algorithms; Proteins; Combinatorial Chemistry Techniques; Probability, Databases: Factual; Sensitivity and Specificity; Monte Carlo Method; Protein Structure: Secondary; Thermodynamics; Temperature; Time Factors; protein design; combinatorial optimization", "note": "\u00a9 2000 Academic Press.\nReceived 27 September 1999; revised 27 January 2000; Accepted 23 February 2000. Available online 25 March 2002.\nEdited by J. Thornton.\nThe work was partially supported by the Howard\nHughes Medical Institute, NIH training grant GM 08346,\nthe Helen G. and Arthur McCallum Foundation (DBG),\nand a National Science Foundation Graduate Fellowship\n(CAV).", "abstract": "Finding the minimum energy amino acid side-chain conformation is a fundamental problem in both homology modeling and protein design. To address this issue, numerous computational algorithms have been proposed. However, there have been few quantitative comparisons between methods and there is very little general understanding of the types of problems that are appropriate for each algorithm. Here, we study four common search techniques: Monte Carlo (MC) and Monte Carlo plus quench (MCQ); genetic algorithms (GA); self-consistent mean field (SCMF); and dead-end elimination (DEE). Both SCMF and DEE are deterministic, and if DEE converges, it is guaranteed that its solution is the global minimum energy conformation (GMEC). This provides a means to compare the accuracy of SCMF and the stochastic methods. For the side-chain placement calculations, we find that DEE rapidly converges to the GMEC in all the test cases. The other algorithms converge on significantly incorrect solutions; the average fraction of incorrect rotamers for SCMF is 0.12, GA 0.09, and MCQ 0.05. For the protein design calculations, design positions are progressively added to the side-chain placement calculation until the time required for DEE diverges sharply. As the complexity of the problem increases, the accuracy of each method is determined so that the results can be extrapolated into the region where DEE is no longer tractable. We find that both SCMF and MCQ perform reasonably well on core calculations (fraction amino acids incorrect is SCMF 0.07, MCQ 0.04), but fail considerably on the boundary (SCMF 0.28, MCQ 0.32) and surface calculations (SCMF 0.37, MCQ 0.44).", "date": "2000-06-09", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "299", "number": "3", "publisher": "Elsevier", "pagerange": "789-803", "id_number": "CaltechAUTHORS:20110620-160433649", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160433649", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Training Grant Fellowship", "grant_number": "GM 08346" }, { "agency": "Helen G. and Arthur McCallum Foundation" }, { "agency": "NSF Graduate Fellowship" } ] }, "doi": "10.1006/jmbi.2000.3758", "resource_type": "article", "pub_year": "2000", "author_list": "Voigt, Christopher A.; Gordon, D. Benjamin; et el." }, { "id": "https://authors.library.caltech.edu/records/4wr3m-2pz76", "eprint_id": 24134, "eprint_status": "archive", "datestamp": "2023-08-19 05:47:52", "lastmod": "2023-10-23 20:19:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Street-A-G", "name": { "family": "Street", "given": "Arthur G." } }, { "id": "Datta-D", "name": { "family": "Datta", "given": "Deepshikha" } }, { "id": "Gordon-D-B", "name": { "family": "Gordon", "given": "D. Benjamin" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Designing protein \u03b2-sheet surfaces by Z-score optimization", "ispublished": "pub", "full_text_status": "public", "keywords": "Protein Structure: Secondary, Proteins, Thermodynamics, Models: Chemical", "note": "\u00a9 2000 American Physical Society.\nReceived 27 September 1999; published in the issue dated 22 May 2000.\n\nPublished - Street_2000_Phys_Rev_Lett_Designing_protein_beta-sheet_surfaces_by.pdf
", "abstract": "Studies of lattice models of proteins have suggested that the appropriate energy expression for protein design may include nonthermodynamic terms to accommodate negative design concerns. One method, developed in lattice model studies, maximizes a quantity known as the \"Z-score,\" which compares the lowest energy sequence whose ground state structure is the target structure to an ensemble of random sequences. Here we show that, in certain circumstances, the technique can be applied to real proteins. The resulting energy expression is used to design the \u03b2-sheet surfaces of two real proteins. We find experimentally that the designed proteins are stable and well folded, and in one case is even more thermostable than the wild type.", "date": "2000-05-22", "date_type": "published", "publication": "Physical Review Letters", "volume": "84", "number": "21", "publisher": "American Physical Society", "pagerange": "5010-5013", "id_number": "CaltechAUTHORS:20110620-160435469", "issn": "0031-9007", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160435469", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1103/PhysRevLett.84.5010", "primary_object": { "basename": "Street_2000_Phys_Rev_Lett_Designing_protein_beta-sheet_surfaces_by.pdf", "url": "https://authors.library.caltech.edu/records/4wr3m-2pz76/files/Street_2000_Phys_Rev_Lett_Designing_protein_beta-sheet_surfaces_by.pdf" }, "resource_type": "article", "pub_year": "2000", "author_list": "Street, Arthur G.; Datta, Deepshikha; et el." }, { "id": "https://authors.library.caltech.edu/records/2pb5f-jfs64", "eprint_id": 24083, "eprint_status": "archive", "datestamp": "2023-08-21 20:55:47", "lastmod": "2023-10-23 20:18:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Strop-P", "name": { "family": "Strop", "given": "Pavel" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Contribution of surface salt bridges to protein stability", "ispublished": "pub", "full_text_status": "public", "keywords": "Solvents; Bacterial Proteins; Hydrogen Bonding; Solutions; Mutagenesis: Site-Directed; Pyrococcus furiosus; Crystallography: X-Ray; Protein Denaturation; Nuclear Magnetic Resonance: Biomolecular; Rubredoxins; Salts; Thermodynamics; Guanidine", "note": "\u00a9 2000 American Chemical Society. \n\nReceived September 27, 1999; Revised Manuscript Received November 16, 1999. Published on Web 01/19/2000. \n\nThis work was supported by the Howard Huges Medical Institute\n(S.L.M.) and a NSF fellowship (P.S.). The coordinates for the structure have been deposited in the Protein Data Bank (file 1qcv). \n\nWe thank M. K. Eidsness for the wild-type P. furiosus rubredoxin gene used in this study, S. Ross for NMR spectroscopy, and S. Ross and C. Sarisky for help with the NMR structure determination.\n\nAccepted Version - Strop_2000_Biochemistry_Contribution_of_surface_salt_bridges.pdf
", "abstract": "The role of surface salt bridges in protein stabilization has been a source of controversy. Here we present the NMR structure of a hyperthermophilic rubredoxin variant (PFRD-XC4) and the thermodynamic analysis of two surface salt bridges by double mutant cycles. This analysis shows that the surface side chain to side chain salt bridge between Lys 6 and Glu 49 does not stabilize PFRD-XC4. The main chain to side chain salt bridge between the N-terminus and Glu 14 was, however, found to stabilize PFRD-XC4 by 1. 5 kcal mol^(-1). The entropic cost of making a surface salt bridge involving the protein's backbone is reduced, since the backbone has already been immobilized upon protein folding.", "date": "2000-02-15", "date_type": "published", "publication": "Biochemistry", "volume": "39", "number": "6", "publisher": "American Chemical Society", "pagerange": "1251-1255", "id_number": "CaltechAUTHORS:20110620-160425030", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160425030", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF Graduate Research Fellowship" } ] }, "doi": "10.1021/bi992257j", "primary_object": { "basename": "Strop_2000_Biochemistry_Contribution_of_surface_salt_bridges.pdf", "url": "https://authors.library.caltech.edu/records/2pb5f-jfs64/files/Strop_2000_Biochemistry_Contribution_of_surface_salt_bridges.pdf" }, "resource_type": "article", "pub_year": "2000", "author_list": "Strop, Pavel and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/7azde-8kv47", "eprint_id": 24115, "eprint_status": "archive", "datestamp": "2023-08-22 14:02:10", "lastmod": "2023-10-23 20:18:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gordon-D-B", "name": { "family": "Gordon", "given": "D. Benjamin" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Branch-and-terminate: a combinatorial optimization algorithm for protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Protein Engineering; Models: Molecular; Algorithms; Proteins; Molecular Structure; Branch-and-Bound; dead-end elimination; global energy minimum; protein design; rotamers", "note": "\u00a9 1999 Elsevier Science Ltd.\nReceived 8 February 1999; revised 14 May 1999; Accepted 18 May 1999. Available online 20 January 2000.\n\nWe wish to thank AG Street for invaluable feedback throughout the process\nof developing the algorithm. We also wish to thank EM Reingold, R\nManohar, and N Pierce for helpful discussions. This work was supported by\nthe Howard Hughes Medical Institute (SLM), training grant GM 07616C-19\nfrom the National Institutes of Health (DBG), the Rita Allen Foundation, and\nthe David and Lucile Packard Foundation.", "abstract": "Background: Several deterministic and stochastic combinatorial optimization algorithms have been applied to computational protein design and homology modeling. As structural targets increase in size, however, it has become necessary to find more powerful methods to address the increased combinatorial complexity.\n\nResults: We present a new deterministic combinatorial search algorithm called 'Branch-and-Terminate' (B&T), which is derived from the Branch-and-Bound search method. The B&T approach is based on the construction of an efficient but very restrictive bounding expression, which is used for the search of a combinatorial tree representing the protein system. The bounding expression is used both to determine the optimal organization of the tree and to perform a highly effective pruning procedure named 'termination'. For some calculations, the B&T method rivals the current deterministic standard, dead-end elimination (DEE), sometimes finding the solution up to 21 times faster. A more significant feature of the B&T algorithm is that it can provide an efficient way to complete the optimization of problems that have been partially reduced by a DEE algorithm.\n\nConclusions: The B&T algorithm is an effective optimization algorithm when used alone. Moreover, it can increase the problem size limit of amino acid sidechain placement calculations, such as protein design, by completing DEE optimizations that reach a point at which the DEE criteria become inefficient. Together the two algorithms make it possible to find solutions to problems that are intractable by either algorithm alone.", "date": "1999-09-15", "date_type": "published", "publication": "Structure", "volume": "7", "number": "9", "publisher": "Cell Press", "pagerange": "1089-1098", "id_number": "CaltechAUTHORS:20110620-160432352", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160432352", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "GM 07616C-19" }, { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" } ] }, "doi": "10.1016/S0969-2126(99)80176-2", "resource_type": "article", "pub_year": "1999", "author_list": "Gordon, D. Benjamin and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/xz59v-qq944", "eprint_id": 648, "eprint_status": "archive", "datestamp": "2023-08-22 13:56:46", "lastmod": "2023-10-23 19:11:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Street-A-G", "name": { "family": "Street", "given": "Arthur G." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Intrinsic \u03b2-sheet propensities result from van der Waals interactions between side chains and the local backbone", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1999 by The National Academy of Sciences \n\nCommunicated by William A. Goddard, III, California Institute of Technology, Pasadena, CA, May 27, 1999 (received for review January 12, 1999) \n\nWe thank D. B. Gordon, B. I. Dahiyat, and D. W. Vernooy for helpful discussions. This work was supported by the Rita Allen Foundation and the David and Lucile Packard Foundation. A.G.S. was partially supported by a grant from the National Institutes of Health. \n\nThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. \u00a71734 solely to indicate this fact.\n\nPublished - STRpnas99.pdf
", "abstract": "The intrinsic secondary structure-forming propensities of the naturally occurring amino acids have been measured both experimentally in host-guest studies and statistically by examination of the protein structure databank. There has been significant progress in understanding the origins of intrinsic alpha -helical propensities, but a unifying theme for understanding intrinsic beta -sheet propensities has remained elusive. To this end, we modeled dipeptides by using a van der Waals energy function and derived Ramachandran plots for each of the amino acids. These data were used to determine the entropy and Helmholtz free energy of placing each amino acid in the beta -sheet region of phi ---psi space. We quantitatively establish that the dominant cause of intrinsic beta -sheet propensity is the avoidance of steric clashes between an amino acid side chain and its local backbone. Standard implementations of coulombic and solvation effects are seen to be less important.", "date": "1999-08-03", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "96", "number": "16", "publisher": "National Academy of Sciences", "pagerange": "9074-9076", "id_number": "CaltechAUTHORS:STRpnas99", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:STRpnas99", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "NIH" } ] }, "pmcid": "PMC17734", "primary_object": { "basename": "STRpnas99.pdf", "url": "https://authors.library.caltech.edu/records/xz59v-qq944/files/STRpnas99.pdf" }, "resource_type": "article", "pub_year": "1999", "author_list": "Street, Arthur G. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/bbn7d-xjc14", "eprint_id": 24160, "eprint_status": "archive", "datestamp": "2023-08-19 04:33:56", "lastmod": "2023-10-23 20:21:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gordon-D-B", "name": { "family": "Gordon", "given": "D. Benjamin" } }, { "id": "Marshall-S-A", "name": { "family": "Marshall", "given": "Shannon A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Energy functions for protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Protein Engineering, Hydrogen Bonding, Models: Molecular, Solubility, Entropy, Chemistry: Physical, Physicochemical Phenomena, Computer Simulation, Static Electricity, Energy Metabolism, Drug Design, Models: Chemical", "note": "\u00a9 1999 Elsevier Science Ltd.\nAvailable online 22 September 1999. \n\nWe wish to thank AG Street for helpful comments on the manuscript. This\nwork was supported by the Howard Hughes Medical Institute (SLM), the\nHelen G and Arthur McCallum Foundation (DBG), a National Institutes of\nHealth NRSA training grant and the Caltech Initiative in Computational\nMolecular Biology program, awarded by the Burroughs Wellcome Fund (SAM).", "abstract": "Recent successes in protein design have illustrated the promise of computational approaches. These methods rely on energy expressions to evaluate the quality of different amino acid sequences for target protein structures. The force fields optimized for design differ from those typically used in molecular mechanics and molecular dynamics calculations.", "date": "1999-08", "date_type": "published", "publication": "Current Opinion in Structural Biology", "volume": "9", "number": "4", "publisher": "Elsevier", "pagerange": "509-513", "id_number": "CaltechAUTHORS:20110621-154505395", "issn": "0959-440X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110621-154505395", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Helen G and Arthur McCallum Foundation" }, { "agency": "NIH NRSA Training Grant" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1016/S0959-440X(99)80072-4", "resource_type": "article", "pub_year": "1999", "author_list": "Gordon, D. Benjamin; Marshall, Shannon A.; et el." }, { "id": "https://authors.library.caltech.edu/records/sx2g6-s1z69", "eprint_id": 24131, "eprint_status": "archive", "datestamp": "2023-08-19 04:21:39", "lastmod": "2023-10-23 20:19:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Street-A-G", "name": { "family": "Street", "given": "Arthur G." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Computational protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Protein Conformation, Proteins, Algorithms", "note": "\u00a9 1999 Elsevier Science Ltd.\nAvailable online 6 July 1999.", "abstract": "A 'protein design cycle', involving cycling between theory and experiment, has led to recent advances in rational protein design. A reductionist approach, in which protein positions are classified by their local environments, has aided development of an appropriate energy expression. The computational principles and practicalities of the protein design cycle are discussed.", "date": "1999-05-15", "date_type": "published", "publication": "Structure", "volume": "7", "number": "5", "publisher": "Cell Press", "pagerange": "R105-R109", "id_number": "CaltechAUTHORS:20110620-160435008", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160435008", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/S0969-2126(99)80062-8", "resource_type": "article", "pub_year": "1999", "author_list": "Street, Arthur G. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/swfpd-hzv11", "eprint_id": 24068, "eprint_status": "archive", "datestamp": "2023-08-19 04:10:27", "lastmod": "2023-10-23 20:17:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Strop-P", "name": { "family": "Strop", "given": "Pavel" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Rubredoxin Variant Folds without Iron", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1999 American Chemical Society. Received October 1, 1998. Publication Date (Web): March 5, 1999. We thank M. K. Eidness for the wild type Pyroccocus furiosus rubredoxin gene used in this study, S. M. Malakauskas, S. Ross, and C. Sarisky for technical assistance and discussions, and B. I. Dahiyat for discussions. The work was supported by the Howard Hughes Medical Institute (S.L.M.) and a NIH training grant (P.S.).\n\nPublished - Strop_1999_J_Am_Chem_Soc_Rubredoxin_variant_folds_without_iron.pdf
", "abstract": "Pyroccocus furiosus rubredoxin (PFRD), like most studied hyperthermophilic proteins, does not undergo reversible folding. The irreversibility of folding is thought to involve PFRD's iron-binding site. Here we report a PFRD variant (PFRD-XC4) whose iron binding site was redesigned to eliminate iron binding using a computational design algorithm. PFRD-XC4 folds without iron and exhibits reversible folding with a melting temperature of 82 \u00b0C, a thermodynamic stability of 3.2 kcal mol^(-1) at 1 \u00b0C, and NMR chemical shifts similar to that of the wild-type protein. This variant should provide a tractable model system for studying the thermodynamic origins of protein hyperthermostability.", "date": "1999-03-24", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "121", "number": "11", "publisher": "American Chemical Society", "pagerange": "2341-2345", "id_number": "CaltechAUTHORS:20110620-160421544", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160421544", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH Training Grant" } ] }, "doi": "10.1021/ja9834780", "primary_object": { "basename": "Strop_1999_J_Am_Chem_Soc_Rubredoxin_variant_folds_without_iron.pdf", "url": "https://authors.library.caltech.edu/records/swfpd-hzv11/files/Strop_1999_J_Am_Chem_Soc_Rubredoxin_variant_folds_without_iron.pdf" }, "resource_type": "article", "pub_year": "1999", "author_list": "Strop, Pavel and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/sktfm-kjj95", "eprint_id": 24079, "eprint_status": "archive", "datestamp": "2023-08-22 13:02:01", "lastmod": "2023-10-23 20:17:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Street-A-G", "name": { "family": "Street", "given": "Arthur G." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Pairwise calculation of protein solvent-accessible surface areas", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Surface Properties; Databases: Factual; Algorithms; Solvents; Proteins; dead-end elimination; hydrophobic burial; pairwise surface area; protein design; solvent-accessible surface area", "note": "\u00a9 1998 Current Biology Ltd.\nReceived: 12 January 1998;\nRevisions requested: 16 February 1998;\nRevisions received: 16 March 1998;\nAccepted: 23 March 1998;\nPublished: 03 June 1998.\nAvailable online 2 July 2005.\n\nWe thank D.B. Gordon and B.I. Dahiyat for helpful discussions and assistance.\nThis work was supported by the Rita Allen Foundation, the David and\nLucile Packard Foundation and the Searle Scholars Program/The Chicago\nCommunity Trust. A.G.S. is partially supported by the Eleanor Sophia Wood\nTravelling Scholarship from the University of Sydney, Australia.", "abstract": "Background: The tractability of many algorithms for determining the energy state of a system depends on the pairwise nature of an energy expression. Some energy terms, such as the standard implementation of the van der Waals potential, satisfy this criterion whereas others do not. One class of important potentials that are not pairwise involves benefits and penalties for burying hydrophobic and/or polar surface areas. It has been found previously that, in some cases, a pairwise approximation to these surface areas correlates with the true surface areas. We set out to generalize the applicability of this approximation.\n\nResults: We develop a pairwise expression with one scalable parameter that closely reproduces both the true buried and the true exposed solvent- accessible surface areas. We then refit our previously published coiled-coil stability data to give solvation parameters of 26 cal/mol \u00c5^2 favoring hydrophobic burial and 100 cal/mol \u00c5^2 opposing polar burial.\n\nConclusions: An accurate pairwise approximation to calculate exposed and buried protein solvent-accessible surface area is achieved.", "date": "1998-08", "date_type": "published", "publication": "Folding and Design", "volume": "3", "number": "4", "publisher": "Current Biology Ltd", "pagerange": "253-258", "id_number": "CaltechAUTHORS:20110620-160423998", "issn": "1359-0278", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160423998", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program/Chicago Community Trust" }, { "agency": "Eleanor Sophia Wood Traveling Scholarship from University of Sydney, Australia" } ] }, "doi": "10.1016/S1359-0278(98)00036-4", "resource_type": "article", "pub_year": "1998", "author_list": "Street, Arthur G. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/y3aqb-qdv50", "eprint_id": 52096, "eprint_status": "archive", "datestamp": "2023-08-19 03:02:32", "lastmod": "2023-10-18 19:33:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Duplicate Publication", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1998 American Association for the Advancement of Science.", "abstract": "We recently reported our progress toward the fully automated selection of amino acid sequences for target protein folds (1). In this communication, we described both the computational and experimental results associated with a sequence calculation that encompassed 20 of 28 residue positions in a target zinc finger fold. The success of this partial design led rapidly to a fully automated design of a new amino acid sequence for an entire protein fold (2). In our haste to report the full sequence design result, we used text and phraseology from the Journal of Molecular Biology article in the Science article. In addition, because of the closeness in time of the two publications, we did not change a reference of \"unpublished results\" in the Science article to a citation of the Journal of Molecular Biology communication, which clearly preceded the work reported in Science. We regret any confusion these events may have caused the editors and readers of Science and the Journal of Molecular Biology.", "date": "1998-06-19", "date_type": "published", "publication": "Science", "volume": "280", "number": "5371", "publisher": "American Association for the Advancement of Science", "pagerange": "1815", "id_number": "CaltechAUTHORS:20141124-105728014", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141124-105728014", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1126/science.280.5371.1815h", "resource_type": "article", "pub_year": "1998", "author_list": "Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/8t7re-2x187", "eprint_id": 24074, "eprint_status": "archive", "datestamp": "2023-08-22 12:55:29", "lastmod": "2023-10-23 20:17:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Malakauskas-S-M", "name": { "family": "Malakauskas", "given": "Sandra M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Design, structure and stability of a hyperthermophilic protein variant", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Hot Temperature; Computer Simulation; Protein Engineering; Thermodynamics; Models: Molecular; Nuclear Magnetic Resonance: Biomolecular; Streptococcus; Mutagenesis: Site-Directed; Algorithms; Protein Structure: Tertiary; Structure-Activity Relationship; Bacterial Proteins; Circular Dichroism", "note": "\u00a9 1998 Nature Publishing Group. Received March 20, 1998; accepted May 1, 1998. We thank P. Poon for sedimentation equilibrium measurements and discussions, B. Dahiyat, A. Su, S. Ross, D. B\u00f6kenkamp, and C. Sariskyfor technical assistance and discussions, and G. Hathaway for mass spectrometry. Supported by the Howard Hughes Medical Institute (S.L.M.), the Rita Alien Foundation, the Chandler Family Trust, the Booth Ferris Foundation, the David and Lucile Packard Foundation, the Searle Scholars Program and The Chicago Community Trust and an NIH training grant (S.M.M.)", "abstract": "Here we report the use of an objective computer algorithm in the design of a hyperstable variant of the Streptococcal protein G\u03b21 domain (G\u03b21). The designed seven-fold mutant, G\u03b21-c3b4, has a melting temperature in excess of 100 degrees C and an enhancement in thermodynamic stability of 4.3 kcal mol^(-1) at 50 degrees C over the wild-type protein. G\u03b21-c3b4 maintains the G\u03b21 fold, as determined by nuclear magnetic resonance spectroscopy, and also retains a significant level of binding to human IgG in qualitative comparisons with wild type. The basis of the stability enhancement appears to have multiple components including optimized core packing, increased burial of hydrophobic surface area, more favorable helix dipole interactions, and improvement of secondary structure propensity. The design algorithm is able to model such complex contributions simultaneously using empirical physical/chemical potential functions and a combinatorial optimization algorithm based on the dead-end elimination theorem. Because the design methodology is based on general principles, there is the potential of applying the methodology to the stabilization of other unrelated protein folds.", "date": "1998-06-01", "date_type": "published", "publication": "Nature Structural Biology", "volume": "5", "number": "6", "publisher": "Nature Publishing Group", "pagerange": "470-475", "id_number": "CaltechAUTHORS:20110620-160422818", "issn": "1072-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160422818", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Rita Allen Foundation" }, { "agency": "Chandler Family Trust" }, { "agency": "Booth Ferris Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" }, { "agency": "Chicago Community Trust" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "doi": "10.1038/nsb0698-470", "resource_type": "article", "pub_year": "1998", "author_list": "Malakauskas, Sandra M. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/mkezp-djv41", "eprint_id": 24073, "eprint_status": "archive", "datestamp": "2023-08-19 02:24:50", "lastmod": "2023-10-23 20:17:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "B\u00f6kenkamp-D", "name": { "family": "B\u00f6kenkamp", "given": "Dirk" } }, { "id": "Desai-A", "name": { "family": "Desai", "given": "Amish" } }, { "id": "Yang-Xing", "name": { "family": "Yang", "given": "Xing" } }, { "id": "Tai-Yu-Chong", "name": { "family": "Tai", "given": "Yu-Chong" }, "orcid": "0000-0001-8529-106X" }, { "id": "Marzluff-E-M", "name": { "family": "Marzluff", "given": "Elaine M." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Microfabricated Silicon Mixers for Submillisecond Quench-Flow Analysis", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1998 American Chemical Society. Received for review July 30, 1997. Accepted October 22, 1997. Publication Date (Web): January 15, 1998. Abstract published in Advance ACS Abstracts, December 15, 1997. This work was supported by the Rita Allen Foundation, the David and Lucile Packard Foundation and the Searle Scholars Program/The Chicago Community Trust. D.B. acknowledges support from the Deutsche Forschungsgemeinschaft.", "abstract": "Elucidation of fast chemical reactions such as protein folding requires resolution on a submillisecond time scale. However, most quench-flow and stop-flow techniques only allow chemical processes to be studied after a few milliseconds have elapsed. In order to shorten the minimum observation time for quench-flow experiments, we designed a miniaturized mixer assembly. Two \"T\" mixers connected by a channel are etched into a 1 cm \u00d7 1 cm silicon chip which is interfaced with a commercially available quench-flow instrument. Decreasing the volume of the mixing chambers and the distance between them results in an instrument with greatly reduced dead times. As a test of submillisecond measurements, we studied the basic hydrolysis of phenyl chloroacetate. This reaction proceeds with a second-order rate constant, k = 430 M^(-1) s^(-1), and shows pseudo-first-order kinetics at high hydroxide concentrations. The chemical reaction data demonstrate that the silicon device is capable of initiating and quenching chemical reactions in time intervals as short as 110 \u03bcs. The performance of these mixers was further confirmed by visualization using acid-base indicators.", "date": "1998-01-15", "date_type": "published", "publication": "Analytical Chemistry", "volume": "70", "number": "2", "publisher": "American Chemical Society", "pagerange": "232-236", "id_number": "CaltechAUTHORS:20110620-160422644", "issn": "0003-2700", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160422644", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)" }, { "agency": "Chicago Community Trust" } ] }, "doi": "10.1021/ac9708250", "resource_type": "article", "pub_year": "1998", "author_list": "B\u00f6kenkamp, Dirk; Desai, Amish; et el." }, { "id": "https://authors.library.caltech.edu/records/5j4rx-32j71", "eprint_id": 24078, "eprint_status": "archive", "datestamp": "2023-08-22 12:00:50", "lastmod": "2023-10-23 20:17:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dahiyat-B-I", "name": { "family": "Dahiyat", "given": "Bassil I." } }, { "id": "Sarisky-C-A", "name": { "family": "Sarisky", "given": "Catherine A." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "De novo protein design: towards fully automated sequence selection", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Protein Engineering; Algorithms; Amino Acid Sequence; Zinc Fingers; Drug Design; Magnetic Resonance Spectroscopy; Circular Dichroism; Protein Conformation; Models: Molecular; Molecular Sequence Data; protein design; NMR; force field; sequence optimization; dead-end elimination", "note": "\u00a9 1997 Academic Press Limited.\nReceived 22 April 1997; received in revised form\n7 August 1997; accepted 7 August 1997.\nAvailable online 22 April 2002.\n\nWe thank Scott Ross for assistance with NMR studies,\nPak Poon of the UCLA Molecular Biology Institute for\nsedimentation equilibrium studies, and Gary Hathaway\nof the Caltech Protein and Peptide Microanalytical Laboratory\nfor mass spectra. We acknowledge financial support\nfrom the Rita Allen Foundation, the David and\nLucile Packard Foundation and the Searle Scholars Program/\nThe Chicago Community Trust. B.I.D. is partially\nsupported by NIH Training Grant GM 08346.", "abstract": "Several groups have applied and experimentally tested systematic, quantitative methods to protein design with the goal of developing general design algorithms. We have sought to expand the range of computational protein design by developing quantitative design methods for residues of all parts of a protein: the buried core, the solvent exposed surface, and the boundary between core and surface. Our goal is an objective, quantitative design algorithm that is based on the physical properties that determine protein structure and stability and which is not limited to specific folds or motifs. We chose the \u03b2\u03b2\u03b1 motif typified by the zinc finger DNA binding module to test our design methodology. Using previously published sequence scoring functions developed with a combined experimental and computational approach and the Dead-End Elimination theorem to search for the optimal sequence, we designed 20 out of 28 positions in the test motif. The resulting sequence has less than 40% homology to any known sequence and does not contain any metal binding sites or cysteine residues. The resulting peptide, pda8d, is highly soluble and monomeric and circular dichroism measurements showed it to be folded with a weakly cooperative thermal unfolding transition. The NMR solution structure of pda8d was solved and shows that it is well-defined with a backbone ensemble rms deviation of 0.55 \u00c5. Pda8d folds into the desired betabetaalpha motif with well-defined elements of secondary structure and tertiary organization. Superposition of the pda8d backbone to the design target is excellent, with an atomic rms deviation of 1.04 \u00c5.", "date": "1997-11-07", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "273", "number": "4", "publisher": "Elsevier", "pagerange": "789-796", "id_number": "CaltechAUTHORS:20110620-160423493", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160423493", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program/Chicago Community Trust" }, { "agency": "National Institutes of Health Training", "grant_number": "GM 08346" } ] }, "doi": "10.1006/jmbi.1997.1341", "resource_type": "article", "pub_year": "1997", "author_list": "Dahiyat, Bassil I.; Sarisky, Catherine A.; et el." }, { "id": "https://authors.library.caltech.edu/records/5c2fm-1f623", "eprint_id": 25472, "eprint_status": "archive", "datestamp": "2023-08-22 11:57:14", "lastmod": "2023-10-24 15:53:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dahiyat-B-I", "name": { "family": "Dahiyat", "given": "Bassil I." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "De novo protein design: fully automated sequence selection", "ispublished": "pub", "full_text_status": "restricted", "keywords": "DNA-Binding Proteins; Protein Engineering; Sequence Alignment; Hydrogen Bonding; Amino Acid Sequence; Models: Molecular; Zinc Fingers; Transcription Factors; Crystallography: X-Ray; Protein Folding; Protein Conformation; Computer Simulation; Protein Structure: Tertiary; Protein Structure: Secondary; Magnetic Resonance Spectroscopy; Solutions; Molecular Sequence Data; Algorithms", "note": "\u00a9 1997 American Association for the Advancement of Science. \nReceived 16 June 1997; accepted 8 September 1997. We thank P. Poon and T. Laue for sedimentation equilibrium measurements and discussions, A. Su for assistance calculating super-secondary structure parameters, S. Ross for assistance with NMR measurements, G. Hathaway for mass spectrometry, J. Abelson and P. Bjorkman for critical reading of the manuscript, and R. A. Olofson for helpful discussions. Supported by the Howard Hughes Medical\nInstitute (S.L.M.), the Rita Allen Foundation, the\nChandler Family Trust, the Booth Ferris Foundation,\nthe David and Lucile Packard Foundation, the Searle\nScholars Program and The Chicago Community Trust, and grant GM08346 from the National Institutes of Health (B.I.D.). Coordinates and NMR restraints have been deposited in the Brookhaven Protein Data Bank with accession numbers 1FSD and\nR1FSDMR, respectively.", "abstract": "The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 x 10^(27) possible amino acid sequences for compatibility with the design target, a \u03b2\u03b2\u03b1 protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.", "date": "1997-10-03", "date_type": "published", "publication": "Science", "volume": "278", "number": "5335", "publisher": "American Association for the Advancement of Science", "pagerange": "82-87", "id_number": "CaltechAUTHORS:20110928-132632399", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110928-132632399", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Rita Allen Foundation" }, { "agency": "Chandler Family Trust" }, { "agency": "Booth Ferris Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" }, { "agency": "Chicago Community Trust" }, { "agency": "NIH", "grant_number": "GM08346" } ] }, "doi": "10.1126/science.278.5335.82", "resource_type": "article", "pub_year": "1997", "author_list": "Dahiyat, Bassil I. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/gqdv6-6rp64", "eprint_id": 646, "eprint_status": "archive", "datestamp": "2023-08-22 11:54:09", "lastmod": "2023-10-23 19:38:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dahiyat-B-I", "name": { "family": "Dahiyat", "given": "Bassil I." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Probing the role of packing specificity in protein design", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1997 by The National Academy of Sciences \n\nCommunicated by William A. Goddard III, California Institute of Technology, Pasadena, CA, June 24, 1997 (received for review March 7, 1997) \n\nWe thank D. B. Gordon for helpful discussions, S. Ross for assistance with the NMR spectroscopy, and G. Hathaway for mass spectra. This work was supported by the Rita Allen Foundation, the David and Lucile Packard Foundation, and the Searle Scholars Program/The Chicago Community Trust. B.I.D. is partially supported by National Institutes of Health Training Grant GM 08346. \n\nThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. \u00a71734 solely to indicate this fact.\n\nPublished - DAHpnas97.pdf
", "abstract": "By using a protein-design algorithm that quantitatively considers side-chain packing, the effect of specific steric constraints on protein design was assessed in the core of the streptococcal protein G beta 1 domain. The strength of packing constraints used in the design was varied, resulting in core sequences that reflected differing amounts of packing specificity. The structural flexibility and stability of several of the designed proteins were experimentally determined and showed a trend from well-ordered to highly mobile structures as the degree of packing specificity in the design decreased. This trend both demonstrates that the inclusion of specific packing interactions is necessary for the design of native-like proteins and defines a useful range of packing specificity for the design algorithm. In addition, an analysis of the modeled protein structures suggested that penalizing for exposed hydrophobic surface area can improve design performance.", "date": "1997-09-16", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "94", "number": "19", "publisher": "National Academy of Sciences", "pagerange": "10172-10177", "id_number": "CaltechAUTHORS:DAHpnas97", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:DAHpnas97", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM 08346" } ] }, "pmcid": "PMC23334", "primary_object": { "basename": "DAHpnas97.pdf", "url": "https://authors.library.caltech.edu/records/gqdv6-6rp64/files/DAHpnas97.pdf" }, "resource_type": "article", "pub_year": "1997", "author_list": "Dahiyat, Bassil I. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/zar9a-wja82", "eprint_id": 24081, "eprint_status": "archive", "datestamp": "2023-08-22 11:50:12", "lastmod": "2023-10-23 20:18:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Morgan-Chantal-S", "name": { "family": "Morgan", "given": "Chantal S." } }, { "id": "Holton-James-M", "name": { "family": "Holton", "given": "James M." } }, { "id": "Olafson-Barry-D", "name": { "family": "Olafson", "given": "Barry D." } }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Circular dichroism determination of class I MHC-peptide equilibrium dissociation constants", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Animals; Hot Temperature; H-2 Antigens; Amino Acid Sequence; Recombinant Proteins; Peptides; Circular Dichroism; Protein Denaturation; Cricetinae; Protein Binding; CHO Cells; classI MHC; dissociation constant", "note": "\u00a9 1997 The Protein Society. \n\nReceived December 26, 1996; Accepted April 23, 1997. \n\nWe thank B. Dahiyat, G. Hathaway, J. Johnson, and D. Penny for technical help, C. White for insightful discussions, and\nM. Ary for comments on the manuscript. C.S.M. is supported by the James Irvine Foundation and ARCS Foundation. P.J.B. acknowledges support from the Arthritis Foundation. S.L.M. acknowledges support from the Rita Allen Foundation, the David and Lucile Packard Foundation, and the Searle Scholars Program/The Chicago Community Trust.", "abstract": "Class I major histocompatibility complex (MHC) molecules bind peptides derived from degraded proteins for display to T cells of the immune system. Peptides bind to MHC proteins with varying affinities, depending upon their sequence and length. We demonstrate that the thermal stability of the MHC-peptide complex depends directly on peptide binding affinity. We use this correlation to develop a convenient method to determine peptide dissociation constants by measuring MHC-peptide complex stability using thermal denaturation profiles monitored by circular dichroism.", "date": "1997-08", "date_type": "published", "publication": "Protein Science", "volume": "6", "number": "8", "publisher": "Wiley", "pagerange": "1771-1773", "id_number": "CaltechAUTHORS:20110620-160424679", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160424679", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "James Irvine Foundation" }, { "agency": "ARCS Foundation" }, { "agency": "Arthritis Foundation" }, { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" } ] }, "doi": "10.1002/pro.5560060819", "pmcid": "PMC2143769", "resource_type": "article", "pub_year": "1997", "author_list": "Morgan, Chantal S.; Holton, James M.; et el." }, { "id": "https://authors.library.caltech.edu/records/t2p3c-t0w98", "eprint_id": 24080, "eprint_status": "archive", "datestamp": "2023-08-22 11:50:04", "lastmod": "2023-10-23 20:17:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Su-Alyce", "name": { "family": "Su", "given": "Alyce" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Coupling backbone flexibility and amino acid sequence selection in protein design", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Circular Dichroism; Protein Structure: Secondary; Amino Acid Sequence; Magnetic Resonance Spectroscopy; Proteins; Algorithms; Thermodynamics; Mutagenesis; backbone degrees of freedom; protein design; protein G; supersecondary structure parameters", "note": "\u00a9 1997 The Protein Society.\n\nReceived January 27, 1997; Accepted March 21, 1997.\n\nArticle first published online: 31 Dec. 2008.\nWe thank M. Ary, S. Malakauskas, and S. Ross for technical assistance, G.\nHathaway of the Caltech Protein and Peptide Microanalytical Facility for\nmass spectra, the Caltech DNA Sequencing Core Facility for DNA sequencing,\nand the Caltech Center for Advanced Computing Research for\nuse of the Intel Delta. This work was supported by the Rita Allen Foundation,\nthe David and Lucile Packard Foundation, and the Searle Scholars\nProgram/The Chicago Community Trust.", "abstract": "Using a protein design algorithm that considers side-chain packing quantitatively, the effect of explicit backbone motion on the selection of amino acids in protein design was assessed in the core of the streptococcal protein G \u03b21 domain (G\u03b21). Concerted backbone motion was introduced by varying G\u03b21's supersecondary structure parameter values. The stability and structural flexibility of seven of the redesigned proteins were determined experimentally and showed that core variants containing as many as 6 of 10 possible mutations retain native-like properties. This result demonstrates that backbone flexibility can be combined explicitly with amino acid side-chain selection and that the selection algorithm is sufficiently robust to tolerate perturbations as large as 15% of G\u03b21's native supersecondary structure parameter values.", "date": "1997-08", "date_type": "published", "publication": "Protein Science", "volume": "6", "number": "8", "publisher": "Wiley", "pagerange": "1701-1707", "id_number": "CaltechAUTHORS:20110620-160424464", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160424464", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" }, { "agency": "Chicago Community Trust" } ] }, "doi": "10.1002/pro.5560060810", "pmcid": "PMC2143777", "resource_type": "article", "pub_year": "1997", "author_list": "Su, Alyce and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/bypjv-bgy05", "eprint_id": 24090, "eprint_status": "archive", "datestamp": "2023-08-22 11:43:11", "lastmod": "2023-10-23 20:18:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dahiyat-B-I", "name": { "family": "Dahiyat", "given": "Bassil I." } }, { "id": "Gordon-D-B", "name": { "family": "Gordon", "given": "D. Benjamin" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Automated design of the surface positions of protein helices", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Hydrogen Bonding; Protein Engineering; Peptides; Circular Dichroism; Models: Molecular; Fungal Proteins; Saccharomyces cerevisiae Proteins; Protein Structure: Secondary; Surface Properties; Computer Simulation; Algorithms; DNA-Binding Proteins; Magnetic Resonance Spectroscopy; Protein Kinases; Models: Chemical; coiled coils; helix propensities; protein design; surface residues", "note": "\u00a9 1997 The Protein Society.\n\nReceived January 13, 1997; Accepted March 11, 1997.\nArticle first published online: 31 Dec. 2008.\n\n\n\nWe wish to thank G. Hathaway and D. Krapf of the Caltech Protein and\nPeptide Microanalytical Laboratory for mass spectra and amino acid analysis\nand the Caltech Center for Advanced Computing Research for use of\nthe Intel Delta. This work was supported by the Rita Allen Foundation, the\nDavid and Lucile Packard Foundation and the Searle Scholars Program/The Chicago Community Trust. B.I.D. is partially supported by NIH Training\nGrant GM 08346. D.B.G. is partially supported by NIH Training Grant\nGM 07616C-19.", "abstract": "Using a protein design algorithm that quantitatively considers side-chain interactions, the design of surface residues of alpha helices was examined. Three scoring functions were tested: a hydrogen-bond potential, a hydrogen-bond potential in conjunction with a penalty for uncompensated burial of polar hydrogens, and a hydrogen-bond potential in combination with helix propensity. The solvent exposed residues of a homodimeric coiled coil based on GCN4-p1 were designed by using the Dead-End Elimination Theorem to find the optimal amino acid sequence for each scoring function. The corresponding peptides were synthesized and characterized by circular dichroism spectroscopy and size exclusion chromatography. The designed peptides were dimeric and nearly 100% helical at 1 \u00b0C, with melting temperatures from 69-72 \u00b0C, over 12 \u00b0C higher than GCN4-p1, whereas a random hydrophilic sequence at the surface positions produced a peptide that melted at 15 \u00b0C. Analysis of the designed sequences suggests that helix propensity is the key factor in sequence design for surface helical positions.", "date": "1997-06", "date_type": "published", "publication": "Protein Science", "volume": "6", "number": "6", "publisher": "Wiley", "pagerange": "1333-1337", "id_number": "CaltechAUTHORS:20110620-160427729", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160427729", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM 07616C-19" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM 08346" }, { "agency": "Chicago Community Trust" } ] }, "doi": "10.1002/pro.5560060622", "pmcid": "PMC2143725", "resource_type": "article", "pub_year": "1997", "author_list": "Dahiyat, Bassil I.; Gordon, D. Benjamin; et el." }, { "id": "https://authors.library.caltech.edu/records/5e57g-wvj29", "eprint_id": 24099, "eprint_status": "archive", "datestamp": "2023-08-22 11:00:49", "lastmod": "2023-10-23 20:18:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dahiyat-B-I", "name": { "family": "Dahiyat", "given": "Bassil I." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Protein design automation", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Circular Dichroism; Viral Proteins; Structure-Activity Relationship; Amino Acid Sequence; Proteins; DNA-Binding Proteins; Computer-Aided Design; Feedback; Protein Conformation; Monte Carlo Method; Repressor Proteins; Computer Simulation; Viral Regulatory and Accessory Proteins; Algorithms; Molecular Sequence Data; computational; dead-end elimination; packing; proteindesign; sidechain", "note": "\u00a9 1996 The Protein Society.\n\nReceived December 5, 1995; Accepted February 7, 1996.\nArticle first published online: 31 Dec. 2008.\n\n\nWe thank J. Desmet and M. De Maeyer for providing us with their rotamer\nlibrary and a manuscript before publication; P.J. Bjorkman, J.\nHolton, E.M. Marzluff, D.B. Gordon, and D.C. Rees for critical comments\non the manuscript; and B.D. Olafson for help with partial atomic\ncharges and critical comments on the manuscript. This work was supported\nby the Rita Allen Foundation, the Chandler Family Trust, the\nBooth Ferris Foundation, the David and Lucile Packard Foundation,\nand the Searle Scholars Program/The Chicago Community Trust. B.I.D.\nis partially supported by NIH training grant GM 08346.", "abstract": "We have conceived and implemented a cyclical protein design strategy that couples theory, computation, and experimental testing. The combinatorially large number of possible sequences and the incomplete understanding of the factors that control protein structure are the primary obstacles in protein design. Our protein design automation algorithm objectively predicts protein sequences likely to achieve a desired fold. Using a rotamer description of the side chains, we implemented a fast discrete search algorithm based on the Dead-End Elimination Theorem to rapidly find the globally optimal sequence in its optimal geometry from the vast number of possible solutions. Rotamer sequences were scored for steric complementarity using a van der Waals potential. A Monte Carlo search was then executed, starting at the optimal sequence, in order to find other high-scoring sequences. As a test of the design methodology, high-scoring sequences were found for the buried hydrophobic residues of a homodimeric coiled coil based on GCN4-p1. The corresponding peptides were synthesized and characterized by CD spectroscopy and size-exclusion chromatography. All peptides were dimeric and nearly 100% helical at 1 \u00b0C, with melting temperatures ranging from 24 \u00b0C to 57 \u00b0C. A quantitative structure activity relation analysis was performed on the designed peptides, and a significant correlation was found with surface area burial. Incorporation of a buried surface area potential in the scoring of sequences greatly improved the correlation between predicted and measured stabilities and demonstrated experimental feedback in a complete design cycle.", "date": "1996-05", "date_type": "published", "publication": "Protein Science", "volume": "5", "number": "5", "publisher": "Wiley", "pagerange": "895-903", "id_number": "CaltechAUTHORS:20110620-160429268", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160429268", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "Chandler Family Trust" }, { "agency": "Booth Ferris Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" }, { "agency": "Chicago Community Trust" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM 08346" } ] }, "doi": "10.1002/pro.5560050511", "pmcid": "PMC2143401", "resource_type": "article", "pub_year": "1996", "author_list": "Dahiyat, Bassil I. and Mayo, Stephen L." }, { "id": "https://authors.library.caltech.edu/records/sg8cb-gz987", "eprint_id": 24103, "eprint_status": "archive", "datestamp": "2023-08-22 10:53:21", "lastmod": "2023-10-23 20:18:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dahiyat-B-I", "name": { "family": "Dahiyat", "given": "Bassil I." } }, { "id": "Meade-T-J", "name": { "family": "Meade", "given": "Thomas J." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Site-specific modification of \u03b1-helical peptides with electron donors and acceptors", "ispublished": "pub", "full_text_status": "restricted", "keywords": "electron transfer; \u03b1-helical peptides complexes; ruthenium complexes", "note": "\u00a9 1996 Elsevier Science S.A.\n\nAvailable online 15 January 1999.\n\nWe thank H. Qian for the computer program implementing\nLifson-Roig theory, O. Hathaway for mass\nspectral analysis and J.P. Kayyem for helpful discussions.\nSLM. acknowledges support from the Rita Allen Foundation, the David and Lucile Packard Foundation and the\nSearle Scholars Program. B.I.D. is partially supported by\nNIH Training Grant GM 08346. T.J.M. acknowledges\nsupport from the Petroleum Research Fund, American\nChemical Society and the Research Corporation.", "abstract": "We have prepared a histidine containing monomeric \u03b1-helical peptide, ETH6 (A_2KA_4KA_2HA_6HA_4KA_4K) in order to study long-range electron transfer (ET). This peptide was site-specifically labelled with a ruthenium (donor) at one histidine and a second ruthenium (acceptor) at a second histidine located on the same peptide. Both the unlabeled peptide and the singly labeled peptide-metal complex, Ru(bpy)_2(im)(His)-ETH6, were shown to form stable monomeric \u03b1-helical structures as determined by circular dichroism. Ru(NH_3)_4(py) was coupled to Ru(bpy_2)(im)(His)-ETH6, forming a Ru(bpy)_2(im)(His)-ETH6-(His)Ru(NH_3)_4(py) donor-acceptor complex. The synthesis and characterization of these peptides provide an entry into a series of molecules that are ideally suited to evaluate pathway differences such as H-bond mediated versus backbone-coupled long-range ET in protein \u03b1-helices.", "date": "1996-02-29", "date_type": "published", "publication": "Inorganica Chimica Acta", "volume": "243", "number": "1-2", "publisher": "Elsevier", "pagerange": "207-212", "id_number": "CaltechAUTHORS:20110620-160429999", "issn": "0020-1693", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160429999", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Searle Scholars Program" }, { "agency": "NIH Training Grant Fellowship", "grant_number": "GM 08346" }, { "agency": "American Chemical Society Petroleum Research Fund" }, { "agency": "Research Corporation" } ] }, "doi": "10.1016/0020-1693(95)04909-6", "resource_type": "article", "pub_year": "1996", "author_list": "Dahiyat, Bassil I.; Meade, Thomas J.; et el." }, { "id": "https://authors.library.caltech.edu/records/bvaxk-gca10", "eprint_id": 24130, "eprint_status": "archive", "datestamp": "2023-08-20 07:11:57", "lastmod": "2023-10-23 20:19:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Su-Alyce", "name": { "family": "Su", "given": "Alyce" } }, { "id": "Mager-S", "name": { "family": "Mager", "given": "Sela" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" } ] }, "title": "A multi-substrate single-file model for ion-coupled transporters", "ispublished": "pub", "full_text_status": "public", "keywords": "GABA Plasma Membrane Transport Proteins, Carrier Proteins, Biophysics, Serotonin, Monosaccharide Transport Proteins, Molecular Structure, Ion Transport, Electrochemistry, Nerve Tissue Proteins, Models: Biological, Animals, Serotonin Plasma Membrane Transport Proteins, Membrane Glycoproteins, Binding Sites, Membrane Transport Proteins, Organic Anion Transporters, Membrane Potentials, Membrane Proteins, gamma-Aminobutyric Acid, Computer Simulation, Sodium, Sodium-Glucose Transporter 1, Biophysical Phenomena", "note": "\u00a9 1996 The Biophysical Society; Published by Elsevier Inc.\nReceived for publication 25 July 1995 and in final form 21 October 1995.\nAvailable online 2 January 2009. \nWe thank Eric Bax, Bassil Dahiyat, Norman Davidson, and Jun Li for\nsuggestions. Scott Fraser suggested the diffusion pump analogy.\nThis work was supported by grants from the National Institute of Neurological\nDiseases and Stroke and the National Institute on Drug Abuse. SLM\nacknowledges support from the Rita Allen Foundation, the David and\nLucille Packard Foundation, and the Searle Scholars Program.\n\nPublished - Su_1996_Biophys_J_A_multi-substrate_single-file_model_for.pdf
", "abstract": "Ion-coupled transporters are simulated by a model that differs from contemporary alternating-access schemes. Beginning with concepts derived from multi-ion pores, the model assumes that substrates (both inorganic ions and small organic molecules) hop a) between the solutions and binding sites and b) between binding sites within a single-file pore. No two substrates can simultaneously occupy the same site. Rate constants for hopping can be increased both a) when substrates in two sites attract each other into a vacant site between them and b) when substrates in adjacent sites repel each other. Hopping rate constants for charged substrates are also modified by the membrane field. For a three-site model, simulated annealing yields parameters to fit steady-state measurements of flux coupling, transport-associated currents, and charge movements for the GABA transporter GAT1. The model then accounts for some GAT1 kinetic data as well. The model also yields parameters that describe the available data for the rat 5-HT transporter and for the rabbit Na(+)-glucose transporter. The simulations show that coupled fluxes and other aspects of ion transport can be explained by a model that includes local substrate-substrate interactions but no explicit global conformational changes.", "date": "1996-02", "date_type": "published", "publication": "Biophysical Journal", "volume": "70", "number": "2", "publisher": "Biophysical Society", "pagerange": "762-777", "id_number": "CaltechAUTHORS:20110620-160434844", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160434844", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute of Neurological Disorders and Stroke (NINDS)" }, { "agency": "National Institute on Drug Abuse" }, { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucille Packard Foundation" }, { "agency": "Searle Scholars Program" } ] }, "doi": "10.1016/S0006-3495(96)79616-9", "pmcid": "PMC1224976", "primary_object": { "basename": "Su_1996_Biophys_J_A_multi-substrate_single-file_model_for.pdf", "url": "https://authors.library.caltech.edu/records/bvaxk-gca10/files/Su_1996_Biophys_J_A_multi-substrate_single-file_model_for.pdf" }, "resource_type": "article", "pub_year": "1996", "author_list": "Su, Alyce; Mager, Sela; et el." }, { "id": "https://authors.library.caltech.edu/records/4dq6s-gsq15", "eprint_id": 24092, "eprint_status": "archive", "datestamp": "2023-08-22 09:58:52", "lastmod": "2023-10-23 20:18:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Qian-Hong", "name": { "family": "Qian", "given": "Hong" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Morton-A", "name": { "family": "Morton", "given": "Andrew" } } ] }, "title": "Protein hydrogen exchange in denaturant: quantitative analysis by a two-process model", "ispublished": "pub", "full_text_status": "public", "keywords": "Ribonuclease: Pancreatic; Models: Biological; Proteins; Thermodynamics; Kinetics; Protein Folding; Protein Denaturation; Hydrogen", "note": "\u00a9 1994 American Chemical Society.\nReceived April 5, 1994; Revised Manuscript Received May 18, 1994.\nH.Q. is a fellow of the Program in Mathematics and Molecular Biology\nat U.C. Berkeley, which is supported by the NSF Grant DMS 8720208.\nS.L.M. acknowledges support from the Rita Allen Foundation and the\nDavid and Lucile Packard Foundation. A.M. is a Howard Hughes\nPredoctoral Fellow.\nWe thank many colleagues, particularly Buzz Baldwin,\nDoug Barrick, Jay Luo, and Alyce Su, for helpful discussions,\nWalter Englander for sending us a copy of his manuscript\nprior to publication, and Rick Dahlquist, Brian Matthews, John Schellman, and Ingrid Vetter for critical reading of the\nmanuscript.\n\nPublished - Qian_1994_Biochemistry_Protein_hydrogen_exchange_in_denaturant.pdf
", "date": "1994-07-12", "date_type": "published", "publication": "Biochemistry", "volume": "33", "number": "27", "publisher": "American Chemical Society", "pagerange": "8167-8171", "id_number": "CaltechAUTHORS:20110620-160428085", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160428085", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of California, Berkeley" }, { "agency": "NSF", "grant_number": "DMS-8720208" }, { "agency": "Rita Allen Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1021/bi00193a001", "primary_object": { "basename": "Qian_1994_Biochemistry_Protein_hydrogen_exchange_in_denaturant.pdf", "url": "https://authors.library.caltech.edu/records/4dq6s-gsq15/files/Qian_1994_Biochemistry_Protein_hydrogen_exchange_in_denaturant.pdf" }, "resource_type": "article", "pub_year": "1994", "author_list": "Qian, Hong; Mayo, Stephen L.; et el." }, { "id": "https://authors.library.caltech.edu/records/abam2-06w39", "eprint_id": 24093, "eprint_status": "archive", "datestamp": "2023-08-22 09:37:23", "lastmod": "2023-10-23 16:54:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Baldwin-R-L", "name": { "family": "Baldwin", "given": "Robert L." } } ] }, "title": "Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Magnetic Resonance Spectroscopy; Thermodynamics; Protein Denaturation; Guanidine; Mathematics; Protein Folding; Hydrogen-Ion Concentration; Hydrogen; Ribonuclease: Pancreatic; Protons; Guanidines; Temperature", "note": "\u00a9 1993 American Association for the Advancement of Science. \n\nReceived 25 March 1993; accepted 20 September 1993. \n\nWe thank D. Barrick, S. W. Englander, T. Kiefhaber, D. Laurents, and A. Robertson for help and discussion. Supported by NIH grant GM 19988.", "abstract": "Amide (NH) proton exchange rates were measured in 0.0 to 0.7 M guanidinium chloride (GdmCl) for 23 slowly exchanging peptide NH protons of ribonuclease A (RNase A) at pH* 5.5 (uncorrected pH measured in D_2O), 34 \u00b0C. The purpose was to find out whether GdmCl induces exchange through binding to exchange intermediates that are partly or wholly unfolded. It was predicted that, when the logarithm of the exchange rate is plotted as a function of the molarity of GdmCl, the slope should be a measure of the amount of buried surface area exposed to GdmCl in the exchange intermediate. The results indicate that these concentrations of GdmCl do induce exchange by means of a partial unfolding mechanism for all 23 protons; this implies that exchange reactions can be used to study the unfolding and stability of local regions. Of the 23 protons, nine also show a second mechanism of exchange at lower concentrations of GdmCl, a mechanism that is nearly independent of GdmCl concentration and is termed \"limited structural fluctuation.\"", "date": "1993-11-05", "date_type": "published", "publication": "Science", "volume": "262", "number": "5135", "publisher": "American Association for the Advancement of Science", "pagerange": "873-876", "id_number": "CaltechAUTHORS:20110620-160428244", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160428244", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 19988" } ] }, "doi": "10.1126/science.8235609", "resource_type": "article", "pub_year": "1993", "author_list": "Mayo, Stephen L. and Baldwin, Robert L." }, { "id": "https://authors.library.caltech.edu/records/76hyc-cjr81", "eprint_id": 24133, "eprint_status": "archive", "datestamp": "2023-08-19 23:24:22", "lastmod": "2023-10-23 20:19:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Olafson-Barry-D", "name": { "family": "Olafson", "given": "Barry D." } }, { "id": "Goddard-W-A-III", "name": { "family": "Goddard", "given": "William A., III" }, "orcid": "0000-0003-0097-5716" } ] }, "title": "DREIDING: A generic force field for molecular simulations", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1990 American Chemical Society. \n\nReceived: October 2, 1989; In Final Form: February 2, 1990. Publication Date: December 1990. \n\nWe thank Professor Anthony K. Rapp\u00e9 and Dr. Carla J. Casewit for providing stimulating discussions and carrying out tests of these force fields while on sabbatical at BioDesign. We thank Drs. Walter E. Reiher III and Paul W. Saxe for stimulating discussions and assistance in the calculations. We thank Adria McMillan and Carol Scrivnor for typing various versions of the text and Dr. Marie Ary for reformatting the text and preparing the 76 structures in the figures and the long tables (Tables VIII-XIII). Initial development of the DREIDING force field was carried out at Caltech and supported by a grant from the Department of Energy, Energy Conversion and Utilization Technologies Program (DOE-ECUT). More recent developments of the DREIDING force field were carried out at BioDesign.", "abstract": "We report the parameters for a new generic force field, DREIDING, that we find useful for predicting structures and dynamics of organic, biological, and main-group inorganic molecules. The philosophy in DREIDING is to use general force constants and geometry parameters based on simple hybridization considerations rather than individual force constants and geometric parameters that depend on the particular combination of atoms involved in the bond, angle, or torsion terms. Thus all bond distances are derived from atomic radii, and there is only one force constant each for bonds, angles, and inversions and only six different values for torsional barriers. Parameters are defined for all possible combinations of atoms and new atoms can be added to the force field rather simply. This paper reports the parameters for the \"nonmetallic\" main-group elements (B, C, N, 0, F columns for the C, Si, Ge, and Sn rows) plus H and a few metals (Na, Ca, Zn, Fe). The accuracy of the DREIDING force field is tested by comparing with (i) 76 accurately determined crystal structures of organic compounds involving H, C, N, 0, F, P, S, CI, and Br, (ii) rotational barriers of a number of molecules, and (iii) relative conformational energies and barriers of a number of molecules. We find excellent results for these systems.", "date": "1990-12-27", "date_type": "published", "publication": "Journal of Physical Chemistry", "volume": "94", "number": "26", "publisher": "American Chemical Society", "pagerange": "8897-8909", "id_number": "CaltechAUTHORS:20110620-160435314", "issn": "0022-3654", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160435314", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)" } ] }, "doi": "10.1021/j100389a010", "resource_type": "article", "pub_year": "1990", "author_list": "Mayo, Stephen L.; Olafson, Barry D.; et el." }, { "id": "https://authors.library.caltech.edu/records/4n53b-24f05", "eprint_id": 24124, "eprint_status": "archive", "datestamp": "2023-08-19 22:00:10", "lastmod": "2023-10-23 20:19:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bowler-B-E", "name": { "family": "Bowler", "given": "Bruce E." } }, { "id": "Meade-T-J", "name": { "family": "Meade", "given": "Thomas J." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Richards-J-H", "name": { "family": "Richards", "given": "John H." } }, { "id": "Gray-H-B", "name": { "family": "Gray", "given": "Harry B." }, "orcid": "0000-0002-7937-7876" } ] }, "title": "Long-range electron transfer in structurally engineered pentaammineruthenium (histidine-62) cytochrome c", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1989 American Chemical Society.\n\nReceived July 19, 1989.\n\nWe thank Professor Judith L. Campbell, Dr. Guy Guillemette, Dr. Alfred Gartner, and Professor A. G. Mauk for helpful discussions and Dr. Adrienne Raphael for assistance with the electrochemical (differential pulse polarography) measurements. Large-scale fermentations were done with the aid of Dr. Tom Sutherland at the UCLA Molecular Biology Institute. B.E.B. acknowledges the Medical Research Council (Canada) for a postdoctoral fellowship. This research was supported by National Science Foundation Grant CHE88-14222", "abstract": "In many biological processes, long-range electron transfer (ET) plays a key role. When the three-dimensional structures of proteins are accurately known, use of modified proteins and protein-protein complexes provides an experimental approach to study ET rates between two metal centers. For Ru(His)- modified proteins, the introduction of histidine residues at any desired surface location by site-directed mutagenesis opens the way for systematic investigations of ET pathways.", "date": "1989-11-08", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "111", "number": "23", "publisher": "American Chemical Society", "pagerange": "8757-8759", "id_number": "CaltechAUTHORS:20110620-160433811", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160433811", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Medical Research Council (Canada)" }, { "agency": "NSF", "grant_number": "CHE88-14222" } ] }, "doi": "10.1021/ja00205a049", "resource_type": "article", "pub_year": "1989", "author_list": "Bowler, Bruce E.; Meade, Thomas J.; et el." }, { "id": "https://authors.library.caltech.edu/records/1ye1b-azm52", "eprint_id": 24139, "eprint_status": "archive", "datestamp": "2023-08-19 21:30:37", "lastmod": "2023-10-23 20:19:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Maryanoff-B-E", "name": { "family": "Maryanoff", "given": "Bruce E." } }, { "id": "McComsey-D-F", "name": { "family": "McComsey", "given": "David F." } }, { "id": "Inners-R-R", "name": { "family": "Inners", "given": "Ruth R." } }, { "id": "Mutter-M-S", "name": { "family": "Mutter", "given": "Martin S." } }, { "id": "Wooden-G-P", "name": { "family": "Wooden", "given": "Gary P." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Olofson-R-A", "name": { "family": "Olofson", "given": "R. A." } } ] }, "title": "Stereochemical studies on protonated bridgehead amines. ^1H NMR determination of cis and trans B-C ring-fused structures for salts of hexahydropyrrolo [2,1-a] isoquinolines and related C ring homologs. Capture of unstable ring-fused structures in the solid state", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1989 American Chemical Society.\nReceived January 11, 1988.\nPublication Date: March 1989.\nThis paper was presented in part in the \"Symposium on Heterocyclic\nChemistry\" at the 18th Middle Atlantic Regional Meeting of the American\nChemical Society, Newark, NJ, May 1984; paper ORGN-246. It was also\npresented at the 194th National Meeting of the American Chemical Society,\nNew Orleans, LA, Sept 1987; paper ORGN-122.\n\nWe thank Dr. Harold R. Almond, Jr., for\nconducting the MM2 and MNDO calculations.\n\nPublished - Maryanoff_1989_J_Am_Chem_Soc_Stereochemical_studies_on_protonated_bridgehead.pdf
", "abstract": "Acid-addition salts of tricyclic isoquinolines 2a/b, 3a/b, 4a-4c, 5, 6a/b, 7, 8a/b, 9a/b, and 17a/b were studied by high-field ^1H NMR in CDCl_3 solution. Cis (e.g., 14 and 15 in Figure 1) and trans (e.g., 13)B-C ring-fused structures were identified by using the vicinal ^3J(CH-NH) coupling constants, which demonstrate a Karplus-like behavior. In some cases, we initially observed a trans form, which converted to a cis A form by N H proton exchange. For 4c.HBr, the exchange process was slowed by addition of trifluoroacetic acid. In many cases, cis A and cis B structures were preferred in solution. The pendant phenyl group exerted a strong influence on the preferred solution structure. Observation of the initial, unstable trans-fused structures was related to their capture in the solid state and release intact on dissolution. X-ray diffraction was performed on the HBr salts of 2a (B-C cis), 2b (B-C cis), and 4c (B-C trans). The result for 4c.HBr confirmed the connection between the initial trans form in solution and the solid state. For 17b.HCI two conformers, associated with hindered rotation about the bond connecting the 2,6-disubstituted phenyl group to the tricyclic array, were detected at ambient probe temperature; however, rotamers were not observed for either of the two forms (trans and cis A) of 17a.HBr. Two conformers were also found for 16b.HBr. Temperature-dependent behavior was recorded in the ^1H NMR spectra of 17b.HBr and 16b.HBr; the activation free energy for interconversion of conformers was estimated to be in the vicinity of 17 kcal/mol for the former and 14-15 kcal/mol for the latter. The ^1H NMR spectrum of butaclamol hydrochloride (20.HC1), a potent neuroleptic agent, in Me_2SO-d_6 revealed two species in a ratio of 81:19, which were assigned as trans and cis A forms, respectively. ^1H NMR data for various free bases are also presented and discussed. Empirical force field calculations on three model hydrocarbons are discussed from a perspective of finding an explanation for the configurational/conformational behavior of the bridgehead ammonium salts. Diverse literature examples of structures for protonated bridgehead amines are also discussed. A tentative rationale is suggested for the preference of cis A forms in some protonated tetrahydroisoquinoline derivatives.", "date": "1989-03-29", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "111", "number": "7", "publisher": "American Chemical Society", "pagerange": "2487-2496", "id_number": "CaltechAUTHORS:20110620-160436278", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160436278", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1021/ja00189a020", "primary_object": { "basename": "Maryanoff_1989_J_Am_Chem_Soc_Stereochemical_studies_on_protonated_bridgehead.pdf", "url": "https://authors.library.caltech.edu/records/1ye1b-azm52/files/Maryanoff_1989_J_Am_Chem_Soc_Stereochemical_studies_on_protonated_bridgehead.pdf" }, "resource_type": "article", "pub_year": "1989", "author_list": "Maryanoff, Bruce E.; McComsey, David F.; et el." }, { "id": "https://authors.library.caltech.edu/records/d884v-18y52", "eprint_id": 25476, "eprint_status": "archive", "datestamp": "2023-08-19 20:40:47", "lastmod": "2023-10-24 15:54:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Haddon-R-C", "name": { "family": "Haddon", "given": "R. C." } }, { "id": "Chichester-Hicks-S-V", "name": { "family": "Chichester-Hicks", "given": "S. V." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Phenalene-phosphazene complexes: effect of exocyclic charge densities on the cyclotriphosphazene ring system", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1988 American Chemical Society.\nReceived October 27, 1987.\nPublication Date: June 1988.\n\nPublished - HADDON_1988_Inorganic_Chemistry_PHENALENE_PHOSPHAZENE_COMPLEXES_-_EFFECT.pdf
", "abstract": "The synthesis and properties of a new series of 1,9-diamino-substituted phenalene complexes of the cyclotriphosphazene ring system is described. One of the compounds is shown to be amphoteric, and this behavior allows an examination of the response of the phosphazene linkage to variations in exocyclic charge density at the spiro center in a plane perpendicular to the cyclotriphosphazene ring system. ^(31)P NMR spectroscopy indicates that substituent lone pairs with this orientation are not effective in long-range delocalization within the phosphazene linkage (in accord with our theoretical model of spiro delocalization). An X-ray crystal structure of one compound (7) identifies the presence of clathrated molecules of chloroform together with doubly hydrogen-bonded pairs of the phenalene-phosphazene complexes in the lattice. Crystal data for 7 (C_(13)H_8Cl_4N_5P_3\u2022CHCl_3): monoclinic space group P2_1/c, a = 12.401 (4) \u00c5, b = 28.404 (6) \u00c5, c = 12.962 (3) \u00c5, \u03b2 = 91.76 (2)\u00b0, V = 4564 (2) \u00c5^3, Z = 8, R = 0.050 for 4525 reflections.", "date": "1988-06-01", "date_type": "published", "publication": "Inorganic Chemistry", "volume": "27", "number": "11", "publisher": "American Chemical Society", "pagerange": "1911-1915", "id_number": "CaltechAUTHORS:20110928-144707183", "issn": "0020-1669", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110928-144707183", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1021/ic00284a019", "primary_object": { "basename": "HADDON_1988_Inorganic_Chemistry_PHENALENE_PHOSPHAZENE_COMPLEXES_-_EFFECT.pdf", "url": "https://authors.library.caltech.edu/records/d884v-18y52/files/HADDON_1988_Inorganic_Chemistry_PHENALENE_PHOSPHAZENE_COMPLEXES_-_EFFECT.pdf" }, "resource_type": "article", "pub_year": "1988", "author_list": "Haddon, R. C.; Chichester-Hicks, S. V.; et el." }, { "id": "https://authors.library.caltech.edu/records/nbks5-30s45", "eprint_id": 24137, "eprint_status": "archive", "datestamp": "2023-08-19 20:22:27", "lastmod": "2023-10-23 20:19:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Axup-A-W", "name": { "family": "Axup", "given": "Andrew W." } }, { "id": "Albin-M", "name": { "family": "Albin", "given": "Michael" } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Crutchley-R-J", "name": { "family": "Crutchley", "given": "Robert J." } }, { "id": "Gray-H-B", "name": { "family": "Gray", "given": "Harry B." }, "orcid": "0000-0002-7937-7876" } ] }, "title": "Distance dependence of photoinduced long-range electron transfer in zinc/ruthenium-modified myoglobins", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1988 American Chemical Society.\nReceived May 8, 1987.\nPublication Date: January 1988.\nContribution No. 7588 from the Arthur Amos Noyes Laboratory, California Institute of\nTechnology, Pasadena, California 91125.\nWe thank Charlie Lieber, Jenny Karas,\nWalther Ellis, Lome Reid, Jose Onuchic, David Beratan, A. Kuki,\nHarvey Schugar, R. A. Marcus, and Jay Winkler for helpful\ndiscussions. A.W.A. acknowledges a fellowship from the Fannie\nand John Hertz Foundation. S.L.M. acknowledges a fellowship\nfrom AT&T Bell Laboratories. This research was supported by\nNational Science Foundation Grants CHE85-18793 and\nCHE85-09637.\n\nPublished - Axup_1988_J_Am_Chem_Soc_Distance_dependence_of_photoinduced_long-range.pdf
", "abstract": "An experimental investigation of the distance dependence of long-range electron transfer in zinc/ruthenium-modified myoglobins has been performed. The modified proteins were prepared by substitution of zinc mesoporphyrin IX diacid (ZnP) for the heme in each of four previously characterized pentaammineruthenium(III) (a_5Ru;a = NH_3) derivatives of sperm whale myoglobin (Mb): a_5Ru(His-48)Mb, a_5Ru(His-12)Mb, a_5Ru(His-116)Mb, a_5Ru(His-81)Mb. Electron transfer from the ZnP triplet excited state (^3ZnP*) to Ru^3+, ^3ZnP*-Ru^3+ \u2192 ZnP^+-Ru^2+ (\u0394E\u00b0 ~ 0.8V) was measured by time-resolved transient absorption spectroscopy: rate constants (k_f) are 7.0 \u00d7 10^4 (His-48), 1.0 \u00d7 10^2 (His-12), 8.9 \u00d7 10^1 (His-116), and 8.5 \u00d7 10^1 (His-81) s^-1 at 25 \u00b0C. Activation enthalpies calculated from the temperature dependences of the electron-transfer rates over the range 5-40 \u00b0C are 1.7 \u00b1 1.6 (His-48), 4.7 \u00b1 0.9 (His-12), 5.4 \u00b1 0.4 (His-116), and 5.6 \u00b1 2.5 (His-81) kcal mol^-1. Electron-transfer distances (d = closest ZnP edge to a_5Ru(His) edge; angstroms) were calculated to fall in the following ranges: His-48, 11.8-16.6; His-12, 21.5-22.3; His-116, 19.8-20.4; His-81, 18.8-19.3. The rate-distance equation is k_f = 7.8 \u00d7 10^8 exp[-0.9l(d - 3)] s^-1 . The data indicate that the ^3ZnP*-Ru(His-12)^3+ electronic coupling may be enhanced by an intervening tryptophan (Trp-14).", "date": "1988-01-20", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "110", "number": "2", "publisher": "American Chemical Society", "pagerange": "435-439", "id_number": "CaltechAUTHORS:20110620-160435945", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160435945", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Fannie and John Hertz Foundation" }, { "agency": "AT&T Bell Laboratories" }, { "agency": "NSF", "grant_number": "CHE85-18793" }, { "agency": "NSF", "grant_number": "CHE85-09637" } ] }, "doi": "10.1021/ja00210a020", "primary_object": { "basename": "Axup_1988_J_Am_Chem_Soc_Distance_dependence_of_photoinduced_long-range.pdf", "url": "https://authors.library.caltech.edu/records/nbks5-30s45/files/Axup_1988_J_Am_Chem_Soc_Distance_dependence_of_photoinduced_long-range.pdf" }, "resource_type": "article", "pub_year": "1988", "author_list": "Axup, Andrew W.; Albin, Michael; et el." }, { "id": "https://authors.library.caltech.edu/records/76ad2-50411", "eprint_id": 24127, "eprint_status": "archive", "datestamp": "2023-08-19 18:47:14", "lastmod": "2023-10-23 20:19:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Ellis-W-R-Jr", "name": { "family": "Ellis", "given": "Walther R., Jr." } }, { "id": "Crutchley-R-J", "name": { "family": "Crutchley", "given": "Robert J." } }, { "id": "Gray-H-B", "name": { "family": "Gray", "given": "Harry B." }, "orcid": "0000-0002-7937-7876" } ] }, "title": "Long-range electron transfer in heme proteins", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Thermodynamics, Cytochrome c Group, Pseudomonas aeruginosa, Hemeproteins, Myoglobin, Electron Transport, Metalloporphyrins, Animals, Horses", "note": "\u00a9 1986 American Association for the Advancement of Science. \n\n Supported by grants from the National Science Foundation (CHE85-09637 and CHE85-18793). S.L.M. is an AT&T Bell Laboratories predoctoral fellow (1983 to the present). R.J.C. held a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada during 1982-84. H.B.G. was Visiting Miller Research Professor at the Department of Chemistry, University of California, Berkeley, when the manuscript was completed. We thank the following colleagues for helpful discussion: K. M. Yocom, J. R. Winkler, E. Bordignon, D. G. Nocera, J. B. Shelton, J. R. Shelton, W. A. Schroeder, J. N. Onuchic, G. Worosila, S. S. Isied, B. M. Hoffman, G. L. McLendon, R. A. Scott, A. G. Mauk, M. R. Mauk, N. S. Hush, R. A. Marcus, N. Sutin, J. J. Hopfield, D. N. Beratan, G. L. Closs, M. Smith, G. Pielak, B. D. Olafson, J. L. Campbell, J. H. Richards, W. A. Goddard III, I. Pecht, A. W. Axup, A. A. da Gama, M. Albin, J. H. Dawson, H. Taube, J. R. Miller, B. G. Malmstrom, W. R. Scheidt, and S. Larsson. Contribution 7334 from the Arthur Amos Noyes Laboratory.", "abstract": "Kinetic experiments have conclusively shown that electron transfer can take place over large distances (greater than 10 angstroms) through protein interiors. Current research focuses on the elucidation of the factors that determine the rates of long-range electron-transfer reactions in modified proteins and protein complexes. Factors receiving experimental and theoretical attention include the donor-acceptor distance, changes in geometry of the donor and acceptor upon electron transfer, and the thermodynamic driving force. Recent experimental work on heme proteins indicates that the electron-transfer rate falls off exponentially with donor-acceptor distance at long range. The rate is greatly enhanced in proteins in which the structural changes accompanying electron transfer are very small.", "date": "1986-08-29", "date_type": "published", "publication": "Science", "volume": "233", "number": "4767", "publisher": "American Association for the Advancement of Science", "pagerange": "948-952", "id_number": "CaltechAUTHORS:20110620-160434289", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160434289", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CHE85-18793" }, { "agency": "NSF", "grant_number": "CHE85-09637" }, { "agency": "AT&T Bell Laboratories" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" } ] }, "other_numbering_system": { "items": [ { "id": "7334", "name": "Caltech Arthur Amos Noyes Laboratory" } ] }, "doi": "10.1126/science.3016897", "resource_type": "article", "pub_year": "1986", "author_list": "Mayo, Stephen L.; Ellis, Walther R., Jr.; et el." }, { "id": "https://authors.library.caltech.edu/records/e5as1-p4r74", "eprint_id": 24120, "eprint_status": "archive", "datestamp": "2023-08-19 18:03:07", "lastmod": "2023-10-23 20:18:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Brunschwig-B-S", "name": { "family": "Brunschwig", "given": "Bruce S." }, "orcid": "0000-0002-6135-6727" }, { "id": "DeLaive-P-J", "name": { "family": "DeLaive", "given": "Patricia J." } }, { "id": "English-A-M", "name": { "family": "English", "given": "Ann M." } }, { "id": "Goldberg-M", "name": { "family": "Goldberg", "given": "Michael" } }, { "id": "Gray-H-B", "name": { "family": "Gray", "given": "Harry B." }, "orcid": "0000-0002-7937-7876" }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Sutin-N", "name": { "family": "Sutin", "given": "Norman" } } ] }, "title": "Kinetics and mechanisms of electron transfer between blue copper proteins and electronically excited chromium and ruthenium polypyridine complexes", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1985 American Chemical Society. \n\nReceived January 28, 1985. Publication Date: November 1985. \n\nResearch at the California Institute of Technology was supported by National Institutes of Health Grant AM19038, and research at Brookhaven National Laboratory was carried out under contract DE-AC02-76CH00016 with the U.S. Department of Energy and supported by its Division of Chemical Sciences and Office of Basic Energy Sciences. A.M.E. acknowledges a postdoctoral fellowship from the NSERC (1980-1981). S.L.M. thanks AT&T Bell Laboratories for a predoctoral fellowship (1983-present). We wish to acknowledge helpful discussions with Dr. C. Creutz and the assistance of J. Horwitz of the University of California at Santa Cruz and Dr. R. Humphry-Baker of L'Ecole Polytechnique Fiderale de Lausanne during the early stages of this work.", "abstract": "The kinetics of the quenching of the long-lived excited states of CrL_3^(3+) and RuL_3^(2+) complexes (L is 1,10-phenanthroline and 2,2'-bipyridine or substituted derivatives) by the copper proteins plastocyanin, azurin, and stellacyanin have been studied in aqueous solution. The rate constants for quenching by the Cu(I) proteins approach a limiting value of ~10^(6) s^(-1) at high protein concentration. The kinetic behavior for plastocyanin is discussed in terms of a model in which the metal complex binds at a remote site 10-12 \u00c5 from the copper center. The model allows for electron transfer both from this remote site and by attack of the metal complex adjacent to the copper center. The results show that at low protein concentration the adjacent pathway is about 10 times faster than the remote pathway. The rate constant for the intramolecular electron transfer from the remote site is consistent with the value expected on the basis of theoretical calculations.", "date": "1985-11", "date_type": "published", "publication": "Inorganic Chemistry", "volume": "24", "number": "23", "publisher": "American Chemical Society", "pagerange": "3743-3749", "id_number": "CaltechAUTHORS:20110620-160433152", "issn": "0020-1669", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160433152", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AM19038" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-76CH00016" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "AT&T Bell Laboratories" } ] }, "doi": "10.1021/ic00217a010", "resource_type": "article", "pub_year": "1985", "author_list": "Brunschwig, Bruce S.; DeLaive, Patricia J.; et el." }, { "id": "https://authors.library.caltech.edu/records/j1d7z-yt974", "eprint_id": 25475, "eprint_status": "archive", "datestamp": "2023-08-19 17:23:40", "lastmod": "2023-10-24 15:54:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Haddon-R-C", "name": { "family": "Haddon", "given": "R. C." } }, { "id": "Chichester-S-V", "name": { "family": "Chichester", "given": "S. V." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" } ] }, "title": "Direct Amination of 9-Hydroxy-1-oxophenalene to Produce 9-Amino-1-oxophenalene and Related Compounds", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1985 Georg Thieme Verlag. Received: October 29, 1984.\nRevised form: December 12, 1984.\n\nPublished - Haddon_1985_Synthesis_Direct_amination_of_9-hydroxy-1-oxophenalene_to.pdf
", "abstract": "In connection with our studies of organo-non-metallic complexes of the 1,9-disubstituted phenalene unit 1 we required access to compounds possessing a total of just two ionizable hydrogen atoms in the A,B groups of 1. The prototypical compound in this series, 9-amino-1-oxophenalene (2), is not known although 9-hydroxy-l-oxophenalene (3) was first prepared in 1941 and a number\nof derivatives of 1 possessing one or three ionizable hydrogen atoms in the A,B groups have recently become available. We have found that the high-pressure reaction between 9-hydroxy-1-oxophenalene (3) and aqueous ammonia\naffords the desired 9-amino-1-oxophenalene (2) in high yield and good purity under relatively mild conditions. In addition 2 may be alkylated to produce the 9-amino-l-ethoxyphenalenylium salt which serves as a precursor\nfor the other derivatives in this series with two ionizable hydrogen atoms in the A,B groups of 1.", "date": "1985", "date_type": "published", "publication": "Synthesis-Stuttgart", "volume": "1985", "number": "6-7", "publisher": "Georg Thieme Verlag", "pagerange": "639-641", "id_number": "CaltechAUTHORS:20110928-141129059", "issn": "0039-7881", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110928-141129059", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1055/s-1985-34145", "primary_object": { "basename": "Haddon_1985_Synthesis_Direct_amination_of_9-hydroxy-1-oxophenalene_to.pdf", "url": "https://authors.library.caltech.edu/records/j1d7z-yt974/files/Haddon_1985_Synthesis_Direct_amination_of_9-hydroxy-1-oxophenalene_to.pdf" }, "resource_type": "article", "pub_year": "1985", "author_list": "Haddon, R. C.; Chichester, S. V.; et el." }, { "id": "https://authors.library.caltech.edu/records/6a820-6py24", "eprint_id": 24118, "eprint_status": "archive", "datestamp": "2023-08-19 17:16:45", "lastmod": "2023-10-23 20:18:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bemis-G-W", "name": { "family": "Bemis", "given": "Guy W." } }, { "id": "Whittle-R-R", "name": { "family": "Whittle", "given": "Robert R." } }, { "id": "Mayo-S-L", "name": { "family": "Mayo", "given": "Stephen L." }, "orcid": "0000-0002-9785-5018" }, { "id": "Olofson-R-A", "name": { "family": "Olofson", "given": "R. A." } } ] }, "title": "1,3,4,6-Tetramethyl-1,4-dihydro-1,2,4,5-tetrazine, C_6H_(12)N_4", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1984 International Union of Crystallography.\nReceived 16 April 1984; accepted 8 August 1984. \nWe thank Drs H. Kohn and D. Hoskin for useful discussions. We also are grateful to the National Institutes of Health and McNeil Pharmaceutical for grants that supported this investigation.\n\n", "abstract": "M_r =140\u221919, monoclinic, P2_1/n, a = 10\u2219612(3), b=6\u2219820(1), c= 10\u2219975 (2) \u00c5, \u03b2=95\u221931(2)\u00b0, V=790.9(5) \u00c5^3, Z=4, D_m=1.13(5) (flotation), D_x = 1\u2219177 g cm^(-3), Mo K\u03b1, \u03bb = 0.71073 \u00c5, \u03bc= 0.848 cm^(-1), F(000) = 304, T= 295 K, R = 0\u2219077 for 704 observed reflections. This potentially antiaromatic or homoaromatic ring system has a flattened boat conformation with both N-methyls in equatorial positions. Bond angles and distances (excluding H's) predicted to be symmetry equivalent exhibit variations of 0.002-0.014 \u00c5 and 0.0-2.0\u00b0. Substantial delocalization of the electron lone pairs of N(1) and N(4) is found.", "date": "1984-12", "date_type": "published", "publication": "Acta Crystallographica Section C", "volume": "40", "number": "12", "publisher": "International Union of Crystallography", "pagerange": "2076-2078", "id_number": "CaltechAUTHORS:20110620-160432815", "issn": "0108-2701", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160432815", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "McNeil Pharmaceutical" } ] }, "doi": "10.1107/S0108270184010684", "primary_object": { "basename": "Bemis_1984_Acta_Crystallographica_Section_C_Crystal_Structure_Communications_1_3_4_6-Tetramethyl-1_4-dihydro-1.pdf", "url": "https://authors.library.caltech.edu/records/6a820-6py24/files/Bemis_1984_Acta_Crystallographica_Section_C_Crystal_Structure_Communications_1_3_4_6-Tetramethyl-1_4-dihydro-1.pdf" }, "resource_type": "article", "pub_year": "1984", "author_list": "Bemis, Guy W.; Whittle, Robert R.; et el." } ]