[ { "id": "https://authors.library.caltech.edu/records/pbtnb-6k609", "eprint_id": 115443, "eprint_status": "archive", "datestamp": "2023-08-22 15:42:13", "lastmod": "2023-10-24 16:31:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Wang-Vincent-C-C", "name": { "family": "Wang", "given": "Vincent C.-C." } }, { "id": "Chen-Peter-P-Y", "name": { "family": "Chen", "given": "Peter P.-Y." } }, { "id": "Yu-Steve-S-F", "name": { "family": "Yu", "given": "Steve S.-F." } } ] }, "title": "Methane oxidation by the copper methane monooxygenase: Before and after the cryogenic electron microscopy structure of particulate methane monooxygenase from Methylococcus capsulatus (Bath)", "ispublished": "pub", "full_text_status": "public", "keywords": "biocatalysis; copper monooxygenase; methane oxidation; oxene chemistry; tricopper cluster; General Chemistry", "note": "\u00a9 2022 Chemical Society Located in Taipei and Wiley-VCH GmbH. \n\nVersion of Record online: 23 May 2022; Manuscript accepted: 08 May 2022; Manuscript received: 13 April 2022. \n\nDedicated to the memory of Robert H. Grubbs, a great scientist and human being. \n\nFunding information: Ministry of Science and Technology, Taiwan, Grant/Award Numbers: 110-2113-M-001-038, 109-2113-M-001-003; Academia Sinica, Grant/Award Numbers: AS-KPQ-106-DDPP, AS-TP-108-ML07, AS-GCS-107-07", "abstract": "The particulate methane monooxygenase (pMMO) is a copper monooxygenase that converts methane into methanol in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently and selectively under ambient conditions, it has become the paradigm for understanding the design of nature to facilitate this process so that we could develop a biomimetic catalyst to accomplish this difficult C1 chemistry in the laboratory. With the advent of the recent 2.5\u2009\u00c5 cryo-electron microscopy structure of the pMMO from Methylococcus capsulatus (Bath), it is now evident that the catalytic site of hydroxylation in pMMO is a Cu^ICu^ICu^I tricopper cluster (Cu^I: copper ions) sequestered within the transmembrane domain of this protein complex. With three reducing equivalents embodied in this structural motif, the tricopper cluster can react with O\u2082 to irreversibly cleave the O-O bond to harness the highly reactive oxene for rapid and direct insertion into the C-H bonds of methane. Here, we review the structural, biochemical, and biophysical studies over the past three decades that have culminated in this important advance in the chemistry of methane oxidation.", "date": "2022-07-11", "date_type": "published", "publication": "Journal of the Chinese Chemical Society", "publisher": "Chinese Chemical Society", "id_number": "CaltechAUTHORS:20220708-259535200", "issn": "0009-4536", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220708-259535200", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "110-2113-M-001-038" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "109-2113-M-001-003" }, { "agency": "Academia Sinica", "grant_number": "AS-KPQ-106-DDPP" }, { "agency": "Academia Sinica", "grant_number": "AS-TP-108-ML07" }, { "agency": "Academia Sinica", "grant_number": "AS-GCS-107-07" } ] }, "doi": "10.1002/jccs.202200166", "resource_type": "article", "pub_year": "2022", "author_list": "Chan, Sunney I.; Wang, Vincent C.-C.; et el." }, { "id": "https://authors.library.caltech.edu/records/kqw88-mjz51", "eprint_id": 94736, "eprint_status": "archive", "datestamp": "2023-08-22 01:54:42", "lastmod": "2023-10-20 18:13:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lu-Yu-Jhang", "name": { "family": "Lu", "given": "Yu-Jhang" } }, { "id": "Hung-Mu-Cheng", "name": { "family": "Hung", "given": "Mu-Cheng" } }, { "id": "Chang-Brian-T-A", "name": { "family": "Chang", "given": "Brian T.-A." } }, { "id": "Lee-Tsu-Lin", "name": { "family": "Lee", "given": "Tsu-Lin" } }, { "id": "Lin-Zhi-Han", "name": { "family": "Lin", "given": "Zhi-Han" } }, { "id": "Tsai-I-Kuen", "name": { "family": "Tsai", "given": "I-Kuen" } }, { "id": "Chen-Yao-Sheng", "name": { "family": "Chen", "given": "Yao-Sheng" } }, { "id": "Chang-Chin-Shuo", "name": { "family": "Chang", "given": "Chin-Shuo" } }, { "id": "Tsai-Yi-Fang", "name": { "family": "Tsai", "given": "Yi-Fang" } }, { "id": "Chen-Kelvin-H-C", "name": { "family": "Chen", "given": "Kelvin H.-C." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Yu-Steve-S-F", "name": { "family": "Yu", "given": "Steve S.-F." }, "orcid": "0000-0002-3462-065X" } ] }, "title": "PmoB subunit of particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath): The Cu^I sponge and its function", "ispublished": "pub", "full_text_status": "public", "keywords": "Copper sites; Particulate methane monooxygenase (pMMO); Membrane protein; Methane oxidation; Oxygen/hydrogen-peroxide redox loop; X-ray absorption spectroscopy", "note": "\u00a9 2019 Published by Elsevier Inc. \n\nReceived 2 September 2018, Revised 28 February 2019, Accepted 8 April 2019, Available online 15 April 2019. \n\nThis work was supported in whole or in part by Academia Sinica (AS-107-TP-ML07 and AS-KPQ-106-DDPP) and grants from the Ministry of Science and Technology, Taiwan (MOST 94-2113-M-001-016, 101-2113-M-001-007-MY3 and 104-2113-M-001-013-MY3 to S.S.F.Y.; and MOST 101-2113-M-001-013 to S.I.C.). We are grateful to Dr. Jyh-Fu Lee and his staffs at the National Synchrotron Radiation Research Center, Hsinchu, Taiwan, for their kind assistance with the X-ray absorption measurements. Mr. Tai-Lang Lin assisted us with the electron microscopy analyses at the EM Core Facility of the Institute of Cellular and Organismic Biology, Academia Sinica. \n\nThe contributions of the coauthors to this article are: Y.-J.L., Z.-H.L., T.-L.L. and Y.-S.C. constructed and designed the expression vectors for protein expression; M.-C.H., C.-S.C. and Y.-S.C. conducted the mutagenesis studies; Y.-J.L., M.-C.H., B.T.-A.C. and C.-S.C. carried out the specific activity measurements on the recombinant PmoB constructs; B.T.-A.C. purified the MBP-PmoB55\u2013414; Y.-J.L., B.T.-A.C., Y.-F.T. and S.S.-F.Y. conducted the EPR and/or XAS experiments; M.-C.H., B.T.-A.C., Z.-H.L., I.-K.T., C.-S.C. and Y.-S.C. performed the quantification of the copper contents in the proteins, and the protein quantification using antibodies; B.T.-A.C., Z.-H. L., I.-K.T. and C.-S.C. grew the E. coli cells for the biochemical and biophysical characterization of the recombinant proteins; K.H.-C.C., S.S.-F.Y. and S.I.C. designed the research; S.S.-F.Y. and S.I.C. wrote the paper.\n\n
Supplemental Material - 1-s2.0-S0162013418305166-mmc1.docx
", "abstract": "In this study, we describe efforts to clarify the role of the copper cofactors associated with subunit B (PmoB) of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) (M. capsulatus). This subunit exhibits strong affinity toward Cu^I ions. To elucidate the high copper affinity of the subunit, the full-length PmoB, and the N-terminal truncated mutants PmoB_(33\u2013414) and PmoB_(55\u2013414), each fused to the maltose-binding protein (MBP), are cloned and over-expressed into Escherichia coli (E. coli) K12 TB1 cells. The Y374F, Y374S and M300L mutants of these protein constructs are also studied. When this E. coli is grown with the pmoB gene in 1.0\u202fmM Cu^(II), it behaves like M. capsulatus (Bath) cultured under high copper stresswith abundant membrane accumulation and high CuI content. The recombinantPmoB proteins are verified by Western blotting of antibodies directed against the MBP sub-domain in each of the copper-enriched PmoB proteins. Cu K-edge X-rayabsorption near edge spectroscopy (XANES) of the copper ions confirms that all the PmoB recombinants are Cu^I proteins. All the PmoB proteins show evidence of a \"dicopper site\" according to analysis of the Cu extended X-ray absorption edge fine structure (EXAFS) of the membranes. No specific activities toward methane and propene oxidation are observed with the recombinant membrane-bound PmoB proteins. However, significant production of hydrogen peroxide is observed in the case of the PmoB_(33\u2013414) mutant. Reaction of the dicopper site with dioxygenproduces hydrogen peroxide and leads to oxidation of the CuI ions residing in the C-terminal sub-domain of the PmoB subunit.", "date": "2019-07", "date_type": "published", "publication": "Journal of Inorganic Biochemistry", "volume": "196", "publisher": "Elsevier", "pagerange": "Art. No. 110691", "id_number": "CaltechAUTHORS:20190417-075957631", "issn": "0162-0134", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190417-075957631", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academia Sinica", "grant_number": "AS-107-TP-ML07" }, { "agency": "Academia Sinica", "grant_number": "AS-KPQ-106-DDPP" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "94-2113-M-001-016" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "101-2113-M-001-007-MY3" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "104-2113-M-001-013-MY3" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "101-2113-M-001-013" } ] }, "doi": "10.1016/j.jinorgbio.2019.04.005", "primary_object": { "basename": "1-s2.0-S0162013418305166-mmc1.docx", "url": "https://authors.library.caltech.edu/records/kqw88-mjz51/files/1-s2.0-S0162013418305166-mmc1.docx" }, "resource_type": "article", "pub_year": "2019", "author_list": "Lu, Yu-Jhang; Hung, Mu-Cheng; et el." }, { "id": "https://authors.library.caltech.edu/records/kaas6-key07", "eprint_id": 93376, "eprint_status": "archive", "datestamp": "2023-08-22 00:56:45", "lastmod": "2023-10-20 17:05:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Nai-Chi", "name": { "family": "Chen", "given": "Nai-Chi" } }, { "id": "Yoshimura-Masato", "name": { "family": "Yoshimura", "given": "Masato" }, "orcid": "0000-0002-7466-2192" }, { "id": "Miyazaki-Naoyuki", "name": { "family": "Miyazaki", "given": "Naoyuki" } }, { "id": "Guan-Hong-Hsiang", "name": { "family": "Guan", "given": "Hong-Hsiang" } }, { "id": "Chuankhayan-Phimonphan", "name": { "family": "Chuankhayan", "given": "Phimonphan" } }, { "id": "Lin-Chien-Chih", "name": { "family": "Lin", "given": "Chien-Chih" } }, { "id": "Chen-Shao-Kang", "name": { "family": "Chen", "given": "Shao-Kang" } }, { "id": "Lin-Pei-Ju", "name": { "family": "Lin", "given": "Pei-Ju" } }, { "id": "Huang-Yen-Chieh", "name": { "family": "Huang", "given": "Yen-Chieh" } }, { "id": "Iwasaki-Kenji", "name": { "family": "Iwasaki", "given": "Kenji" } }, { "id": "Nakagawa-Atsushi", "name": { "family": "Nakagawa", "given": "Atsushi" }, "orcid": "0000-0002-1700-7861" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Chen-Chun-Jung", "name": { "family": "Chen", "given": "Chun-Jung" }, "orcid": "0000-0002-5157-4288" } ] }, "title": "The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism", "ispublished": "pub", "full_text_status": "public", "keywords": "Electron microscopy; Virus structures; X-ray crystallography", "note": "\u00a9 2019 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 24 August 2018; Accepted 17 January 2019; Published 20 February 2019. \n\nData availability: Coordinates for the cryo-EM and crystal structures of PvNV and MrNV are deposited in the Protein Data Bank under accession codes 6AB5, 6AB6, 5YKU, 5YKV, 5YKX, 5YKZ, 5YL0, and 5YL1. Cryo-EM reconstructions of the T\u2009=\u20093 and T\u2009=\u20091 PvNV-LPs are deposited in the EM Data Bank under accession codes EMD-9576 and EMD-6999, respectively. All relevant data supporting the findings of this study are available from the authors upon request. \n\nWe are indebted to staff at beamlines TPS 05A, TLS 13B1, 13C1, and 15A1 at the National Synchrotron Radiation Research Center (NSRRC) in Taiwan, Eiki Yamashita at the Beamline BL44XU, and Taiwan beamline BL12B2 at SPring-8 in Japan for technical assistance under the proposal numbers 2015A6600, 2015A4000, 2015B6600, 2015B4004, 2015B4010, 2016A6600, 2016A6659, 2016A4012, 2016B6600, 2016B4000, 2017A4000, 2017A6600, and 2017B6659, partly supported by the International Collaborative Research Program of the Institute for Protein Research, Osaka University (ICR-16-05). We thank Tomitake Tsukihara for valuable discussions. We are also grateful for Shang-Rung Wu for the assistance of the negative-staining EM measurement at National Cheng Kung University (NCKU). Portions of this research were carried out at the NSRRC-NCKU Protein Crystallography Laboratory. This work was supported in part by National Science Council (NSC) and Ministry of Science and Technology (MOST) grants 101-2628-B-213-001-MY4, 102-2627-M-213-001-MY3, 105-2311-B-213-001-MY3 and NSRRC grants to C.-J. Chen. \n\nAuthor Contributions: C.J.C. initiated the project and designed the research; N.C.C. designed, expressed, purified and crystallized proteins and viral particles; N.C.C., M.Y., H.H.G., P.C., C.C.L, S.K.C, P.J.L., Y.C.H., and C.J.C. performed X-ray data collection and analyses; N.C.C., M.Y., and C.J.C. determined and refined crystal structures; N.M. and K.I. provided cryo-EM facilities, carried out cryo-EM experiment and EM maps; N.C.C., N.M., M.Y., and C.J.C. built and refined cryo-EM structures; N.C.C., M.Y., N.M., H.H.G., and C.J.C. analyzed structures; A.N. provided the collaborative BL44XU beamtime and discussion; N.C.C., M.Y., and C.J.C. wrote the manuscript and prepared the figures; N.C.C., M.Y., C.J.C., and S.I.C. edited and revised the manuscript. \n\nThe authors declare no competing interests.\n\nPublished - s42003-019-0311-z.pdf
Supplemental Material - 42003_2019_311_MOESM1_ESM.pdf
Supplemental Material - 42003_2019_311_MOESM2_ESM.pdf
", "abstract": "Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T\u2009=\u20093 and T\u2009=\u20091 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the \u2206N-ARM-PvNV shell-domain (S-domain) in T\u2009=\u20091 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N-terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T\u2009=\u20093 and T\u2009=\u20091 assemblies. Increasing the N/C-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.", "date": "2019-02-20", "date_type": "published", "publication": "Communications Biology", "volume": "2", "publisher": "Springer Nature", "pagerange": "Art. No. 72", "id_number": "CaltechAUTHORS:20190301-081007422", "issn": "2399-3642", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190301-081007422", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Osaka University", "grant_number": "ICR-16-05" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "101-2628-B-213-001-MY4" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "102-2627-M-213-001-MY3" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "105-2311-B-213-001-MY3" }, { "agency": "National Synchrotron Radiation Research Center" } ] }, "doi": "10.1038/s42003-019-0311-z", "pmcid": "PMC6382870", "primary_object": { "basename": "42003_2019_311_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/kaas6-key07/files/42003_2019_311_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "42003_2019_311_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/kaas6-key07/files/42003_2019_311_MOESM2_ESM.pdf" }, { "basename": "s42003-019-0311-z.pdf", "url": "https://authors.library.caltech.edu/records/kaas6-key07/files/s42003-019-0311-z.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Chen, Nai-Chi; Yoshimura, Masato; et el." }, { "id": "https://authors.library.caltech.edu/records/1jcam-2jp16", "eprint_id": 90274, "eprint_status": "archive", "datestamp": "2023-08-19 11:54:08", "lastmod": "2023-10-18 23:20:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Guan-Hong-Hsiang", "name": { "family": "Guan", "given": "Hong-Hsiang" } }, { "id": "Hsieh-Yin-Cheng", "name": { "family": "Hsieh", "given": "Yin-Cheng" } }, { "id": "Lin-Pei-Ju", "name": { "family": "Lin", "given": "Pei-Ju" } }, { "id": "Huang-Yen-Chieh", "name": { "family": "Huang", "given": "Yen-Chieh" } }, { "id": "Yoshimura-Masato", "name": { "family": "Yoshimura", "given": "Masato" }, "orcid": "0000-0002-7466-2192" }, { "id": "Chen-Li-Ying", "name": { "family": "Chen", "given": "Li-Ying" } }, { "id": "Chen-Shao-Kang", "name": { "family": "Chen", "given": "Shao-Kang" } }, { "id": "Chuankhayan-P", "name": { "family": "Chuankhayan", "given": "Phimonphan" } }, { "id": "Lin-Chien-Chih", "name": { "family": "Lin", "given": "Chien-Chih" } }, { "id": "Chen-Nai-Chi", "name": { "family": "Chen", "given": "Nai-Chi" } }, { "id": "Nakagawa-Atsushi", "name": { "family": "Nakagawa", "given": "Atsushi" }, "orcid": "0000-0002-1700-7861" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Chen-Chun-Jung", "name": { "family": "Chen", "given": "Chun-Jung" }, "orcid": "0000-0002-5157-4288" } ] }, "title": "Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 29 March 2018; Accepted 18 September 2018; Published 08 October 2018. \n\n\nAccession Codes: The structural factors and coordinates have been deposited in the RCSB Protein Data Bank. The PDB code is 5XMJ. \n\nWe are indebted to the Yuch-Cheng Jean and staff at TLS beamlines BL13B1, BL13C1 and BL15A1 and TPS 05\u2009A at the National Synchrotron Radiation Research Center (NSRRC) in Taiwan and Hirofumi Ishii at the Taiwan contracted beamline BL12B2 and Eiki Yamashita and Akifumi Higashiura at the BL44XU at SPring-8 in Japan for technical assistance under the proposal numbers 2014B6600, 2014B6965, 2015A6600, 2015A4000, 2015B6600, 2015B4004, 2015B4010, 2016A6600, 2016A6659, 2016A4012, 2016B6600, 2016B4000, 2017A4000, 2017A6600, 2017B4000, 2017B6769 and 2017B6600. This work was in part performed under the International Collaborative Research Program of Institute for Protein Research, Osaka University, ICR-17-05. Portions of this research were carried out at the NSRRC-NCKU Protein Crystallography Laboratory at National Cheng Kung University (NCKU). This work was supported in part by National Science Council (NSC) grants 101\u20132628-B-213-001-MY4, 102-2627-M-213-001-MY3, Ministry of Science and Technology (MOST) 105-2311-B-231-001-MY3 and NSRRC grants 1034RSB02, 1044RSB02, 1054RSB02 and 1064RSB02 to C.-J. Chen. \n\nAuthor Contributions: Yin-Cheng Hsieh, Yen-Chieh Huang and Pei-Ju Lin performed the cell culturing of D. gigas and QFR protein purification and characterization; Yin-Cheng Hsieh carried out the crystallization and the crystal optimization; Yin-Cheng Hsieh and Masato Yoshimura did the data collection and diffraction data analyses; Hong-Hsiang Guan determined and refined the structure; Hong-Hsiang Guan, Li-Ying Chen, Phimonphan Chuankhayan, Chien-Chih Lin, Nai-Chi Chen, Shao-Kang Chen and Sunney I. Chan analyzed the structure and interpret the functional mechanism. Atsushi Nakagawa provided the collaborative BL44XU beamtime and discussion. Chun-Jung Chen initiated the project and designed the research; Hong-Hsiang Guan, Sunney I. Chan and Chun-Jung Chen wrote and edited the paper. \n\nThe authors declare no competing interests.\n\nPublished - 41598_2018_Article_33193.pdf
Supplemental Material - 41598_2018_33193_MOESM1_ESM.pdf
", "abstract": "The membrane-embedded quinol:fumarate reductase (QFR) in anaerobic bacteria catalyzes the reduction of fumarate to succinate by quinol in the anaerobic respiratory chain. The electron/proton-transfer pathways in QFRs remain controversial. Here we report the crystal structure of QFR from the anaerobic sulphate-reducing bacterium Desulfovibrio gigas (D. gigas) at 3.6\u2009\u00c5 resolution. The structure of the D. gigas QFR is a homo-dimer, each protomer comprising two hydrophilic subunits, A and B, and one transmembrane subunit C, together with six redox cofactors including two b-hemes. One menaquinone molecule is bound near heme b_L in the hydrophobic subunit C. This location of the menaquinone-binding site differs from the menaquinol-binding cavity proposed previously for QFR from Wolinella succinogenes. The observed bound menaquinone might serve as an additional redox cofactor to mediate the proton-coupled electron transport across the membrane. Armed with these structural insights, we propose electron/proton-transfer pathways in the quinol reduction of fumarate to succinate in the D. gigas QFR.", "date": "2018-10-08", "date_type": "published", "publication": "Scientific Reports", "volume": "8", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 14935", "id_number": "CaltechAUTHORS:20181016-085612513", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181016-085612513", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Science Council (Taipei)", "grant_number": "101-2628-B-213-001-MY4" }, { "agency": "National Science Council (Taipei)", "grant_number": "102-2627-M-213-001-MY3" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "105-2311-B-231-001-MY3" }, { "agency": "National Synchrotron Radiation Research Center", "grant_number": "1034RSB02" }, { "agency": "National Synchrotron Radiation Research Center", "grant_number": "1044RSB02" }, { "agency": "National Synchrotron Radiation Research Center", "grant_number": "1054RSB02" }, { "agency": "National Synchrotron Radiation Research Center", "grant_number": "1064RSB02" } ] }, "doi": "10.1038/s41598-018-33193-5", "pmcid": "PMC6175931", "primary_object": { "basename": "41598_2018_33193_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/1jcam-2jp16/files/41598_2018_33193_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "41598_2018_Article_33193.pdf", "url": "https://authors.library.caltech.edu/records/1jcam-2jp16/files/41598_2018_Article_33193.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Guan, Hong-Hsiang; Hsieh, Yin-Cheng; et el." }, { "id": "https://authors.library.caltech.edu/records/wh5t5-t9885", "eprint_id": 74432, "eprint_status": "archive", "datestamp": "2023-08-19 04:07:01", "lastmod": "2023-10-24 22:38:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Vincent-C-C", "name": { "family": "Wang", "given": "Vincent C.-C." } }, { "id": "Maji-S", "name": { "family": "Maji", "given": "Suman" } }, { "id": "Chen-Peter-P-Y", "name": { "family": "Chen", "given": "Peter P.-Y." } }, { "id": "Lee-Hung-Kay", "name": { "family": "Lee", "given": "Hung Kay" } }, { "id": "Yu-Steve-S-F", "name": { "family": "Yu", "given": "Steve S.-F." }, "orcid": "0000-0002-3462-065X" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Alkane Oxidation: Methane Monooxygenases, Related Enzymes, and Their Biomimetics", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2017 American Chemical Society. \n\nReceived: September 11, 2016; Published: February 16, 2017. \n\nThis work was supported by the National Taiwan University and Academia Sinica Innovative Joint Program (NTU-SINICA-104R104502 and NTU-SINICA-105R104502) and the Academia Sinica Research Program on Nanoscience and Nanotechnology (2393-105-0200). V.C.-C. W. thanks Dr. Tiow-Gan Ong for financial support from Academia Sinica Career Development Award (104-CDA-M08). \n\nThe authors declare no competing financial interest.", "abstract": "Methane monooxygenases (MMOs) mediate the facile conversion of methane into methanol in methanotrophic bacteria with high efficiency under ambient conditions. Because the selective oxidation of methane is extremely challenging, there is considerable interest in understanding how these enzymes carry out this difficult chemistry. The impetus of these efforts is to learn from the microbes to develop a biomimetic catalyst to accomplish the same chemical transformation. Here, we review the progress made over the past two to three decades toward delineating the structures and functions of the catalytic sites in two MMOs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO). sMMO is a water-soluble three-component protein complex consisting of a hydroxylase with a nonheme diiron catalytic site; pMMO is a membrane-bound metalloenzyme with a unique tricopper cluster as the site of hydroxylation. The metal cluster in each of these MMOs harnesses O_2 to functionalize the C\u2014H bond using different chemistry. We highlight some of the common basic principles that they share. Finally, the development of functional models of the catalytic sites of MMOs is described. These efforts have culminated in the first successful biomimetic catalyst capable of efficient methane oxidation without overoxidation at room temperature.", "date": "2017-07-12", "date_type": "published", "publication": "Chemical Reviews", "volume": "117", "number": "13", "publisher": "American Chemical Society", "pagerange": "8574-8621", "id_number": "CaltechAUTHORS:20170221-133527458", "issn": "0009-2665", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170221-133527458", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Taiwan University", "grant_number": "NTU-SINICA-104R104502" }, { "agency": "National Taiwan University", "grant_number": "NTU-SINICA-105R104502" }, { "agency": "Academia Sinica", "grant_number": "2393-105-0200" }, { "agency": "Academia Sinica", "grant_number": "104-CDA-M08" } ] }, "doi": "10.1021/acs.chemrev.6b00624", "resource_type": "article", "pub_year": "2017", "author_list": "Wang, Vincent C.-C.; Maji, Suman; et el." }, { "id": "https://authors.library.caltech.edu/records/7er4b-vsa80", "eprint_id": 59845, "eprint_status": "archive", "datestamp": "2023-08-22 16:54:30", "lastmod": "2023-10-23 22:46:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pham-Minh-D", "name": { "family": "Pham", "given": "Minh D." } }, { "id": "Lin-Ya-Ping", "name": { "family": "Lin", "given": "Ya-Ping" } }, { "id": "Vuong-Quan-Van", "name": { "family": "Vuong", "given": "Quan Van" } }, { "id": "Nagababu-P", "name": { "family": "Nagababu", "given": "Penumaka" } }, { "id": "Chang-Brian-T-A", "name": { "family": "Chang", "given": "Brian T.-A." } }, { "id": "Ng-Kok-Yaoh", "name": { "family": "Ng", "given": "Kok Yaoh" } }, { "id": "Chen-Chein-Hung", "name": { "family": "Chen", "given": "Chein-Hung" } }, { "id": "Han-Chau-Chung", "name": { "family": "Han", "given": "Chau-Chung" } }, { "id": "Chen-Chung-Hsuan", "name": { "family": "Chen", "given": "Chung-Hsuan" } }, { "id": "Li-Mai-Suan", "name": { "family": "Li", "given": "Mai Suan" } }, { "id": "Yu-Steve-S-F", "name": { "family": "Yu", "given": "Steve S.-F." }, "orcid": "0000-0002-3462-065X" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Inactivation of the particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath) by acetylene", "ispublished": "pub", "full_text_status": "public", "keywords": "Acetylene; Mechanism-based inactivation; Particulate methane monooxygenase; Methylococcus capsulatus (Bath); Mass spectrometry; Computational simulation", "note": "\u00a9 2015 Elsevier B.V. \n\nReceived date: 16 June 2015; Revised date: 29 July 2015; Accepted date: 9 August 2015. \n\nThis work was supported by Academia Sinica and by research grants from the National Science Council of the Republic of China (NSC 98-2113-M-001-026; NSC 99-2119-M-001-003; NSC 100-2113-M-001-002; and 101-2113-M-001-013- to SIC; and NSC 101-2113-M-001-007-MY3 to SSFY). The computer simulations were supported by the Department of Science and Technology at Ho Chi Minh City, Vietnam and Narodowe Centrum Nauki in Poland (grant 2011/01/B/NZ1/01622 to MSL). \n\nWe acknowledge numerous scientific discussions on this work with Dr. Chia-Min Yang (Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan). M.D.P. is also grateful to Dr. Yang for serving as his academic advisor.\n\nSupplemental Material - mmc1.pdf
", "abstract": "Acetylene (HCCH) has a long history as a mechanism-based enzyme inhibitor and is considered an active-site probe of the particulate methane monooxygenase (pMMO). Here, we report how HCCH inactivates pMMO in Methylococcus capsulatus (Bath) by using high-resolution mass spectrometry and computational simulation. High-resolution MALDI-TOF MS of intact pMMO complexes has allowed us to confirm that the enzyme oxidizes HCCH to the ketene (C_2H_2O) intermediate, which then forms an acetylation adduct with the transmembrane PmoC subunit. LC-MS/MS analysis of the peptides derived from in-gel proteolytic digestion of the protein subunit identifies K196 of PmoC as the site of acetylation. No evidence is obtained for chemical modification of the PmoA or PmoB subunit. The inactivation of pMMO by a single adduct in the transmembrane PmoC domain is intriguing given the complexity of the structural fold of this large membrane-protein complex as well as the complicated roles played by the various metal cofactors in the enzyme catalysis. Computational studies suggest that the entry of hydrophobic substrates to, and migration of products from, the catalytic site of pMMO is controlled tightly within the transmembrane domain. Support of these conclusions is provided by parallel experiments with two related alkynes: propyne (CH3CCH) and trifluoropropyne (CF_3CCH). Finally, we discuss the implication of these findings to the location of the catalytic site in pMMO.", "date": "2015-12", "date_type": "published", "publication": "Biochimica et Biophysica Acta - Proteins and Proteomics", "volume": "1854", "number": "12", "publisher": "Elsevier", "pagerange": "1842-1852", "id_number": "CaltechAUTHORS:20150824-122929840", "issn": "1570-9639", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150824-122929840", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academia Sinica" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 98-2113-M-001-026" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 99-2119-M-001-003" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 100-2113-M-001-002" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 101-2113-M-001-013" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 101-2113-M-001-007-MY3" }, { "agency": "Department of Science and Technology (Vietnam)" }, { "agency": "National Science Centre (Poland)", "grant_number": "2011/01/B/NZ1/01622" } ] }, "doi": "10.1016/j.bbapap.2015.08.004", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/7er4b-vsa80/files/mmc1.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Pham, Minh D.; Lin, Ya-Ping; et el." }, { "id": "https://authors.library.caltech.edu/records/6ak7e-a3y89", "eprint_id": 61785, "eprint_status": "archive", "datestamp": "2023-08-20 08:23:32", "lastmod": "2023-10-25 15:44:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Nai-Chi", "name": { "family": "Chen", "given": "Nai-Chi" } }, { "id": "Yoshimura-Masato", "name": { "family": "Yoshimura", "given": "Masato" }, "orcid": "0000-0002-7466-2192" }, { "id": "Guan-Hong-Hsiang", "name": { "family": "Guan", "given": "Hong-Hsiang" } }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "Ting-Yu" } }, { "id": "Misumi-Yuko", "name": { "family": "Misumi", "given": "Yuko" } }, { "id": "Lin-Chien-Chih", "name": { "family": "Lin", "given": "Chien-Chih" } }, { "id": "Chuankhayan-P", "name": { "family": "Chuankhayan", "given": "Phimonphan" } }, { "id": "Nakagawa-Atsushi", "name": { "family": "Nakagawa", "given": "Atsushi" }, "orcid": "0000-0002-1700-7861" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Tsukihara-Tomitake", "name": { "family": "Tsukihara", "given": "Tomitake" } }, { "id": "Chen-Tzong-Yueh", "name": { "family": "Chen", "given": "Tzong-Yueh" } }, { "id": "Chen-Chun-Jung", "name": { "family": "Chen", "given": "Chun-Jung" }, "orcid": "0000-0002-5157-4288" } ] }, "title": "Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Chen 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 31, 2015; Accepted: September 11, 2015; Published: October 22, 2015. \n\nThis work was supported in part by Ministry of Science and Technology (MOST) grants 98-2313-B-009-001-MY3, 101-2628-B-213-001-MY4, 102-2627-M-213-001-MY3 and NSRRC grants 1023RSB02, 1023RSB14, 10324RSB02 and 10324RSB14 to C-J Chen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funders had no role in study design, data collection and\nanalysis, decision to publish, or preparation of the manuscript.\n\nThe authors have declared that no competing interests exist.\n\nWe are indebted to the staff at beamlines BL13B1, BL13C1 and BL15A1 at the National Synchrotron Radiation Research Center (NSRRC) in Taiwan and the staff at the Taiwan contracted beamline BL12B2 and Eiki Yamashita at the BL44XU at SPring-8 in Japan for technical assistance under the proposal numbers 2012A4009, 2012A6760, 2012A6600, 2012B4002, 2012B4012, 2012B6600, 2013A4011, 2013A6600, 2013B4000, 2013B6600, 2014A4000, 2014A6600, 2014A6965 and 2014A4004. We thank Ting-Fang Wang for the SUMO expression vector. We thank Christina Ling Chang, Yee-Shin Lin and KC Han-Ching Wang for valuable discussion. Portions of this research were carried out at the NSRRC-NCKU Protein Crystallography Laboratory of the University Center for Bioscience and Biotechnology of National Cheng Kung University (NCKU).\n\nAuthor Contributions: Conceived and designed the experiments: CJC TYC NCC. Performed the experiments: NCC YM HHG TYW CCL PC CJC. Analyzed the data: NCC MY TT TYW TYC CJC. Contributed reagents/materials/analysis tools: AN. Wrote the paper: NCC CJC. Revised the paper: NCC MY SIC AN TYC CJC.\n\nPublished - journal.ppat.1005203.pdf
Supplemental Material - journal.ppat.1005203.s001.TIFF
Supplemental Material - journal.ppat.1005203.s002.TIFF
Supplemental Material - journal.ppat.1005203.s003.TIFF
Supplemental Material - journal.ppat.1005203.s004.TIFF
Supplemental Material - journal.ppat.1005203.s005.TIFF
Supplemental Material - journal.ppat.1005203.s006.TIFF
Supplemental Material - journal.ppat.1005203.s007.TIFF
Supplemental Material - journal.ppat.1005203.s008.TIFF
", "abstract": "Betanodaviruses cause massive mortality in marine fish species with viral nervous necrosis. The structure of a T = 3 Grouper nervous necrosis virus-like particle (GNNV-LP) is determined by the ab initio method with non-crystallographic symmetry averaging at 3.6 \u00c5 resolution. Each capsid protein (CP) shows three major domains: (i) the N-terminal arm, an inter-subunit extension at the inner surface; (ii) the shell domain (S-domain), a jelly-roll structure; and (iii) the protrusion domain (P-domain) formed by three-fold trimeric protrusions. In addition, we have determined structures of the T = 1 subviral particles (SVPs) of (i) the delta-P-domain mutant (residues 35\u2212217) at 3.1 \u00c5 resolution; and (ii) the N-ARM deletion mutant (residues 35\u2212338) at 7 \u00c5 resolution; and (iii) the structure of the individual P-domain (residues 214\u2212338) at 1.2 \u00c5 resolution. The P-domain reveals a novel DxD motif asymmetrically coordinating two Ca2+ ions, and seems to play a prominent role in the calcium-mediated trimerization of the GNNV CPs during the initial capsid assembly process. The flexible N-ARM (N-terminal arginine-rich motif) appears to serve as a molecular switch for T = 1 or T = 3 assembly. Finally, we find that polyethylene glycol, which is incorporated into the P-domain during the crystallization process, enhances GNNV infection. The present structural studies together with the biological assays enhance our understanding of the role of the P-domain of GNNV in the capsid assembly and viral infection by this betanodavirus.", "date": "2015-10", "date_type": "published", "publication": "PLoS Pathogens", "volume": "11", "number": "10", "publisher": "Public Library of Science", "pagerange": "Art. No. e1005203", "id_number": "CaltechAUTHORS:20151103-082920090", "issn": "1553-7366", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151103-082920090", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "98-2313-B-009-001-MY3" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "101-2628-B-213-001-MY4" }, { "agency": "Ministry of Science and Technology (Taipei)", "grant_number": "102-2627-M-213-001-MY3" }, { "agency": "National Synchrotron Radiation Research Center (NSRRC)", "grant_number": "1023RSB02" }, { "agency": "National Synchrotron Radiation Research Center (NSRRC)", "grant_number": "1023RSB14" }, { "agency": "National Synchrotron Radiation Research Center (NSRRC)", "grant_number": "10324RSB02" }, { "agency": "National Synchrotron Radiation Research Center (NSRRC)", "grant_number": "10324RSB14" } ] }, "doi": "10.1371/journal.ppat.1005203", "pmcid": "PMC4619592", "primary_object": { "basename": "journal.ppat.1005203.s002.TIFF", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.s002.TIFF" }, "related_objects": [ { "basename": "journal.ppat.1005203.s003.TIFF", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.s003.TIFF" }, { "basename": "journal.ppat.1005203.s005.TIFF", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.s005.TIFF" }, { "basename": "journal.ppat.1005203.s006.TIFF", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.s006.TIFF" }, { "basename": "journal.ppat.1005203.s008.TIFF", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.s008.TIFF" }, { "basename": "journal.ppat.1005203.pdf", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.pdf" }, { "basename": "journal.ppat.1005203.s004.TIFF", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.s004.TIFF" }, { "basename": "journal.ppat.1005203.s007.TIFF", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.s007.TIFF" }, { "basename": "journal.ppat.1005203.s001.TIFF", "url": "https://authors.library.caltech.edu/records/6ak7e-a3y89/files/journal.ppat.1005203.s001.TIFF" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Chen, Nai-Chi; Yoshimura, Masato; et el." }, { "id": "https://authors.library.caltech.edu/records/jeaqt-ejp77", "eprint_id": 120761, "eprint_status": "archive", "datestamp": "2023-08-22 13:42:53", "lastmod": "2023-10-23 18:00:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Cheng", "name": { "family": "Hu", "given": "Cheng" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Sawyer-Elizabeth-B", "name": { "family": "Sawyer", "given": "Elizabeth B." }, "orcid": "0000-0003-0389-2692" }, { "id": "Yu-Yang", "name": { "family": "Yu", "given": "Yang" } }, { "id": "Wang-Jiangyun", "name": { "family": "Wang", "given": "Jiangyun" } } ] }, "title": "Metalloprotein design using genetic code expansion", "ispublished": "pub", "full_text_status": "public", "keywords": "General Chemistry", "note": "We gratefully acknowledge the Major State Basic Research Program of China (2010CB912301, 2011CBA00800), National Science Foundation of China (91313301, 21325211), and a CAS grant (KJZD-EW-L01) to Y. Y and J. Y. W.\n\nPublished - c4cs00018h.pdf
", "abstract": "More than one third of all proteins are metalloproteins. They catalyze important reactions such as photosynthesis, nitrogen fixation and CO\u2082 reduction. Metalloproteins such as the olfactory receptors also serve as highly elaborate sensors. Here we review recent developments in functional metalloprotein design using the genetic code expansion approach. We show that, through the site-specific incorporation of metal-chelating unnatural amino acids (UAAs), proton and electron transfer mediators, and UAAs bearing bioorthogonal reaction groups, small soluble proteins can recapitulate and expand the important functions of complex metalloproteins. Further developments along this route may result in cell factories and live-cell sensors with unprecedented efficiency and selectivity.", "date": "2014-09-21", "date_type": "published", "publication": "Chemical Society Reviews", "volume": "43", "number": "18", "publisher": "Royal Society of Chemistry", "pagerange": "6498-6510", "id_number": "CaltechAUTHORS:20230411-407202000.2", "issn": "0306-0012", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230411-407202000.2", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Major State Basic Research Program of China", "grant_number": "2010CB912301" }, { "agency": "Major State Basic Research Program of China", "grant_number": "2011CBA00800" }, { "agency": "National Natural Science Foundation of China", "grant_number": "91313301" }, { "agency": "National Natural Science Foundation of China", "grant_number": "21325211" }, { "agency": "Chinese Academy of Sciences", "grant_number": "KJZD-EW-L01" } ] }, "doi": "10.1039/c4cs00018h", "primary_object": { "basename": "c4cs00018h.pdf", "url": "https://authors.library.caltech.edu/records/jeaqt-ejp77/files/c4cs00018h.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Hu, Cheng; Chan, Sunney I.; et el." }, { "id": "https://authors.library.caltech.edu/records/4ce45-spp80", "eprint_id": 45212, "eprint_status": "archive", "datestamp": "2023-08-19 23:40:38", "lastmod": "2023-10-26 17:52:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-C", "name": { "family": "Chen", "given": "C." } }, { "id": "Hsieh-Y", "name": { "family": "Hsieh", "given": "Y." } }, { "id": "Yang-Y", "name": { "family": "Yang", "given": "Y." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "S. I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Crystal Structure of Dihydropyrimidinase from Tetraodon nigroviridis with Lysine Carboxylation: Metal Requirement for Post-translational Modification and Function", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2014 Springer.", "abstract": "Lysine carboxylation, a post-translational, facilitates metal coordination for specific enzymatic activities. We have determined structures of the vertebrate dihydropyrimidinase from Tetraodon nigroviridis (TnDhp) in various states: the apo enzyme as well as two forms of the holo enzyme with one and two metals at the catalytic site.", "date": "2014-03", "date_type": "published", "publication": "Journal of Biological Inorganic Chemistry", "volume": "19", "number": "S1", "publisher": "Springer", "pagerange": "S91", "id_number": "CaltechAUTHORS:20140425-084531804", "issn": "0949-8257", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140425-084531804", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1007/s00775-014-1095-8", "resource_type": "article", "pub_year": "2014", "author_list": "Chen, C.; Hsieh, Y.; et el." }, { "id": "https://authors.library.caltech.edu/records/8t4aa-2f773", "eprint_id": 43831, "eprint_status": "archive", "datestamp": "2023-08-22 10:38:08", "lastmod": "2023-10-25 23:55:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hsieh-Yin-Cheng", "name": { "family": "Hsieh", "given": "Yin-Cheng" } }, { "id": "Chen-Mei-Chun", "name": { "family": "Chen", "given": "Mei-Chun" } }, { "id": "Hsu-Ching-Chen", "name": { "family": "Hsu", "given": "Ching-Chen" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Yang-Yuh-Shyong", "name": { "family": "Yang", "given": "Yuh-Shyong" } }, { "id": "Chen-Chun-Jung", "name": { "family": "Chen", "given": "Chun-Jung" }, "orcid": "0000-0002-5157-4288" } ] }, "title": "Crystal Structures of Vertebrate Dihydropyrimidinase and Complexes from Tetraodon nigroviridis with Lysine Carbamylation", "ispublished": "pub", "full_text_status": "public", "keywords": "Crystal Structure; Crystallography; Metalloenzymes Post-translational Modification; Protein Carboxylation; Protein Complexes", "note": "\u00a9 2013 American Society for Biochemistry and Molecular Biology, Inc. \n\nReceived July 11, 2013; Revision received August 26, 2013. First Published on September 4, 2013. \n\nWe are indebted to the supporting staffs at beamlines BL13B1 and BL13C1 of the National Synchrotron Radiation Research Center and to Masato Yoshimura and Hirofumi Ishii at Beamlines BL12B2 and BL44XU of SPring-8. \n\nThis work was supported in part by National Science Council (NSC) Grants NSC 98-2311-B-213-MY3 and NSC 101-2628-B-213-MY4 and National Synchrotron Radiation Center Grants 1003RSB02 and 1013RSB02 (to C. J. C.) and NSC Grant NSC 99-2311-B-009-004-MY3 and the Aiming for the Top University and Elite Research Center Development Plan of Ministry of Education (MOE-ATU Plan) (to Y. S. Y.).\n\nPublished - J._Biol._Chem.-2013-Hsieh-30645-58.pdf
", "abstract": "Lysine carbamylation, a post-translational modification, facilitates metal coordination for specific enzymatic activities. We have determined structures of the vertebrate dihydropyrimidinase from Tetraodon nigroviridis (TnDhp) in various states: the apoenzyme as well as two forms of the holoenzyme with one and two metals at the catalytic site. The essential active-site structural requirements have been identified for the possible existence of four metal-mediated stages of lysine carbamylation. Only one metal is sufficient for stabilizing lysine carbamylation; however, the post-translational lysine carbamylation facilitates additional metal coordination for the regulation of specific enzymatic activities through controlling the conformations of two dynamic loops, Ala^(69)\u2013Arg^(74) and Met^(158)\u2013Met^(165), located in the tunnel for the substrate entrance. The substrate/product tunnel is in the \"open form\" in the apo-TnDhp, in the \"intermediate state\" in the monometal TnDhp, and in the \"closed form\" in the dimetal TnDhp structure, respectively. Structural comparison also suggests that the C-terminal tail plays a role in the enzymatic function through interactions with the Ala^(69)\u2013Arg^(74) dynamic loop. In addition, the structures of the dimetal TnDhp in complexes with hydantoin, N-carbamyl-\u03b2-alanine, and N-carbamyl-\u03b2-amino isobutyrate as well as apo-TnDhp in complex with a product analog, N-(2-acetamido)-iminodiacetic acid, have been determined. These structural results illustrate how a protein exploits unique lysines and the metal distribution to accomplish lysine carbamylation as well as subsequent enzymatic functions.", "date": "2013-10-18", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "288", "number": "42", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "30645-30658", "id_number": "CaltechAUTHORS:20140214-093236082", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140214-093236082", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Science Council (Tapiei)", "grant_number": "NSC 98-2311-B-213-MY3" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 101-2628-B-213-MY4" }, { "agency": "National Synchrotron Radiation Center", "grant_number": "1003RSB02" }, { "agency": "National Synchrotron Radiation Center", "grant_number": "1013RSB02" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 99-2311-B-009-004-MY3" }, { "agency": "Ministry of Education (Taipei)" } ] }, "doi": "10.1074/jbc.M113.496778", "pmcid": "PMC3798535", "primary_object": { "basename": "J._Biol._Chem.-2013-Hsieh-30645-58.pdf", "url": "https://authors.library.caltech.edu/records/8t4aa-2f773/files/J._Biol._Chem.-2013-Hsieh-30645-58.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Hsieh, Yin-Cheng; Chen, Mei-Chun; et el." }, { "id": "https://authors.library.caltech.edu/records/7wdah-b8x04", "eprint_id": 24145, "eprint_status": "archive", "datestamp": "2023-08-19 06:54:38", "lastmod": "2023-10-23 20:20:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fang-Jou-Yin", "name": { "family": "Fang", "given": "Jou-Yin" } }, { "id": "Chiang-Yuan-Lan", "name": { "family": "Chiang", "given": "Yuan-Lan" } }, { "id": "Hsieh-Yin-Cheng", "name": { "family": "Hsieh", "given": "Yin-Cheng" } }, { "id": "Wang-Vincent-C-C", "name": { "family": "Wang", "given": "Vincent C.-C." } }, { "id": "Huang-Yen-Chieh", "name": { "family": "Huang", "given": "Yen-Chieh" } }, { "id": "Chuankhayan-P", "name": { "family": "Chuankhayan", "given": "Phimonphan" } }, { "id": "Yang-Ming-Chi", "name": { "family": "Yang", "given": "Ming-Chi" } }, { "id": "Liu-Ming-Yih", "name": { "family": "Liu", "given": "Ming-Yih" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Chen-Chun-Jung", "name": { "family": "Chen", "given": "Chun-Jung" }, "orcid": "0000-0002-5157-4288" } ] }, "title": "Crystallization of Adenylylsulfate Reductase from Desulfovibrio gigas: A Strategy Based on Controlled Protein Oligomerization", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2011 American Chemical Society. Received: October 15, 2010. Revised: April 1, 2011. Published: April 05, 2011. \n\nPublished as part of the Crystal Growth & Designvirtual special issue on the 13th International Conference on the Crystallization of Biological Macromolecules (ICCBM13).\n\n\nWe are indebted to Yuch-Cheng Jean and the supporting staff\nat beamlines BL13B1 and BL13C1 at the National Synchrotron\nRadiation Research Center (NSRRC) and Masato Yoshimura,\nJeyakanthan Jeyaraman, and Hirofumi Ishii at the Taiwan contracted beamline BL12B2 at SPring-8 for technical assistance. Portions of this research were carried out at the NSRRC-NCKU Protein Crystallography Laboratory at National Cheng Kung University (NCKU). We thank Prof. Rong-Long Pan and Prof. Ping-Ling Ong for discussions and suggestions. This work was supported in part by grants from the National Science Council [NSC 95-2313-B-213-001, 95-2313-B-009-001-MY, and 98-2311-B-213-MY3] and the National Synchrotron Radiation Center [NSRRC 983RSB02 and 993RSB02] to C.-J.C.", "abstract": "Adenylylsulfate reductase (adenosine 5\u2032-phosphosulfate reductase, APS reductase or APSR, E.C.1.8.99.2) catalyzes the conversion of APS to sulfite in dissimilatory sulfate reduction. APSR was isolated and purified directly from massive anaerobically grown Desulfovibrio gigas, a strict anaerobe, for structure and function investigation. Oligomerization of APSR to form dimers\u2013\u03b1_2\u03b2_2, tetramers\u2013\u03b1_4\u03b2_4, hexamers\u2013\u03b1_6\u03b2_6, and larger oligomers was observed during purification of the protein. Dynamic light scattering and ultracentrifugation revealed that the addition of adenosine monophosphate (AMP) or adenosine 5\u2032-phosphosulfate (APS) disrupts the oligomerization, indicating that AMP or APS binding to the APSR dissociates the inactive hexamers into functional dimers. Treatment of APSR with \u03b2-mercaptoethanol decreased the enzyme size from a hexamer to a dimer, probably by disrupting the disulfide Cys156\u2014Cys162 toward the C-terminus of the \u03b2-subunit. Alignment of the APSR sequences from D. gigas and A. fulgidus revealed the largest differences in this region of the \u03b2-subunit, with the D. gigas APSR containing 16 additional amino acids with the Cys156\u2014Cys162 disulfide. Studies in a pH gradient showed that the diameter of the APSR decreased progressively with acidic pH. To crystallize the APSR for structure determination, we optimized conditions to generate a homogeneous and stable form of APSR by combining dynamic light scattering, ultracentrifugation, and electron paramagnetic resonance methods to analyze the various oligomeric states of the enzyme in varied environments.", "date": "2011-06", "date_type": "published", "publication": "Crystal Growth and Design", "volume": "11", "number": "6", "publisher": "American Chemical Society", "pagerange": "2127-2134", "id_number": "CaltechAUTHORS:20110621-085539646", "issn": "1528-7483", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110621-085539646", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Science Council (Taipei)", "grant_number": "95-2313-B-213-001" }, { "agency": "National Science Council (Taipei)", "grant_number": "95-2313-B-009-001-MY" }, { "agency": "National Science Council (Taipei)", "grant_number": "98-2311-B-213-MY3" }, { "agency": "National Synchrotron Radiation Research Center", "grant_number": "983RSB02" }, { "agency": "National Synchrotron Radiation Research Center", "grant_number": "993RSB02" } ] }, "doi": "10.1021/cg1013818", "resource_type": "article", "pub_year": "2011", "author_list": "Fang, Jou-Yin; Chiang, Yuan-Lan; et el." }, { "id": "https://authors.library.caltech.edu/records/25nkr-yxy96", "eprint_id": 21559, "eprint_status": "archive", "datestamp": "2023-08-19 04:31:22", "lastmod": "2023-10-21 00:08:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hsieh-Yin-Cheng", "name": { "family": "Hsieh", "given": "Yin-Cheng" } }, { "id": "Liu-Ming-Yih", "name": { "family": "Liu", "given": "Ming-Yih" } }, { "id": "Wang-Vincent-C-C", "name": { "family": "Wang", "given": "Vincent C.-C." } }, { "id": "Chiang-Yen-Lung", "name": { "family": "Chiang", "given": "Yen-Lung" } }, { "id": "Liu-En-Huang", "name": { "family": "Liu", "given": "En-Huang" } }, { "id": "Wu-Wen-guey", "name": { "family": "Wu", "given": "Wen-guey" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Chen-Chun-Jung", "name": { "family": "Chen", "given": "Chun-Jung" }, "orcid": "0000-0002-5157-4288" } ] }, "title": "Structural insights into the enzyme catalysis from comparison of three forms of dissimilatory sulphite reductase from Desulfovibrio gigas", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Blackwell Publishing Ltd. \n\nAccepted 1 September, 2010. Article first published online: 28 Sep. 2010. \n\nWe are indebted to the Yuch-Cheng Jean and supporting\nstaffs at beamlines BL13B1 and BL13C1 at the National\nSynchrotron Radiation Research Center (NSRRC), and\nJeyakanthan Jeyaraman, Masato Yoshimura and Hirofumi\nIshii at the Taiwan contracted beamline BL12B2 at SPring-8,\nfor their assistance. We are also grateful to Go Ueno and his\nstaff for assistance at BL26-I and -II of SPring-8 at RIKEN.\nPortions of this research were carried out at the NSRRCNCKU\nProtein Crystallography Laboratory at National Cheng\nKung University (NCKU). We thank Yi-Hong Lin for protein\nsequencing; Yu-Jhang Lu for assistance with the low temperature EPR experiments on the anaerobically purified Dsr\nproteins; and Wen-Hsiung Li, James Ketudat Cairns and\nChien-Te Chen for discussions. This work was supported in\npart by grants from the National Synchrotron Radiation\nResearch Center (NSRRC) (NSRRC 954RSB03, 963RSB03\nand 973RSB02 and from the National Science Council (NSC)\n(NSC 95-2311-B213-001-MY3, NSC 95-2923-B-213-001-\nMY3 and NSC 98-2311-B-213-MY3) of Taiwan.\n\nSupplemental Material - MMI_7390_sm_SuppInfor.doc
", "abstract": "The crystal structures of two active forms of dissimilatory sulphite reductase (Dsr) from Desulfovibrio gigas, Dsr-I and Dsr-II, are compared at 1.76 and 2.05 \u00c5 resolution respectively. The dimeric \u03b1_2\u03b2_2\u03b3_2 structure of Dsr-I contains eight [4Fe\u20134S] clusters, two saddle-shaped sirohaems and two flat sirohydrochlorins. In Dsr-II, the [4Fe\u20134S] cluster associated with the sirohaem in Dsr-I is replaced by a [3Fe\u20134S] cluster. Electron paramagnetic resonance (EPR) of the active Dsr-I and Dsr-II confirm the co-factor structures, whereas EPR of a third but inactive form, Dsr-III, suggests that the sirohaem has been demetallated in addition to its associated [4Fe\u20134S] cluster replaced by a [3Fe\u20134S] centre. In Dsr-I and Dsr-II, the sirohydrochlorin is located in a putative substrate channel connected to the sirohaem. The \u03b3-subunit C-terminus is inserted into a positively charged channel formed between the \u03b1- and \u03b2-subunits, with its conserved terminal Cys\u03b3104 side-chain covalently linked to the CHA atom of the sirohaem in Dsr-I. In Dsr-II, the thioether bond is broken, and the Cys\u03b3104 side-chain moves closer to the bound sulphite at the sirohaem pocket. These different forms of Dsr offer structural insights into a mechanism of sulphite reduction that can lead to S_3O_6^(2\u2212), S_2O_3^(2\u2212) and S^(2\u2212).", "date": "2010-12", "date_type": "published", "publication": "Molecular Microbiology", "volume": "78", "number": "5", "publisher": "Wiley-Blackwell", "pagerange": "1101-1116", "id_number": "CaltechAUTHORS:20110104-081227286", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110104-081227286", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Synchrotron Radiation Research Center (NSRRC)", "grant_number": "954RSB03" }, { "agency": "National Synchrotron Radiation Research Center (NSRRC)", "grant_number": "963RSB03" }, { "agency": "National Synchrotron Radiation Research Center (NSRRC)", "grant_number": "973RSB02" }, { "agency": "National Science Council (Taipei)", "grant_number": "95-2311-B213-001-MY3" }, { "agency": "National Science Council (Taipei)", "grant_number": "95-2923-B-213-001-MY3" }, { "agency": "National Science Council (Taipei)", "grant_number": "98-2311-B-213-MY3" } ] }, "doi": "10.1111/j.1365-2958.2010.07390.x", "primary_object": { "basename": "MMI_7390_sm_SuppInfor.doc", "url": "https://authors.library.caltech.edu/records/25nkr-yxy96/files/MMI_7390_sm_SuppInfor.doc" }, "resource_type": "article", "pub_year": "2010", "author_list": "Hsieh, Yin-Cheng; Liu, Ming-Yih; et el." }, { "id": "https://authors.library.caltech.edu/records/a1p2b-fn162", "eprint_id": 18629, "eprint_status": "archive", "datestamp": "2023-08-19 02:32:26", "lastmod": "2023-10-20 16:36:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Proton pumping in cytochrome c oxidase: The coupling between proton and electron gating", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 by the National Academy of Sciences.\nPublished online before print May 10, 2010.\nAuthor contributions: S.I.C. wrote the paper.\n\nPublished - Chan2010p10146P_Natl_Acad_Sci_Usa.pdf
", "abstract": "Comment on\nBovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate. [Proc Natl Acad Sci U S A. 2010]", "date": "2010-05-11", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "107", "number": "19", "publisher": "National Academy of Sciences", "pagerange": "8505-8506", "id_number": "CaltechAUTHORS:20100610-081630636", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100610-081630636", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1073/pnas.1004050107", "pmcid": "PMC2889352", "primary_object": { "basename": "Chan2010p10146P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/a1p2b-fn162/files/Chan2010p10146P_Natl_Acad_Sci_Usa.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/37dhh-21j11", "eprint_id": 15012, "eprint_status": "archive", "datestamp": "2023-08-21 21:31:38", "lastmod": "2023-10-18 20:27:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "A physical chemist's expedition to explore the world of membrane proteins", "ispublished": "pub", "full_text_status": "restricted", "keywords": "NMR of base-stacking interactions in nucleic acids in solution; dynamic structure of bilayer membranes; membrane biophysics; metal cofactor structure and function; redox linkage and proton pumping in cytochrome c oxidase; methane hydroxylation by the particulate methane monooxygenase; early kinetic events in protein folding", "note": "\u00a9 2009 Annual Reviews.\nI am indebted to Drs. Steve S.-F.Yu and Joseph J.-T. Huang of the Institute of Chemistry, Academia Sinica, for advice and assistance with the preparation of the manuscript.", "abstract": "Despite growing up amid humble surroundings, I ended up receiving an excellent education at the University of California at Berkeley and postdoctoral training at Harvard. My academic career at Caltech was shaped by serendipity, inspirational colleagues, and a stimulating research environment, as well as smart, motivated students and postdocs who were willing to join my search for molecular understanding of complex biological systems. From chemical physics I allowed my research to evolve, beginning with the application of NMR to investigate the base stacking of nucleic acid bases in solution, the dynamic structure of membranes, and culminating with the use of various forms of spectroscopy to elucidate the structure and function of membrane proteins and the early kinetic events in protein folding. The journey was a biased random walk driven by my own intellectual curiosity and instincts and by the pace at which I learned biochemistry from my students and postdocs, my colleagues, and the literature and through osmosis during seminars and scientific meetings.", "date": "2009-06", "date_type": "published", "publication": "Annual Reviews of Biophysics", "volume": "38", "publisher": "Annual Reviews", "pagerange": "1-27", "id_number": "CaltechAUTHORS:20090813-122034630", "issn": "1936-122X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090813-122034630", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1146/annurev.biophys.050708.133713", "resource_type": "article", "pub_year": "2009", "author_list": "Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/47b9z-8z917", "eprint_id": 73840, "eprint_status": "archive", "datestamp": "2023-08-19 23:23:52", "lastmod": "2023-10-24 21:01:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Yu-Steve-S-F", "name": { "family": "Yu", "given": "Steve S.-F." }, "orcid": "0000-0002-3462-065X" } ] }, "title": "Controlled Oxidation of Hydrocarbons by the Membrane-Bound Methane Monooxygenase: The Case for a Tricopper Cluster", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2008 American Chemical Society. \n\nReceived 13 December 2007. Published online 8 July 2008. Published in print 1 August 2008. \n\nThis work was supported by Academia Sinica and grants from the National Science Council of the Republic China (Grant NSC 95-2113-M-001-046-MY2). We thank Dr. Michael K. Chan (Departments of Chemistry and Biochemistry, The Ohio State University) for helpful discussions on the science as well as the manuscript.", "abstract": "The growing need for inexpensive methods to convert methane to methanol has sparked considerable interest in methods that catalyze this process. The integral membrane protein particulate methane monooxygenase (pMMO) mediates the facile conversion of methane to methanol in methanotrophic bacteria. Most evidence indicates that pMMO is a multicopper enzyme, and these copper ions support redox, dioxygen, and oxo-transfer chemistry. However, the exact identity of the copper species that mediates the oxo-transfer chemistry remains an area of intense debate. This highly complex enzyme is notoriously difficult to purify because of its instability outside the lipid bilayer and tendency to lose its essential metal cofactors. For this reason, pMMO has resisted both initial identification and subsequent isolation and purification for biochemical and biophysical characterization.\n\nIn this Account, we describe evidence that pMMO is a multicopper protein. Its unique trinuclear copper cluster mediates dioxygen chemistry and O-atom transfer during alkane hydroxylation. Although a recent crystal structure did not show this tricopper cluster, we provide compelling evidence for such a cluster through redox potentiometry and EPR experiments on the \"holo\" enzyme in pMMO-enriched membranes. We also identify a site in the structure of pMMO that could accommodate this cluster. A hydrophobic pocket capable of harboring pentane, the enzyme's largest known substrate, lies adjacent to this site.\n\nIn addition, we have designed and synthesized model tricopper clusters to provide further chemical evidence that a tricopper cluster mediates the enzyme's oxo-transfer chemistry. These biomimetic models exhibit similar spectroscopic properties and chemical reactivity to the putative tricopper cluster in pMMO. Based on computational analysis using density functional theory (DFT), triangular tricopper clusters are capable of harnessing a \"singlet oxene\" upon activation by dioxygen. An oxygen atom is then inserted via a concerted process into the C\u2212H bond of an alkane in the transition state during hydroxylation. The turnover frequency and kinetic isotope effect predicted by DFT show excellent agreement with experimental data.", "date": "2008-08", "date_type": "published", "publication": "Accounts of Chemical Research", "volume": "41", "number": "8", "publisher": "American Chemical Society", "pagerange": "969-979", "id_number": "CaltechAUTHORS:20170131-071607269", "issn": "0001-4842", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170131-071607269", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academia Sinica" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 95-2113-M-001-046-MY2" } ] }, "doi": "10.1021/ar700277n", "resource_type": "article", "pub_year": "2008", "author_list": "Chan, Sunney I. and Yu, Steve S.-F." }, { "id": "https://authors.library.caltech.edu/records/5eavz-3fg91", "eprint_id": 9901, "eprint_status": "archive", "datestamp": "2023-08-22 10:00:15", "lastmod": "2023-10-16 22:33:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Peter-P-Y", "name": { "family": "Chen", "given": "Peter P.-Y." } }, { "id": "Yang-Richard-B-G", "name": { "family": "Yang", "given": "Richard B.-G." } }, { "id": "Lee-Jason-C-M", "name": { "family": "Lee", "given": "Jason C.-M." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Facile O-atom insertion into C-C and C-H bonds by a trinuclear copper complex designed to harness a singlet oxene", "ispublished": "pub", "full_text_status": "public", "keywords": "density functional theory; methane monooxygenase; membrane-bound or particulate methane monooxygenase; soluble methane monooxygenase; mass spectroscopy", "note": "\u00a9 2007 by The National Academy of Sciences of the USA. \n\nCommunicated by Harry B. Gray, California Institute of Technology, Pasadena, CA, July 31, 2007 (received for review March 30, 2007). Published online on September 5, 2007, 10.1073/pnas.0707119104. \n\nWe thank Dr. Mei-Chun Tseng of the Institute of Chemistry of Academia Sinica for kind assistance in nanospray ESI-MS, Yi-Hung Liu of the Instrumentation Center of National Taiwan University in Taipei for solving the x-ray structure, and Dr. Michael K. Chan of the Department of Biochemistry and Chemistry at Ohio State University (Columbus, OH) for numerous discussions on this scientific project as well as valuable comments on this manuscript. This work was supported by Academia Sinica and by grants from the National Science Council (NSC95-2113-M-001-046-MY2) in Taiwan. \n\nAuthor contributions: P.P.-Y.C., R.B.-G.Y., and J.C.-M.L. performed research; S.I.C. designed research; S.I.C. contributed new reagents/analytic tools; P.P.-Y.C. and S.I.C. analyzed data; and P.P.-Y.C. and S.I.C. 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/0707119104/DC1.\n\nPublished - CHEpnas07b.pdf
Supplemental Material - CHEpnas07bfig10.pdf
Supplemental Material - CHEpnas07bfig11.pdf
Supplemental Material - CHEpnas07bfig12.pdf
Supplemental Material - CHEpnas07bfig13.pdf
Supplemental Material - CHEpnas07bfig14.pdf
Supplemental Material - CHEpnas07bfig7.pdf
Supplemental Material - CHEpnas07bfig8.pdf
Supplemental Material - CHEpnas07bfig9.pdf
Supplemental Material - CHEpnas07bsupp.pdf
", "abstract": "Two trinuclear copper [CuICuICuI(L)]1+ complexes have been prepared with the multidentate ligands (L) 3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(dimethylamino)ethyl)(methyl)amino)propan-2-ol) (7-Me) and (3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(diethylamino) ethyl)(ethyl) amino)propan-2-ol) (7-Et) as models for the active site of the particulate methane monooxygenase (pMMO). The ligands were designed to form the proper spatial and electronic geometry to harness a \"singlet oxene,\" according to the mechanism previously suggested by our laboratory. Consistent with the design strategy, both [CuICuICuI(L)]1+ reacted with dioxygen to form a putative bis(\u00b53-oxo)CuIICuIICuIII species, capable of facile O-atom insertion across the central C-C bond of benzil and 2,3-butanedione at ambient temperature and pressure. These complexes also catalyze facile O-atom transfer to the C-H bond of CH3CN to form glycolonitrile. These results, together with our recent biochemical studies on pMMO, provide support for our hypothesis that the hydroxylation site of pMMO contains a trinuclear copper cluster that mediates C-H bond activation by a singlet oxene mechanism.", "date": "2007-09-11", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "104", "number": "37", "publisher": "National Academy of Sciences", "pagerange": "14570-14575", "id_number": "CaltechAUTHORS:CHEpnas07b", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHEpnas07b", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academia Sinica" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 95-2113-M-001-046-MY2" } ] }, "doi": "10.1073/pnas.0707119104", "pmcid": "PMC1976241", "primary_object": { "basename": "CHEpnas07bfig11.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bfig11.pdf" }, "related_objects": [ { "basename": "CHEpnas07bfig9.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bfig9.pdf" }, { "basename": "CHEpnas07bfig14.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bfig14.pdf" }, { "basename": "CHEpnas07bfig7.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bfig7.pdf" }, { "basename": "CHEpnas07bfig8.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bfig8.pdf" }, { "basename": "CHEpnas07bsupp.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bsupp.pdf" }, { "basename": "CHEpnas07b.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07b.pdf" }, { "basename": "CHEpnas07bfig10.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bfig10.pdf" }, { "basename": "CHEpnas07bfig12.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bfig12.pdf" }, { "basename": "CHEpnas07bfig13.pdf", "url": "https://authors.library.caltech.edu/records/5eavz-3fg91/files/CHEpnas07bfig13.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Chen, Peter P.-Y.; Yang, Richard B.-G.; et el." }, { "id": "https://authors.library.caltech.edu/records/fgcgy-hd291", "eprint_id": 7092, "eprint_status": "archive", "datestamp": "2023-08-22 04:45:41", "lastmod": "2023-10-16 20:42:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pavlova-S-V", "name": { "family": "Pavlova", "given": "Svetlana V." } }, { "id": "To-Hing-Lun", "name": { "family": "To", "given": "Hing Lun" } }, { "id": "Chan-Edith-S-H", "name": { "family": "Chan", "given": "Edith S. H." } }, { "id": "Li-Hung-Wing", "name": { "family": "Li", "given": "Hung-Wing" } }, { "id": "Mak-Thomas-C-W", "name": { "family": "Mak", "given": "Thomas C. W." } }, { "id": "Lee-Hung-Kay", "name": { "family": "Lee", "given": "Hung Kay" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Synthesis, structure and dioxygen reactivity of a bis(\u00b5-iodo)dicopper(I) complex supported by the [N-(3,5-di-tert-butyl-2-hydroxybenzyl)-N,N-di-(2-pyridylmethyl)]amine ligand", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Royal Society of Chemistry 2006 \n\nReceived 30th September 2005, Accepted 25th January 2006. First published on the web 14th February 2006. \n\nThis work was supported by Academia Sinica and by grants from the National Science Council (NSC 90-2113-M-001-006, 90-2113-M-001-080 and 91-2113-M-006-006). The part of the work done in Hong Kong was supported by a Direct Grant (A/C 2060271) of The Chinese University of Hong Kong. We are grateful to Dr Jyh-Fu Lee of the Research Division of the National Synchrotron Radiation Research Center (NSRRC), Hsinchu, Taiwan for his kind assistance in the X-ray absorption measurements. Miss H.-W. Li and Professor Thomas C. W. Mak of CUHK solved the X-ray structure of [CuL(\u00b5-I)]2\u00b72CH2Cl2, and Mr Yuh-Sheng Wen solved the X-ray structure of [Cu(L)Cl]Cl\u00b72CHCl3. We are indebted to these colleagues for their contributions to the work. Finally, one of us (H.K.L.) would like to thank Dr Yee-Lok Wong for helpful discussions on the synthesis of 1; and S.V.P. and S.I.C. are grateful to Dr Peter P.-Y. Chen for discussions on the interpretation of the EPR results. \n\nSingle crystals of the solvated complex 1\u00b72CH2Cl2 were obtained from a dichloromethane solution. Crystals suitable for crystallographic studies were mounted in Lindemann glass capillaries and sealed under nitrogen. Data were collected using graphite-monochromatized Mo-K radiation ( = 0.71073 \u00c5) on a Bruker SMART CCD diffractometer at 293 K using frames of oscillation range 0.3\u00b0, with 2.19\u00b0 < < 28.02\u00b0. Diffraction measurements for a single crystal of 4\u00b72CHCl3 were carried out with a Bruker-Nonius Apex CCD diffractometer at 100 K using graphite-monochromatized Mo-K radiation ( = 0.71073 \u00c5) and frame of oscillation range 0.5\u00b0, with 2.30\u00b0 < < 27.48\u00b0. An empirical absorption correction was applied using the SADABS program.30 The crystal structures were solved by the direct methods and refined by full-matrix least squares on F2 using the SHELXTL program package.31 \n\nCCDC reference numbers 285531 and 286337. \n\nFor crystallographic data in CIF or other electronic format see DOI: 10.1039/b513898a\n\nPublished - PAVdt06.pdf
Supplemental Material - PAVdt06cryst.txt
Supplemental Material - PAVdt06supp.pdf
Cover Image - PAVdt06diag.gif
", "abstract": "The air-sensitive bis(\u00b5-iodo)dicopper(I) complex 1 supported by [N-(3,5-di-tert-butyl-2-hydroxybenzyl)-N,N-di-(2-pyridylmethyl)]amine (L) has been prepared by treating copper(I) iodide with L in anhydrous THF. Compound 1 crystallizes as a dimer in space group C2/c. Each copper(I) center has distorted tetrahedral N2I2 coordination geometry with Cu\u2013N(pyridyl) distances 2.061(3) and 2.063(3) \u00c5, Cu\u2013I distances 2.6162(5) and 2.7817(5) and a CuCu distance of 2.9086(8) \u00c5. Complex 1 is rapidly oxidized by dioxygen in CH2Cl2 with a 1 : 1 stoichiometry giving the bis(\u00b5-iodo)peroxodicopper(II) complex [Cu(L)(\u00b5-I)]2O2 (2). The reaction of 1 with dioxygen has been characterized by UV-vis, mass spectrometry, EPR and Cu K-edge X-ray absorption spectroscopy at low temperature (193 K) and above. The mass spectrometry and low temperature EPR measurements suggested an equilibrium between the bis(\u00b5-iodo)peroxodicopper(II) complex 2 and its dimer, namely, the tetranuclear (peroxodicopper(II))2 complex [Cu(L)(\u00b5-I)]4O4 (2). Complex 2 undergoes an effective oxo-transfer reaction converting PPh3 into OPPh3 under anaerobic conditions. At sufficiently high concentration of PPh3, the oxygen atom transfer from 2 to PPh3 was followed by the formation of [Cu(PPh3)3I]. The dioxygen reactivity of 1 was compared with that known for other halo(amine)copper(I) dimers.", "date": "2006", "date_type": "published", "publication": "Dalton Transactions", "volume": "2006", "number": "18", "publisher": "Royal Society of Chemistry", "pagerange": "2232-2243", "id_number": "CaltechAUTHORS:PAVdt06", "issn": "1477-9226", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:PAVdt06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academia Sinica" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 90-2113-M-001-006" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 90-2113-M-001-080" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 91-2113-M-006-006" }, { "agency": "Chinese University of Hong Kong", "grant_number": "A/C 2060271" } ] }, "doi": "10.1039/b513898a", "primary_object": { "basename": "PAVdt06.pdf", "url": "https://authors.library.caltech.edu/records/fgcgy-hd291/files/PAVdt06.pdf" }, "related_objects": [ { "basename": "PAVdt06cryst.txt", "url": "https://authors.library.caltech.edu/records/fgcgy-hd291/files/PAVdt06cryst.txt" }, { "basename": "PAVdt06diag.gif", "url": "https://authors.library.caltech.edu/records/fgcgy-hd291/files/PAVdt06diag.gif" }, { "basename": "PAVdt06supp.pdf", "url": "https://authors.library.caltech.edu/records/fgcgy-hd291/files/PAVdt06supp.pdf" }, { "basename": "medium.png", "url": "https://authors.library.caltech.edu/records/fgcgy-hd291/files/medium.png" }, { "basename": "small.png", "url": "https://authors.library.caltech.edu/records/fgcgy-hd291/files/small.png" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Pavlova, Svetlana V.; To, Hing Lun; et el." }, { "id": "https://authors.library.caltech.edu/records/yzm1b-g2587", "eprint_id": 1125, "eprint_status": "archive", "datestamp": "2023-08-22 01:56:24", "lastmod": "2023-10-13 22:37:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Rita-P-Y", "name": { "family": "Chen", "given": "Rita P.-Y." } }, { "id": "Huang-Joseph-J-T", "name": { "family": "Huang", "given": "Joseph J.-T." } }, { "id": "Chen-Hsin-Liang", "name": { "family": "Chen", "given": "Hsin-Liang" } }, { "id": "Jan-H", "name": { "family": "Jan", "given": "Howard" } }, { "id": "Velusamy-M", "name": { "family": "Velusamy", "given": "Marappan" } }, { "id": "Lee-Chung-Tien", "name": { "family": "Lee", "given": "Chung-Tien" } }, { "id": "Fann-Wunshain", "name": { "family": "Fann", "given": "Wunshain" } }, { "id": "Larsen-R-W", "name": { "family": "Larsen", "given": "Randy W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Measuring the refolding of \u03b2-sheets with different turn sequences on a nanosecond time scale", "ispublished": "pub", "full_text_status": "public", "keywords": "SHORT LINEAR PEPTIDE, HAIRPIN FORMATION, AQUEOUS-SOLUTION, DESIGNED PEPTIDES, FOLDING DYNAMICS, B1 DOMAIN, PROTEIN, STABILITY, UBIQUITIN, PHOTOLYSIS", "note": "Copyright \u00a9 2004 by the National Academy of Sciences. \n\nEdited by William F. DeGrado, University of Pennsylvania School of Medicine, Philadelphia, PA, and approved March 19, 2004 (received for review August 4, 2003). Published online before print May 3, 2004, 10.1073/pnas.0304922101 \n\nWe thank Prof. Tien-Yau Luh, Dr. Hsian-Rong Tseng, and Dr. Joern Wirsch in the Department of Chemistry at National Taiwan University for assistance in the synthesis of our linker. This work was supported by a program project grant from Academia Sinica as well as by Grant NSC 91-2119-M-001-012 from the National Science Council, Taiwan. \n\nThis paper was submitted directly (Track II) to the PNAS office.\n\nPublished - CHEpnas04.pdf
", "abstract": "Whether turns play an active or passive role in protein folding remains a controversial issue at this juncture. Here we use a photolabile cage strategy in combination with laser-flash photolysis and photoacoustic calorimetry to study the effects of different turns on the kinetics of beta-hairpin refolding on a nanosecond time scale. This strategy opens up a temporal window to allow the observation of early kinetic events in the protein refolding process at ambient temperature and pH without interference from any denaturants. Our results provide direct evidence demonstrating that even a one-residue difference in the turn region can change the refolding kinetics of a peptide. This observation suggests an active role for turn formation in directing protein folding.", "date": "2004-05-11", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "101", "number": "19", "publisher": "National Academy of Sciences", "pagerange": "7305-7310", "id_number": "CaltechAUTHORS:CHEpnas04", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHEpnas04", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academia Sinica" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 91-2119-M-001-012" } ] }, "doi": "10.1073/pnas.0304922101", "pmcid": "PMC409914", "primary_object": { "basename": "CHEpnas04.pdf", "url": "https://authors.library.caltech.edu/records/yzm1b-g2587/files/CHEpnas04.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Chen, Rita P.-Y.; Huang, Joseph J.-T.; et el." }, { "id": "https://authors.library.caltech.edu/records/13zvv-cmw51", "eprint_id": 73891, "eprint_status": "archive", "datestamp": "2023-08-19 13:28:50", "lastmod": "2023-10-24 21:04:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Chen-Kelvin-H-C", "name": { "family": "Chen", "given": "Kelvin H.-C." } }, { "id": "Yu-Steve-S-F", "name": { "family": "Yu", "given": "Steve S.-F." }, "orcid": "0000-0002-3462-065X" }, { "id": "Chen-Chang-Li", "name": { "family": "Chen", "given": "Chang-Li" } }, { "id": "Kuo-Simon-S-J", "name": { "family": "Kuo", "given": "Simon S.-J." } } ] }, "title": "Toward Delineating the Structure and Function of the Particulate Methane Monooxygenase from Methanotrophic Bacteria", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2004 American Chemical Society. \n\nReceived 3 February 2004. Published online 19 March 2004. Published in print 1 April 2004. \n\nThis work was supported by grants from the National Science Council (NSC 91-2113-M-001-045 and 92-2113-M-001-057) and the National Institute of General Medical Sciences, U.S. Public Health Service (GM22432).", "abstract": "The particulate methane monooxygenase (pMMO) is a complex membrane protein complex that has been difficult to isolate and purify for biochemical and biophysical characterization because of its instability in detergents used to solubilize the enzyme. In this perspective, we summarize the progress recently made toward obtaining a purified pMMO\u2212detergent complex and characterizing the enzyme in pMMO-enriched membranes. The purified pMMO is a multi-copper protein, with ca. 15 copper ions sequestered into five trinuclear copper clusters:\u2009 two for dioxygen chemistry and alkane hydroxylation (catalytic or C-clusters) and three to provide a buffer of reducing equivalents to re-reduce the C-clusters following turnover (electron transfer or E-clusters). The enzyme is functional when all the copper ions are reduced. When the protein is purified under ambient aerobic conditions in the absence of a hydrocarbon substrate, only the C-clusters are oxidized; there is an apparent kinetic barrier for electron transfer from the E-cluster copper ions to the C-clusters under these conditions. Evidence is provided in support of both C-clusters participating in the dioxygen chemistry, but only one C-cluster supporting alkane hydroxylation. Acetylene modification of the latter C-cluster in the hydrophobic pocket of the active site lowers or removes the kinetic barrier for electron transfer from the E-clusters to the C-clusters so that all the copper ions could be fully oxidized by dioxygen. A model for the hydroxylation chemistry when a hydrocarbon substrate is bound to the active site of the hydroxylation C-cluster is presented. Unlike soluble methane monooxygenase (sMMO), pMMO exhibits limited substrate specificity, but the hydroxylation chemistry is highly regioselective and stereoselective. In addition, the hydroxylation occurs with total retention of configuration of the carbon center that is oxidized. These results are consistent with a concerted mechanism involving direct side-on insertion of an active singlet \"oxene\" from the activated copper cluster across the \"C\u2212H\" bond in the active site. Finally, in our hands, both the purified pMMO\u2212detergent complex and pMMO-enriched membranes exhibit high NADH-sensitive as well as duroquinol-sensitive specific activity. A possible role for the two reductants in the turnover of the enzyme is proposed.", "date": "2004-04-20", "date_type": "published", "publication": "Biochemistry", "volume": "43", "number": "15", "publisher": "American Chemical Society", "pagerange": "4421-4430", "id_number": "CaltechAUTHORS:20170131-140941315", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170131-140941315", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Science Council (Taipei)", "grant_number": "NSC 91-2113-M-001-045" }, { "agency": "National Science Council (Taipei)", "grant_number": "92-2113-M-001-057" }, { "agency": "NIH", "grant_number": "GM22432" } ] }, "doi": "10.1021/bi0497603", "resource_type": "article", "pub_year": "2004", "author_list": "Chan, Sunney I.; Chen, Kelvin H.-C.; et el." }, { "id": "https://authors.library.caltech.edu/records/g2s3f-p9f62", "eprint_id": 7090, "eprint_status": "archive", "datestamp": "2023-08-22 01:18:08", "lastmod": "2023-10-16 20:42:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pavlova-S-V", "name": { "family": "Pavlova", "given": "Svetlana V." } }, { "id": "Chen-Kelvin-H-C", "name": { "family": "Chen", "given": "Kelvin H.-C." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Spectroscopic characterization of the oxo-transfer reaction from a bis(\u00b5-oxo)dicopper(III) complex to triphenylphosphine", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 Royal Society of Chemistry 2004. \n\nReceived 4th May 2004, Accepted 17th August 2004. First published on the web 31st August 2004. \n\nThis work was supported by Academia Sinica and by grants from the National Science Council (NSC 90-2113-M-001-006, 90-2113-M-001-080 and 91-2113-M-006-006). We are grateful to Dr Jyh-Fu Lee of the Research Division of the National Synchrotron Radiation Research Center (NSRRC), Hsinchu, Taiwan for his kind assistance in the X-ray absorption measurements. We thank Mr Yuh-Sheng Wen for solving the X-ray structure of [CuII2(\u00b5-OH)2(L)2](ClO4)2. We also thank Prof. J.F. Biellmann for helpful discussions. \n\nCrystal data. C20H50Cl2Cu2N4O10, M = 704.62, monoclinic, space group P21/c (no. 14), a = 7.6177(10), b = 17.850(3), c = 13.9471(17) , = 122.147(12)\u00b0, U = 1605.7(4) 3, T = 298(2) K, Z = 2, \u00b5(Mo-K) = 1.542 mm\u20131, 3036 reflection measured, 2814 unique (Rint = 0.0220) which were used in all calculations. The final wR(F2) was 0.1084 (all data). \n\nCCDC reference number 245728. \n\nSee http://www.rsc.org/suppdata/dt/b4/b406692h/ for crystallographic data in CIF or other electronic format.\n\nPublished - PAVdt04.pdf
Supplemental Material - PAVdt04cifdata.txt
Supplemental Material - PAVdt04supp.pdf
Cover Image - PAVdt04fig.gif
", "abstract": "The oxygen-atom transfer reaction from the bis(\u00b5-oxo)dicopper(III) complex [CuIII2(\u00b5-O)2(L)2]2+1, where L =N,N,N,N -tetraethylethylenediamine, to PPh3 has been studied by UV-vis, EPR, 1H NMR and Cu K-edge X-ray absorption spectroscopy in parallel at low temperatures (193 K) and above. Under aerobic conditions (excess dioxygen), 1 reacted with PPh3, giving OPPh3 and a diamagnetic species that has been assigned to an oxo-bridged dicopper(II) complex on the basis of EPR and Cu K-edge X-ray absorption spectroscopic data. Isotope-labeling experiments (18O2) established that the oxygen atom incorporated into the triphenylphosphine oxide came from both complex 1 and exogenous dioxygen. Detailed kinetic studies revealed that the process is a third-order reaction; the rate law is first order in both complex 1 and triphenylphosphine, as well as in dioxygen. At temperatures above 233 K, reaction of 1 with PPh3 was accompanied by ligand degradation, leading to oxidative N-dealkylation of one of the ethyl groups. By contrast, when the reaction was performed in the absence of excess dioxygen, negligible substrate (PPh3) oxidation was observed. Instead, highly symmetrical copper complexes with a characteristic isotropic EPR signal at g= 2.11 were formed. These results are discussed in terms of parallel reaction channels that are activated under various conditions of temperature and dioxygen.", "date": "2004", "date_type": "published", "publication": "Dalton Transactions", "volume": "2004", "number": "20", "publisher": "Royal Society of Chemistry", "pagerange": "3261-3272", "id_number": "CaltechAUTHORS:PAVdt04", "issn": "1477-9226", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:PAVdt04", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academia Sinica" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 90-2113-M-001-006" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 90-2113-M-001-080" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 91-2113-M-006-006" } ] }, "doi": "10.1039/B406692H", "primary_object": { "basename": "PAVdt04cifdata.txt", "url": "https://authors.library.caltech.edu/records/g2s3f-p9f62/files/PAVdt04cifdata.txt" }, "related_objects": [ { "basename": "PAVdt04fig.gif", "url": "https://authors.library.caltech.edu/records/g2s3f-p9f62/files/PAVdt04fig.gif" }, { "basename": "PAVdt04supp.pdf", "url": "https://authors.library.caltech.edu/records/g2s3f-p9f62/files/PAVdt04supp.pdf" }, { "basename": "medium.png", "url": "https://authors.library.caltech.edu/records/g2s3f-p9f62/files/medium.png" }, { "basename": "small.png", "url": "https://authors.library.caltech.edu/records/g2s3f-p9f62/files/small.png" }, { "basename": "PAVdt04.pdf", "url": "https://authors.library.caltech.edu/records/g2s3f-p9f62/files/PAVdt04.pdf" } ], "resource_type": "article", "pub_year": "2004", "author_list": "Pavlova, Svetlana V.; Chen, Kelvin H.-C.; et el." }, { "id": "https://authors.library.caltech.edu/records/51a9m-dcm55", "eprint_id": 1853, "eprint_status": "archive", "datestamp": "2023-09-13 16:43:13", "lastmod": "2023-10-23 20:36:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yu-Steve-S-F", "name": { "family": "Yu", "given": "Steve S.-F." }, "orcid": "0000-0002-3462-065X" }, { "id": "Chen-Kelvin-H-C", "name": { "family": "Chen", "given": "Kelvin H.-C." } }, { "id": "Tseng-Mandy-Y-H", "name": { "family": "Tseng", "given": "Mandy Y.-H." } }, { "id": "Wang-Yane-Shih", "name": { "family": "Wang", "given": "Yane-Shih" } }, { "id": "Tseng-Chiu-Feng", "name": { "family": "Tseng", "given": "Chiu-Feng" } }, { "id": "Chen-Yu-Ju", "name": { "family": "Chen", "given": "Yu-Ju" } }, { "id": "Huang-Ded-Shih", "name": { "family": "Huang", "given": "Ded-Shih" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Production of High-Quality Particulate Methane Monooxygenase in High Yields from Methylococcus capsulatus (Bath) with a Hollow-Fiber Membrane Bioreactor", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2003, American Society for Microbiology. \n\nReceived 12 May 2003/ Accepted 18 July 2003 \n\nThis work was supported by grants NSC 90-2113-M-001-006, NSC 90-2113-M-001-080, and NSC 91-2113-M-006-006 from the National Science Council.\n\nWe are grateful to Jyh-Fu Lee of the Research Division of the National Synchrotron Radiation Research Center, Hsinchu, Taiwan, for his kind assistance with the X-ray absorption measurements.\n\nPublished - YUSjbact03.pdf
", "abstract": "In order to obtain particulate methane monooxygenase (pMMO)-enriched membranes from Methylococcus capsulatus (Bath) with high activity and in high yields, we devised a method to process cell growth in a fermentor adapted with a hollow-fiber bioreactor that allows easy control and quantitative adjustment of the copper ion concentration in NMS medium over the time course of cell culture. This technical improvement in the method for culturing bacterial cells allowed us to study the effects of copper ion concentration in the growth medium on the copper content in the membranes, as well as the specific activity of the enzyme. The optimal copper concentration in the growth medium was found to be 30 to 35 \u00b5M. Under these conditions, the pMMO is highly expressed, accounting for 80% of the total cytoplasmic membrane proteins and having a specific activity as high as 88.9 nmol of propylene oxide/min/mg of protein with NADH as the reductant. The copper stoichiometry is ~13 atoms per pMMO molecule. Analysis of other metal contents provided no evidence of zinc, and only traces of iron were present in the pMMO-enriched membranes. Further purification by membrane solubilization in dodecyl \u00df-D-maltoside followed by fractionation of the protein-detergent complexes according to molecular size by gel filtration chromatography resulted in a good yield of the pMMO-detergent complex and a high level of homogeneity. The pMMO-detergent complex isolated in this way had a molecular mass of 220 kDa and consisted of an {alpha}\u00df{gamma} protein monomer encapsulated in a micelle consisting of ca. 240 detergent molecules. The enzyme is a copper protein containing 13.6 mol of copper/mol of pMMO and essentially no iron (ratio of copper to iron, 80:1). Both the detergent-solubilized membranes and the purified pMMO-detergent complex exhibited reasonable, if not excellent, specific activity. Finally, our ability to control the level of expression of the pMMO allowed us to clarify the sensitivity of the enzyme to NADH and duroquinol, the two common reductants used to assay the enzyme.", "date": "2003-10-15", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "185", "number": "20", "publisher": "American Society for Microbiology", "pagerange": "5915-5924", "id_number": "CaltechAUTHORS:YUSjbact03", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:YUSjbact03", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Science Council (Taipei)", "grant_number": "NSC 90-2113-M-001-006" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 90-2113-M-001-080" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 91-2113-M-006-006" } ] }, "doi": "10.1128/JB.185.20.5915-5924.2003", "pmcid": "PMC225036", "primary_object": { "basename": "YUSjbact03.pdf", "url": "https://authors.library.caltech.edu/records/51a9m-dcm55/files/YUSjbact03.pdf" }, "resource_type": "article", "pub_year": "2003", "author_list": "Yu, Steve S.-F.; Chen, Kelvin H.-C.; et el." }, { "id": "https://authors.library.caltech.edu/records/h6bwg-mf176", "eprint_id": 1472, "eprint_status": "archive", "datestamp": "2023-08-21 23:46:15", "lastmod": "2023-10-13 22:50:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Peter-P-Y", "name": { "family": "Chen", "given": "Pei-Yeh" } }, { "id": "Lin-Chun-Cheng", "name": { "family": "Lin", "given": "Chun-Cheng" } }, { "id": "Chang-Yin-Ting", "name": { "family": "Chang", "given": "Yin-Ting" } }, { "id": "Lin-Su-Ching", "name": { "family": "Lin", "given": "Su-Ching" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "One O-linked sugar can affect the coil-to-\u03b2 structural transition of the prion peptide", "ispublished": "pub", "full_text_status": "public", "keywords": "TRANSMISSIBLE SPONGIFORM ENCEPHALOPATHIES; SOLID-PHASE SYNTHESIS; N-ACETYLGLUCOSAMINE; SCRAPIE ISOFORM; ALPHA-HELICES; CELLULAR PRP; PROTEIN; GLYCOSYLATION; PROPAGATION; NUCLEAR", "note": "Copyright \u00a9 2002 by the National Academy of Sciences. \n\nEdited by Douglas C. Rees, California Institute of Technology, Pasadena, CA, and approved July 29, 2002 (received for review March 8, 2002). Published online before print September 16, 2002, 10.1073/pnas.192137799. \n\nThe electron microscopy was obtained on a ZEISS 902 electron microscope in the Institute of Molecular Biology, Academia Sinica, and we thank Dr. Sue Lin-Chao and Ms. Sue-Ping Lee for access to this facility as well as their kind assistance in the use of microscope. This work was supported by a Program Project grant awarded by Academia Sinica as well as a grant from the National Scientific Council, Taiwan (NSC90-2119-M001-010). This paper was submitted directly (Track II) to the PNAS office.\n\nPublished - CHEpnas02.pdf
", "abstract": "It has been known that the structural transition from PrPC to PrPSc leads to the prion formation. This putative conformational change challenges the central dogma of the protein folding theory-\"one sequence, one structure.\" Generally, scientists believe that there must be either a posttranslational modification or environmental factors involved in this event. However, all of the efforts to solve the mystery of the PrPC to PrPSc transition have ended in vain so far. Here we provide evidence linking O-linked glycosylation to the structural transition based on prion peptide studies. We find that the O-linked alpha-GaINAc at Ser-135 suppresses the formation of amyloid fibril formation of the prion peptide at physiological salt concentrations, whereas the peptide with the same sugar at Ser-132 shows the opposite effect. Moreover, this effect is sugar specific. Replacing alpha-GaINAc with beta-GIcNAc does not yield the same effect.", "date": "2002-10-01", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "99", "number": "20", "publisher": "National Academy of Sciences", "pagerange": "12633-12638", "id_number": "CaltechAUTHORS:CHEpnas02", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHEpnas02", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academia Sinica" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 90-2119-M001-010" } ] }, "doi": "10.1073/pnas.192137799", "pmcid": "PMC130512", "primary_object": { "basename": "CHEpnas02.pdf", "url": "https://authors.library.caltech.edu/records/h6bwg-mf176/files/CHEpnas02.pdf" }, "resource_type": "article", "pub_year": "2002", "author_list": "Chen, Pei-Yeh; Lin, Chun-Cheng; et el." }, { "id": "https://authors.library.caltech.edu/records/zzaa1-dqk17", "eprint_id": 503, "eprint_status": "archive", "datestamp": "2023-08-21 22:57:20", "lastmod": "2023-10-13 21:50:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhong-Dongping", "name": { "family": "Zhong", "given": "Dongping" } }, { "id": "Pal-S-K", "name": { "family": "Pal", "given": "Sumir Kumar" } }, { "id": "Zhang-Deqiang", "name": { "family": "Zhang", "given": "Deqiang" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Zewail-A-H", "name": { "family": "Zewail", "given": "Ahmed H." } } ] }, "title": "Femtosecond dynamics of rubredoxin: Tryptophan solvation and resonance energy transfer in the protein", "ispublished": "pub", "full_text_status": "public", "keywords": "tryptophan, formylmethionine variant of Pyrococcus furiosus\nrubredoxin, resonance energy transfer, N-acetyl-L-tryptophanamide, N-acetyl-L-Trp ethyl ester", "note": "\u00a9 2002, The National Academy of Sciences. \n\nContributed by Ahmed H. Zewail, October 31, 2001. \n\nWe like to thank Prof. Michael W. W. Adams and Dr. Francis E. Jenney, Jr. (University of Georgia) for the generous gift of all proteins reported here. We acknowledge the assistance of Dr. Spencer Baskin for the measuring of the lifetime of the apoprotein and for helpful discussion. This work was supported by the National Science Foundation. \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 - ZHOpnas02.pdf
", "abstract": "We report here studies of tryptophan (Trp) solvation dynamics in water and in the Pyrococcus furiosus rubredoxin protein, including the native and its apo and denatured forms. We also report results on energy transfer from Trp to the iron-sulfur [Fe-S] cluster. Trp fluorescence decay with the onset of solvation dynamics of the chromophore in water was observed with femtosecond resolution (approx 160 fs; 65% component), but the emission extended to the picosecond range (1.1 ps; 35% component). In contrast, the decay is much slower in the native rubredoxin; the Trp fluorescence decay extends to 10 ps and longer, reflecting the local rigidity imposed by residues and by the surface water layer. The dynamics of resonance energy transfer from the two Trps to the [Fe-S] cluster in the protein was observed to follow a temporal behavior characterized by a single exponential (15-20 ps) decay. This unusual observation in a protein indicates that the resonance transfer is to an acceptor of a well-defined orientation and separation. From studies of the mutant protein, we show that the two Trp residues have similar energy-transfer rates. The critical distance for transfer (R0) was determined, by using the known x-ray data, to be 19.5 \u00c5 for Trp-36 and 25.2 \u00c5 for Trp-3, respectively. The orientation factor (kappa 2) was deduced to be 0.13 for Trp-36, clearly indicating that molecular orientation of chromophores in the protein cannot be isotropic with kappa 2 value of 2/3. These studies of solvation and energy-transfer dynamics, and of the rotational anisotropy, of the wild-type protein, the (W3Y, I23V, L32I) mutant, and the fmetPfRd variant at various pH values reveal a dynamically rigid protein structure, which is probably related to the hyperthermophilicity of the protein.", "date": "2002-01-08", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "99", "number": "1", "publisher": "National Academy of Sciences", "pagerange": "13-18", "id_number": "CaltechAUTHORS:ZHOpnas02.1007", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:ZHOpnas02.1007", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" } ] }, "doi": "10.1073/pnas.012582399", "pmcid": "PMC117505", "primary_object": { "basename": "ZHOpnas02.pdf", "url": "https://authors.library.caltech.edu/records/zzaa1-dqk17/files/ZHOpnas02.pdf" }, "resource_type": "article", "pub_year": "2002", "author_list": "Zhong, Dongping; Pal, Sumir Kumar; et el." }, { "id": "https://authors.library.caltech.edu/records/chpd7-e7997", "eprint_id": 1623, "eprint_status": "archive", "datestamp": "2023-08-21 22:16:49", "lastmod": "2023-10-13 22:54:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schultz-B-E", "name": { "family": "Schultz", "given": "Brian E." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Structures and proton-pumping strategies of mitochondrial respiratory enzymes", "ispublished": "pub", "full_text_status": "public", "keywords": "CRYSTAL STRUCTURES; FREE ENERGY TRANSDUCTION; MITOCHONDRION; REDOX LINKAGE; RESPIRATORY ELECTRON TRANSPORT CHAIN; CYTOCHROME-C-OXIDASE; NADH-UBIQUINONE OXIDOREDUCTASE; BOVINE HEART-MITOCHONDRIA; ELECTRON-PARAMAGNETIC-RESONANCE; COLI FUMARATE REDUCTASE; 2 INDEPENDENT PATHWAYS; STEADY-STATE KINETICS; STRETCHING RAMAN BAND; IRON SULFUR PROTEINS; COMPLEX-I", "note": "\"Reprinted, with permission, from the Annual Review of Biophysics and Biomolecular Structure, Volume 30 copyright 2001 by Annual Reviews, www.annualreviews.org\" \n\nWe would like to thank Tina Iverson for assistance in the preparation of several figures presented in this work and for many helpful discussions.\n\nPublished - SCHarbbs01.pdf
", "abstract": "Enzymes of the mitochondrial respiratory chain serve as proton pumps, using the energy made available from electron transfer reactions to transport protons across the inner mitochondrial membrane and create an electrochemical gradient used for the production of ATP. The ATP synthase enzyme is reversible and can also serve as a proton pump by coupling ATP hydrolysis to proton translocation. Each of the respiratory enzymes uses a different strategy for performing proton pumping. In this work, the strategies are described and the structural bases for the action of these proteins are discussed in light of recent crystal structures of several respiratory enzymes. The mechanisms and efficiency of proton translocation are also analyzed in terms of the thermodynamics of the substrate transformations catalyzed by these enzymes.", "date": "2001-06", "date_type": "published", "publication": "Annual Review of Biophysics and Biomolecular Structure", "volume": "30", "publisher": "Annual Reviews", "pagerange": "23-65", "id_number": "CaltechAUTHORS:SCHarbbs01", "issn": "1056-8700", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SCHarbbs01", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1146/annurev.biophys.30.1.23", "primary_object": { "basename": "SCHarbbs01.pdf", "url": "https://authors.library.caltech.edu/records/chpd7-e7997/files/SCHarbbs01.pdf" }, "resource_type": "article", "pub_year": "2001", "author_list": "Schultz, Brian E. and Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/jkktr-epn63", "eprint_id": 75691, "eprint_status": "archive", "datestamp": "2023-08-19 06:48:38", "lastmod": "2023-10-25 15:13:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hansen-K-C", "name": { "family": "Hansen", "given": "Kirk C." } }, { "id": "Rock-R-S", "name": { "family": "Rock", "given": "Ronald S." } }, { "id": "Larsen-R-W", "name": { "family": "Larsen", "given": "Randy W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "A Method for Photoinitating Protein Folding in a Nondenaturing Environment", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2000 American Chemical Society. \n\nReceived 10 August 2000. Published online 5 November 2000. Published in print 1 November 2000. \n\nFunding for this project came from Grant GM22432 from the National Institutes of Health and from the National Science Foundation, MCB9904713 (R.W.L.). K.C.H. and R.S.R. are the recipients of National Research Service Predoctoral Awards.\n\nSupplemental Material - ja002949r_s.pdf
", "abstract": "The early kinetic events of protein folding are an important part of the folding pathway, yet our understanding towards the process is limited. Information from the study of these early events can allow us to distinguish between the various models that have been proposed to describe the folding of a protein in real time. Unlike \"typical\" chemical kinetics with well-defined initial and final states, the initial state of a denatured protein is relatively ill-defined. This uncertainty introduces ambiguity in the interpretation of the experimental data on the early events in protein folding. Toward developing a unified theory of protein folding, it is necessary to begin the observation of the refolding process from a well-defined initial state, trigger folding as rapidly as possible, and to follow the protein in real time as it samples its conformational space over its highly complex free-energy landscape.", "date": "2000-11-22", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "122", "number": "46", "publisher": "American Chemical Society", "pagerange": "11567-11568", "id_number": "CaltechAUTHORS:20170404-104411405", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-104411405", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NSF", "grant_number": "MCB-9904713" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "doi": "10.1021/ja002949r", "primary_object": { "basename": "ja002949r_s.pdf", "url": "https://authors.library.caltech.edu/records/jkktr-epn63/files/ja002949r_s.pdf" }, "resource_type": "article", "pub_year": "2000", "author_list": "Hansen, Kirk C.; Rock, Ronald S.; et el." }, { "id": "https://authors.library.caltech.edu/records/en1qy-fan23", "eprint_id": 101384, "eprint_status": "archive", "datestamp": "2023-08-21 21:37:28", "lastmod": "2023-10-19 22:40:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hung-Shao-Ching", "name": { "family": "Hung", "given": "Shao-Ching" } }, { "id": "Grant-C-V", "name": { "family": "Grant", "given": "Christopher V." }, "orcid": "0000-0003-1692-5414" }, { "id": "Peloquin-J-M", "name": { "family": "Peloquin", "given": "Jeffrey M." } }, { "id": "Waldeck-A-R", "name": { "family": "Waldeck", "given": "A. Reginald" } }, { "id": "Britt-R-D", "name": { "family": "Britt", "given": "R. David" }, "orcid": "0000-0003-0889-8436" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "ESEEM studies of succinate:ubiquinone reductase from Paracoccus denitrificans", "ispublished": "pub", "full_text_status": "restricted", "keywords": "2Fe-2S cluster; 4Fe-4S cluster; 3Fe-4S cluster; Flavin semiquinone radical; Electron spin-echo envelope modulation spectroscopy", "note": "\u00a9 2000 SBIC. \n\nReceived 29 July 1999; Accepted 16 May 2000; Published online: 27 July 2000. \n\nWe would like to thank Dr. Chrisopher J. Bender and Biotechnology Resource in Pulsed EPR Spectroscopy at Albert Einstein College of Medicine for providing us with a copy of their spectral simulation program. This work was supported by the NIH grants GM22432 to (S.I.C.) and GM48242 (to R.D.B.) from the U.S. Public Health Service.", "abstract": "Electron spin-echo envelope modulation (ESEEM) spectroscopy has been performed in order to obtain structural information about the environment of the reduced [2Fe-2S] cluster (S-1 center), the oxidized [3Fe-4S] cluster (S-3 center), and the flavin semiquinone radical in purified succinate:ubiquinone reductase from Paracoccus denitrificans. Spectral simulations of the ESEEM data from the reduced [2Fe-2S] yielded nuclear quadrupole interaction parameters that are indicative of peptide nitrogens. We also observed a weak interaction between the oxidized [3Fe-4S] cluster and a peptide \u00b9\u2074N. There was no evidence for coordination of any of the Fe atoms to \u00b9\u2074N atoms of imidazole rings. The ESEEM data from the flavin semiquinone radical were more complicated. Here, evidence was obtained for interactions between the unpaired electron and only the two nitrogen atoms in the flavin ring.", "date": "2000-10", "date_type": "published", "publication": "Journal of Biological Inorganic Chemistry", "volume": "5", "number": "5", "publisher": "Springer", "pagerange": "593-602", "id_number": "CaltechAUTHORS:20200219-114918387", "issn": "0949-8257", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200219-114918387", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "NIH", "grant_number": "GM48242" } ] }, "doi": "10.1007/s007750000142", "resource_type": "article", "pub_year": "2000", "author_list": "Hung, Shao-Ching; Grant, Christopher V.; et el." }, { "id": "https://authors.library.caltech.edu/records/576y8-zg603", "eprint_id": 76665, "eprint_status": "archive", "datestamp": "2023-08-19 05:47:36", "lastmod": "2023-10-25 16:11:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hung-Shao-Ching", "name": { "family": "Hung", "given": "Shao-Ching" } }, { "id": "Grant-C-V", "name": { "family": "Grant", "given": "Christopher V." }, "orcid": "0000-0003-1692-5414" }, { "id": "Peloquin-J-M", "name": { "family": "Peloquin", "given": "Jeffrey M." } }, { "id": "Waldeck-A-R", "name": { "family": "Waldeck", "given": "A. Reginald" } }, { "id": "Britt-R-D", "name": { "family": "Britt", "given": "R. David" }, "orcid": "0000-0003-0889-8436" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Electron Spin\u2212Lattice Relaxation Measurement of the 3Fe-4S (S-3) Cluster in Succinate:Ubiquinone Reductase from Paracoccus Denitrificans. A Detailed Analysis Based on a Dipole\u2212Dipole Interaction Model", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2000 American Chemical Society. \n\nReceived: October 18, 1999; In Final Form: January 20, 2000.\nPublication Date (Web): April 4, 2000. \n\nWe thank Dr. Brian E. Schultz and Professor Gary W. Brudvig for numerous discussion on this work. This work was supported by the NIH grants GM22432 (to S.I.C.) and GM48242 (to R.D.B.) from the U.S. Public Health Service.", "abstract": "The electron spin\u2212lattice relaxation for the 3Fe-4S (S-3) center in succinate:ubiquinone reductase has been examined using both inversion recovery and \"picket-fence\" pulse sequences at a temperature range of 4\u22128 K. The latter pulse sequence is used to eliminate the interference of spectral diffusion in frozen solids. An abnormally fast relaxation was observed for the S-3 center. We attribute this rapid relaxation to a magnetic dipolar interaction between the S-3 center and a nearby paramagnetic b-heme (cytochrome b). A model has been developed to treat the interaction between two paramagnetic redox centers in a rigid lattice at a fixed distance apart but with random orientations in a magnetic field. Both the contribution to the spin\u2212lattice relaxation rate from the dipolar interaction (k_(1\u03b8)), which is anisotropic, and the intrinsic electron spin relaxation, which is scalar (k_(1scalar)), have been deduced. We find that the contribution of exchange interaction to the anisotropic part of the relaxation rate (k1\u03b8) is very small. Accordingly, we conclude that k_(1scalar) is dominated by the intrinsic electron spin\u2212lattice relaxation. From k_(1\u03b8), a lower limit (r > 10 \u00c5) has been deduced for the distance between the S-3 center and the b-heme.", "date": "2000-05-18", "date_type": "published", "publication": "Journal of Physical Chemistry A", "volume": "104", "number": "19", "publisher": "American Chemical Society", "pagerange": "4402-4412", "id_number": "CaltechAUTHORS:20170419-092628378", "issn": "1089-5639", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170419-092628378", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "NIH", "grant_number": "GM48242" } ] }, "doi": "10.1021/jp993693i", "resource_type": "article", "pub_year": "2000", "author_list": "Hung, Shao-Ching; Grant, Christopher V.; et el." }, { "id": "https://authors.library.caltech.edu/records/3xbtd-3a157", "eprint_id": 76976, "eprint_status": "archive", "datestamp": "2023-08-19 05:08:51", "lastmod": "2023-10-25 17:02:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schultz-B-E", "name": { "family": "Schultz", "given": "Brian E." } }, { "id": "Hansen-K-C", "name": { "family": "Hansen", "given": "Kirk C." } }, { "id": "Lin-Charles-C", "name": { "family": "Lin", "given": "Charles C." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Rapid Photochemical Generation of Ubiquinol through a Radical Pathway: An Avenue for Probing Submillisecond Enzyme Kinetics", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2000 American Chemical Society. \n\nReceived 10 January 2000. Published online 26 April 2000. Published in print 1 May 2000. \n\nFunding for this work came from grant GM22432 from the National Institutes of Health. K.C.H. is the recipient of a National Research Service Predoctoral Award.", "abstract": "The use of photoreleasable protecting groups (\"cages\") on bioactive molecules provides a means for the rapid initiation of bimolecular reaction chemistry in biological systems.1,2 In this approach, the protecting group renders an otherwise biologically active molecule inert, so that the molecule can be mixed with an enzyme or other biological target molecule without any reaction taking place. Irradiation of the \"caged\" molecule leads to the release of the protecting group, so that the biological substrate is free to react with its target biomolecule. Because the bimolecular chemistry can be initiated by a laser pulse, the time frame over which the reaction can be probed is determined by the photochemistry leading to the release of substrate. This time frame can be much shorter than the time scale of milliseconds associated with stopped-flow and other rapid-mixing techniques. For some caged substrates, such as carboxylic acids and phosphates derivatized with benzoin moieties,3-6 release of active substrate is essentially instantaneous upon irradiation. For alcoholic substrates such as quinols, however, release of free substrate has been limited by chemistry that occurs after photocleavage of the cage molecule. When protecting groups such as \u03b1-carboxynitrobenzyl7 and 3',5'-bis(carboxymethoxy)benzoin8 are used to derivatize quinols, a carbonate linker is required. Upon irradiation, the quinol is released as a carbonate monoester, and the slow decarboxylation of this species is rate-limiting in generating the free quinol.", "date": "2000", "date_type": "published", "publication": "Journal of Organic Chemistry", "volume": "65", "number": "10", "publisher": "American Chemical Society", "pagerange": "3244-3247", "id_number": "CaltechAUTHORS:20170427-080241176", "issn": "0022-3263", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170427-080241176", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "doi": "10.1021/jo000028t", "resource_type": "article", "pub_year": "2000", "author_list": "Schultz, Brian E.; Hansen, Kirk C.; et el." }, { "id": "https://authors.library.caltech.edu/records/hnpe6-q1103", "eprint_id": 28731, "eprint_status": "archive", "datestamp": "2023-08-22 14:07:00", "lastmod": "2023-10-24 18:06:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cheng-Timothy-C", "name": { "family": "Cheng", "given": "Timothy C." } }, { "id": "Ramakrishnan-V", "name": { "family": "Ramakrishnan", "given": "Vijay" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Purification and characterization of a cobalt-activated carboxypeptidase from the hyperthermophilic archaeon Pyrococcus furiosus", "ispublished": "pub", "full_text_status": "restricted", "keywords": "C-terminal sequencing; carboxypeptidase; extremozyme; hyperthermophile; Pyrococcus furiosus", "note": "\u00a9 1999 The Protein Society. Article first published online: 31 Dec 2008. Received May 7, 1999; Accepted August 13, 1999.\nThis research was supported in part by NIH grant GM 22432 from the National Institute of General Medical Sciences, US Public Health Service and grant NSC 88-2113-M-001-037 from the National Science Council, Taiwan. We gratefully acknowledge the technical support of Phil Johnson at the University of Wisconsin Fermentation Facility (Madison, Wisconsin) for assistance in the culturing of P. furiosus cells. N-terminal Edman sequencing and MALDI-TOF mass analysis were carried out at the Caltech Protein and Peptide Microanalytical Laboratory under the direction of Gary M. Hathaway. The MALDI-TOF mass spectrometer was purchased with funds awarded by NIH Shared Instrumentation Grant RR11292.", "abstract": "A novel metallocarboxypeptidase (PfuCP) has been purified to homogeneity from the hyperthermophilic archaeon, Pyrococcus furiosus, with its intended use in C-terminal ladder sequencing of proteins and peptides at elevated temperatures. PfuCP was purified in its inactive state by the addition of ethylenediaminetetraacetic acid (EDTA) and dithiothreitol (DTT) to purification buffers, and the activity was restored by the addition of divalent cobalt (K_d = 24 \u00b1 4 \u03bcM at 80 \u00b0C). The serine protease inhibitor phenylmethylsulfonyl fluoride (PMSF) had no effect on the activity. The molecular mass of monomeric PfuCP is 59 kDa as determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 58 kDa by SDS-PAGE analysis. In solution, PfuCP exists as a homodimer of \u02dc 128 kDa as determined by gel filtration chromatography. The activity of PfuCP exhibits a temperature optimum exceeding 90\u00b0C under ambient pressure, and a narrow pH optimum of 6.2-6.6. Addition of Co^(2+) to the apoPfuCP at room temperature does not alter its far-UV circular dichroism (CD) or its intrinsic fluorescence spectrum. Even when the CoPfuCP is heated to 80 \u00b0C, its far-UV CD shows a minimal change in the global conformation and the intrinsic fluorescence of aromatic residues shows only a partial quenching. Changes in the intrinsic fluorescence appear essentially reversible with temperature. Finally, the far-UV CD and intrinsic fluorescence data suggest that the overall structure of the holoenzyme is extremely thermostable. However, the activities of both the apo and holo enzyme exhibit a similar second-order decay over time, with 50% activity remaining after \u02dc 40 min at 80 \u00b0C. The N-blocked synthetic dipeptide, N-carbobenzoxy-Ala-Arg (ZAR), was used in the purification assay. The kinetic parameters at 80\u00b0C with 0.4 mM CoCl_2 were: K_m, 0.9 \u00b1 0.1 mM; V_(max) 2,300 \u00b1 70 U mg^(\u22121); and turn over number, 600 \u00b1 20 s^(\u22121). Activity against other ZAX substrates (X = V, L, I, M, W, Y, F, N, A, S, H, K) revealed a broad specificity for neutral, aromatic, polar, and basic C-terminal residues. This broad specificity was confirmed by the C-terminal ladder sequencing of several synthetic and natural peptides, including porcine N-acetyl-renin substrate, for which we have observed (by MALDI-TOF MS) stepwise hydrolysis by PfuCP of up to seven residues from the C-terminus: Ac-Asp-Arg-Val-Tyr-Ile-His-Pro-z Phe-His-Leu-Leu-Val-Tyr-Ser.", "date": "1999-11", "date_type": "published", "publication": "Protein Science", "volume": "8", "number": "11", "publisher": "Wiley", "pagerange": "2474-2486", "id_number": "CaltechAUTHORS:20120110-102835248", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120110-102835248", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "National Science Council (Taipei)", "grant_number": "NSC 88-2113-M-001-037" }, { "agency": "NIH", "grant_number": "RR11292" } ] }, "doi": "10.1110/ps.8.11.2474", "pmcid": "PMC2144183", "resource_type": "article", "pub_year": "1999", "author_list": "Cheng, Timothy C.; Ramakrishnan, Vijay; et el." }, { "id": "https://authors.library.caltech.edu/records/w979n-t2v55", "eprint_id": 922, "eprint_status": "archive", "datestamp": "2023-08-22 13:08:58", "lastmod": "2023-10-23 17:49:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schultz-B-E", "name": { "family": "Schultz", "given": "Brian E." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Thermodynamics of electron transfer in Escherichia coli cytochrome bo(3)", "ispublished": "pub", "full_text_status": "public", "keywords": "QUINONE-BINDING SITE, C TERMINAL OXIDASES, UBIQUINOL OXIDASE, BO COMPLEX, SUBUNIT-I, PROTON TRANSLOCATION, 2.8 ANGSTROM, HEME-COPPER, DIOXYGEN, OXYGEN", "note": "\u00a9 1998 by the National Academy of Sciences. \n\nCommunicated by Fred C. Anson, California Institute of Technology, Pasadena, CA, July 27, 1998 (received for review May 10, 1998). \n\nThis work was supported by Grant GM22432 from the National\nInstitutes 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 - SCHpnas98.pdf
", "abstract": "The proton translocation mechanism of the Escherichia coli cytochrome bo(3) complex is intimately tied to the electron transfers within the enzyme. Herein we evaluate two models of proton translocation in this enzyme, a cytochrome c oxidase-type ion-pump and a Q-cycle mechanism, on the basis of the thermodynamics of electron transfer. We conclude that from a thermodynamic standpoint, a Q-cycle is the more favorable mechanism for proton translocation and is likely occurring in the enzyme.", "date": "1998-09-29", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "95", "number": "20", "publisher": "National Academy of Sciences", "pagerange": "11643-11648", "id_number": "CaltechAUTHORS:SCHpnas98", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:SCHpnas98", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" } ] }, "pmcid": "PMC21694", "primary_object": { "basename": "SCHpnas98.pdf", "url": "https://authors.library.caltech.edu/records/w979n-t2v55/files/SCHpnas98.pdf" }, "resource_type": "article", "pub_year": "1998", "author_list": "Schultz, Brian E. and Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/c8ee1-aar40", "eprint_id": 10948, "eprint_status": "archive", "datestamp": "2023-08-22 12:44:55", "lastmod": "2023-10-16 23:11:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Hiep-Hoa-T", "name": { "family": "Nguyen", "given": "Hiep-Hoa T." } }, { "id": "Elliott-S-J", "name": { "family": "Elliott", "given": "Sean J." } }, { "id": "Yip-John-Hon-Kay", "name": { "family": "Yip", "given": "John Hon-Kay" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "The Particulate Methane Monooxygenase from Methylococcus capsulatus (Bath) Is a Novel Copper-containing Three-subunit Enzyme: isolation and charactization", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1998 The American Society for Biochemistry and Molecular Biology, Inc. \n\n(Received for publication, July 7, 1997, and in revised form, December 22, 1997) \n\nWe thank Prof. Mary E. Lidstrom and Drs. Andrei Chistoserdov, Ludmila Chistoserdova, and Roopa Ramamorthi for helpful discussions and Dr. Peter Green for assistance with the inductively coupled plasma-mass spectroscopy analysis. \n\nThis work was supported by NIGMS, National Institutes of Health, Grant GM 22432 (to S.I.C.). Unrestricted financial support was also received from the George Grant Hoag Foundation.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. \n\n[H.-H.T.N. was the] [r]ecipient of a W. R. Grace fellowship and a National Research Service Predoctoral Award.\n\nPublished - NGUjbc98.pdf
", "abstract": "The particulate methane monooxygenase (pMMO) is known to be very difficult to study mainly due to its unusual activity instability in vitro. By cultivating Methylococcus capsulatus (Bath) under methane stress conditions and high copper levels in the growth medium, membranes highly enriched in the pMMO with exceptionally stable activity can be isolated from these cells. Purified and active pMMO can be subsequently obtained from these membrane preparations using protocols in which an excess of reductants and anaerobic conditions were maintained during membrane solubilization by dodecyl beta-D-maltoside and purification by chromatography. The pMMO was found to be the major constituent in these membranes, constituting 60-80% of total membrane proteins. The dominant species of the pMMO was found to consist of three subunits, alpha, beta, and gamma, with an apparent molecular mass of 45, 26, and 23 kDa, respectively. A second species of the pMMO, a proteolytically processed version of the enzyme, was found to be composed of three subunits, alpha', beta, and gamma, with an apparent molecular mass of 35, 26, and 23 kDa, respectively. The alpha and alpha' subunits from these two forms of the pMMO contain identical N-terminal sequences. The gamma subunit, however, exhibits variation in its N-terminal sequence. The pMMO is a copper-containing protein only and shows a requirement for Cu(I) ions. Approximately 12-15 Cu ions per 94-kDa monomeric unit were observed. The pMMO is sensitive to dioxygen tension. On the basis of dioxygen sensitivity, three kinetically distinct forms of the enzyme can be distinguished. A slow but air-stable form, which is converted into a \"pulsed\" state upon direct exposure to atmospheric oxygen pressure, is considered as type I pMMO. This form was the subject of our pMMO isolation effort. Other forms (types II and III) are deactivated to various extents upon exposure to atmospheric dioxygen pressure. Under inactivating conditions, these unstable forms release protons to the buffer (~10 H+/94-kDa monomeric unit) and eventually become completely inactive.", "date": "1998-04-03", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "273", "number": "14", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "7957-7966", "id_number": "CaltechAUTHORS:NGUjbc98", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:NGUjbc98", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "George Grant Hoag Foundation" } ] }, "primary_object": { "basename": "NGUjbc98.pdf", "url": "https://authors.library.caltech.edu/records/c8ee1-aar40/files/NGUjbc98.pdf" }, "resource_type": "article", "pub_year": "1998", "author_list": "Nguyen, Hiep-Hoa T.; Elliott, Sean J.; et el." }, { "id": "https://authors.library.caltech.edu/records/5m3m8-ejg52", "eprint_id": 81590, "eprint_status": "archive", "datestamp": "2023-08-19 02:39:23", "lastmod": "2023-10-17 20:53:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schultz-B-E", "name": { "family": "Schultz", "given": "Brian E." } }, { "id": "Edmondson-D-E", "name": { "family": "Edmondson", "given": "Dale E." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Reaction of Escherichia coli Cytochrome bo_3 with Substoichiometric Ubiquinol-2: A Freeze-Quench Electron Paramagnetic Resonance Investigation", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1998 American Chemical Society. \n\nReceived July 14, 1997; Revised Manuscript Received January 14, 1998. Publication Date (Web): March 5, 1998. \n\nThis work was supported by Grants GM22432 (S.I.C.) and\nGM29433 (D.E.E.) from the National Institutes of Health. B.E.S. is the recipient of a National Science Foundation Postdoctoral Fellowship. \n\nWe would like to thank Siegfried Musser, Robert Gennis, and Jeffrey Osborne for insightful comments, Michael Stowell for the synthesis and purification of the UQ2 used in this work, and Kirk Hansen for experimental assistance.", "abstract": "The reaction of the quinol oxidase cytochrome bo_3 from Escherichia coli with ubiquinol-2 (UQ_2H_2) was carried out using substoichiometric (0.5 equiv) amounts of substrate. Reactions were monitored through the use of freeze-quench EPR spectroscopy. Under 1 atm of argon, semiquinone was formed at the Q_B site of the enzyme with a formation rate constant of 140 s^(-1); the Q_B semiquinone EPR signal decayed with a rate constant of about 5 s^(-1). Heme b and Cu_B were reduced within the 10-ms dead time of the freeze-quench experiment and remained at a constant level of reduction over the 1-s time course of the experiment. Quantitation of the reduction levels of QB and heme b during this reaction yielded a reduction potential of 30\u221260 mV for heme b. Under a dioxygen atmosphere, the rates of semiquinone formation and its subsequent decay were not altered significantly. However, accurate quantitation of the EPR signals for heme band heme o_3 could not be made, due to interference from dioxygen. In the reaction between the Q_B-depleted enzyme and UQ_2H_2 under substoichiometric conditions, there was no observable change in the EPR spectra of the enzyme over the time course of the reaction, suggesting an electron transfer from heme b to the binuclear site in the absence of Q_B which occurs within the dead time of the freeze-quench apparatus. Analysis of the thermodynamics and kinetics of electron transfers in this enzyme suggests that a Q-cycle mechanism for proton translocation is more likely than a cytochrome c oxidase-type ion-pump mechanism.", "date": "1998-03-24", "date_type": "published", "publication": "Biochemistry", "volume": "37", "number": "12", "publisher": "American Chemical Society", "pagerange": "4160-4168", "id_number": "CaltechAUTHORS:20170919-153418165", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170919-153418165", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "NIH", "grant_number": "GM29433" }, { "agency": "NSF Postdoctoral Fellowship" } ] }, "doi": "10.1021/bi971714y", "resource_type": "article", "pub_year": "1998", "author_list": "Schultz, Brian E.; Edmondson, Dale E.; et el." }, { "id": "https://authors.library.caltech.edu/records/hygf1-px436", "eprint_id": 86599, "eprint_status": "archive", "datestamp": "2023-08-19 02:37:03", "lastmod": "2023-10-18 19:45:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cavagnero-S", "name": { "family": "Cavagnero", "given": "Silvia" } }, { "id": "Debe-D-A", "name": { "family": "Debe", "given": "Derek A." } }, { "id": "Zhou-Zhi-H", "name": { "family": "Zhou", "given": "Zhi H." } }, { "id": "Adams-M-W-W", "name": { "family": "Adams", "given": "Michael W. W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Kinetic Role of Electrostatic Interactions in the Unfolding of Hyperthermophilic and Mesophilic Rubredoxins", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1998 American Chemical Society. \n\nReceived September 3, 1997. \n\nWe thank Prof. Doug Rees and Dr. Reginald Waldeck for helpful discussions and critical comments on this work.", "abstract": "The temperature dependence of the unfolding kinetics of rubredoxins from the hyperthermophile Pyrococcus furiosus (RdPf) and the mesophile Clostridium pasteurianum (RdCp) has been studied. Results show that RdPf unfolds much more slowly, under all experimentally accessible temperature regimes, than RdCp and other typical mesophilic proteins. Rates of RdCp and RdPf unfolding decrease upon increasing the pH above 2 and diverge dramatically at pH 7. As shown by detailed electrostatic energy calculations, this is the result of a differential degree of protonation of the negatively charged amino acids, which causes distinct electrostatic configurations as a function of pH. We propose that ion pairs, particularly those that are placed in key surface positions, may play a kinetic role by mildly clamping the protein and thereby influencing the nature and the number of the vibrational normal modes that are thermally accessible upon unfolding. More generally, these modes are also likely to be affected by the favorable electrostatic configurations, which we have shown to be directly linked to the extremely slow unfolding rates of RdPf at neutral pH. Even at pH 2, in the absence of any salt bridges, the unfolding rates of RdPf are much smaller than those of RdCp. This is ascribed to presently unidentified structural elements of nonelectrostatic nature. Since electrostatic effects influence the unfolding kinetics of both mesophilic and thermophilic rubredoxins, these findings may be of general significance for proteins.", "date": "1998-03-10", "date_type": "published", "publication": "Biochemistry", "volume": "37", "number": "10", "publisher": "American Chemical Society", "pagerange": "3369-3376", "id_number": "CaltechAUTHORS:20180524-152540450", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180524-152540450", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1021/bi9721795", "resource_type": "article", "pub_year": "1998", "author_list": "Cavagnero, Silvia; Debe, Derek A.; et el." }, { "id": "https://authors.library.caltech.edu/records/nv5nv-pmg98", "eprint_id": 83568, "eprint_status": "archive", "datestamp": "2023-08-19 02:36:56", "lastmod": "2023-10-17 23:14:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cavagnero-S", "name": { "family": "Cavagnero", "given": "Silvia" } }, { "id": "Zhou-Zhi-H", "name": { "family": "Zhou", "given": "Zhi H." } }, { "id": "Adams-M-W-W", "name": { "family": "Adams", "given": "Michael W. W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Unfolding Mechanism of Rubredoxin from Pyrococcus furiosus", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1998 American Chemical Society. \n\nReceived September 3, 1997. Publication Date (Web): February 18, 1998. \n\nThis work was supported by NIH Grant Nos. GM 22432 (S.I.C.)\nand GM 50736 (M.W.W.A.) from the National Institute of General Medical Sciences, U.S. Public Health Service. \n\nWe thank Prof. Doug Rees, Dr. Reginald Waldeck, Dr. Brian Schultz and Ms. Lisa Bibbs for interesting and pertinent discussions.", "abstract": "As part of our studies on the structural and dynamic properties of hyperthermostable proteins, we have investigated the unfolding pathways of the small iron\u2212sulfur protein rubredoxin from Pyrococcus furiosus (RdPf) at pH 2. Unfolding has been initiated by temperature jump, triggered by manual mixing of a concentrated protein solution into a thermally preequilibrated buffer. The process has been followed in real time by absorption, tryptophan fluorescence emission, and far-UV circular dichroism. Unlike the case of the mesophilic rubredoxin from Clostridium pasteurianum (RdCp), RdPf displays a complex unfolding kinetics, pointing to the formation of at least three intermediates. All of the steps, including the one involving metal ion release, are extremely slow. However, hydrophobic core relaxation not Fe^(3+) loss is rate-determining for RdPf unfolding. This clearly rules out the fact that Fe^(3+) is solely responsible for the kinetic stability of RdPf. Results have been discussed in terms of sequential vs parallel pathways, and the possible role of irreversible phenomena has been taken into consideration. Aggregation does not appear to play a significant role in the observed kinetic complexities. According to a proposed sequential mechanism, partial release of secondary structure elements precedes iron loss, which is then followed by further loss of \u03b2-sheet content and, finally, by hydrophobic relaxation. Although the main features of the RdPf unfolding mechanism remain substantially unchanged over the experimentally accessible temperature range, final hydrophobic relaxation gets faster, relative to the other events, as the temperature is decreased. A qualitative assessment of the unfolding activation parameters suggests that this arises from the very low activation energies (E_a) that characterize this step.", "date": "1998-03-10", "date_type": "published", "publication": "Biochemistry", "volume": "37", "number": "10", "publisher": "American Chemical Society", "pagerange": "3377-3385", "id_number": "CaltechAUTHORS:20171129-131714433", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171129-131714433", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "NIH", "grant_number": "GM 50736" } ] }, "doi": "10.1021/bi9721804", "resource_type": "article", "pub_year": "1998", "author_list": "Cavagnero, Silvia; Zhou, Zhi H.; et el." }, { "id": "https://authors.library.caltech.edu/records/e2y4f-jrd95", "eprint_id": 28966, "eprint_status": "archive", "datestamp": "2023-08-19 01:41:55", "lastmod": "2023-10-24 18:16:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Waldeck-A-R", "name": { "family": "Waldeck", "given": "A. Reginald" } }, { "id": "Stowell-M-H-B", "name": { "family": "Stowell", "given": "Michael H. B." } }, { "id": "Lee-Hung-Kay", "name": { "family": "Lee", "given": "Hung Kay" } }, { "id": "Hung-Shao-Ching", "name": { "family": "Hung", "given": "Shao-Ching" } }, { "id": "Matsson-M", "name": { "family": "Matsson", "given": "Mikael" } }, { "id": "Hederstedt-L", "name": { "family": "Hederstedt", "given": "Lars" } }, { "id": "Ackrel-B-A-C", "name": { "family": "Ackrel", "given": "Brian A. C." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Electron Paramagnetic Resonance Studies of Succinate:Ubiquinone Oxidoreductase from Paracoccus denitrificans", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1997 by The American Society for Biochemistry and Molecular Biology, Inc.\n\n\nReceived for publication, March 17, 1997, and in revised form, May 14, 1997.\n\nWe thank the late Dr. Vladimir Sled for valuable\ncorrespondence. Drs. Siegfried Musser and Brian Schultz are thanked\nfor stimulating discussions and advice with EPR simulations,\nrespectively.\n\nThis work was funded in part by National Institutes of Health\nGrants GM 22432 (to S. I. C.) and HL-16251 (to B. A. C. A.) and a grant\nfrom the Swedish Natural Science Research Council (to L. H.). The\ncosts of publication of this article were defrayed in part by the payment\nof page charges. This article must therefore be hereby marked \"advertisement\"\nin accordance with 18 U.S.C. Section 1734 solely to indicate\nthis fact.\n\nPublished - WALjbc97.pdf
", "abstract": "Electron paramagnetic resonance (EPR) studies of succinate:ubiquinone oxidoreductase (SQR) from Paracoccus denitrificans have been undertaken in the purified and membrane-bound states. Spectroscopic \"signatures\" accounting for the three iron-sulfur clusters (2Fe-2S, 3Fe-4S, and 4Fe-4S), cytochromeb, flavin, and protein-bound ubisemiquinone radicals have been obtained in air-oxidized, succinate-reduced, and dithionite-reduced preparations at 4\u201310 K. Spectra obtained at 170 K in the presence of excess succinate showed a signal typical of that of a flavin radical, but superimposed with another signal. The superimposed signal originated from two bound ubisemiquinones, as shown by spectral simulations. Power saturation measurements performed on the air-oxidized enzyme provided evidence for a weak magnetic dipolar interaction operating between the oxidized 3Fe-4S cluster and the oxidized cytochrome b. Power saturation experiments performed on the succinate- and dithionite-reduced forms of the enzyme demonstrated that the 4Fe-4S cluster is coupled weakly to both the 2Fe-2S and the 3Fe-4S clusters. Quantitative interpretation of these power saturation experiments has been achieved through redox calculations. They revealed that a spin-spin interaction between the reduced 3Fe-4S cluster and the cytochrome b (oxidized) may also exist. These findings form the first direct EPR evidence for a close proximity (\u22642 nm) of the high potential 3Fe-4S cluster, situated in the succinate dehydrogenase part of the enzyme, and the low potential, low spin b-heme in the membrane anchor of the enzyme.", "date": "1997-08-01", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "272", "number": "31", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "19373-19382", "id_number": "CaltechAUTHORS:20120125-131713605", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120125-131713605", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "NIH", "grant_number": "HL-16251" }, { "agency": "Swedish Natural Science Research Council" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1074/jbc.272.31.19373", "primary_object": { "basename": "WALjbc97.pdf", "url": "https://authors.library.caltech.edu/records/e2y4f-jrd95/files/WALjbc97.pdf" }, "resource_type": "article", "pub_year": "1997", "author_list": "Waldeck, A. Reginald; Stowell, Michael H. B.; et el." }, { "id": "https://authors.library.caltech.edu/records/t6g2q-p9g98", "eprint_id": 86667, "eprint_status": "archive", "datestamp": "2023-08-19 01:29:09", "lastmod": "2023-10-18 19:51:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schultz-B-E", "name": { "family": "Schultz", "given": "Brian E." } }, { "id": "Ye-Bao-Hui", "name": { "family": "Ye", "given": "Bao-Hui" } }, { "id": "Li-Xiao-Yuan", "name": { "family": "Li", "given": "Xiao-yuan" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Electronic Paramagnetic Resonance and Magnetic Properties of Model Complexes for Binuclear Active Sites in Hydrolase Enzymes", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1997 American Chemical Society. \n\nReceived August 14, 1996. \n\nFunding for this work was provided by NIH Grant GM22432 from the National Institute of General Medical Sciences, U.S. Public Health Services. X.-y.L. acknowledges the support of this project by RGC-CERG and HKUST. B.E.S. is the recipient of a National Science Foundation Postdoctoral Fellowship. We thank Jeff Clites for experimental assistance.", "abstract": "A set of binuclear metal complexes with the formula M_2(Im)_4(OAc)_4(H_2O), where M = Mn, Co, or Ni, designed as mimics of the active sites of hydrolase enzymes, were subjected to EPR and magnetic susceptibility studies. The manganese complex displayed a broad EPR spectrum over the field range 0\u22125500 G. The 4 K spectrum was simulated as a summation of the S = 1, S = 2, and S = 3 spin manifolds of the coupled dimer, with each manifold weighted by the appropriate Boltzmann factor. Parameters for the best fits of EPR and magnetic susceptibility were g = 1.95, J = \u22121.29 cm^(-1), and D = 0.095 cm^(-1), with line widths of 350, 450, and 550 G for the S = 1, 2, and 3 manifolds, respectively. An alternative simulation, with g = 1.93, J = \u22121.28 cm^(-1), and D = 0.081 cm^(-1) provided a better fit for the central peaks but only accounted for six of the seven observed peaks. The cobalt and nickel complexes are EPR-silent. Magnetic susceptibility measurements of these two dimers showed weak antiferromagnetic coupling; variable-temperature magnetic susceptibility plots were fit with the parameters g = 2.22, J = \u22121.60 cm^(-1) (cobalt) and g = 2.04, J = \u22122.47 cm^(-1) (nickel). The weak coupling highlights the difficulty in detecting bound water in these binuclear complexes or in enzymes and hence in determining active site structure through the physical techniques used in this work.", "date": "1997-06-04", "date_type": "published", "publication": "Inorganic Chemistry", "volume": "36", "number": "12", "publisher": "American Chemical Society", "pagerange": "2617-2622", "id_number": "CaltechAUTHORS:20180529-113543917", "issn": "0020-1669", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180529-113543917", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "Research Grants Council of Hong Kong" }, { "agency": "Hong Kong University of Science and Technology" }, { "agency": "NSF Postdoctoral Fellowship" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1021/ic960988r", "resource_type": "article", "pub_year": "1997", "author_list": "Schultz, Brian E.; Ye, Bao-Hui; et el." }, { "id": "https://authors.library.caltech.edu/records/0nazs-4dx89", "eprint_id": 86668, "eprint_status": "archive", "datestamp": "2023-08-19 01:10:10", "lastmod": "2023-10-18 19:51:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kwong-Daniel-W-J", "name": { "family": "Kwong", "given": "Daniel W. J." } }, { "id": "Chan-O-Y", "name": { "family": "Chan", "given": "O. Y." } }, { "id": "Wong-Ricky-N-S", "name": { "family": "Wong", "given": "Ricky N. S." } }, { "id": "Musser-S-M", "name": { "family": "Musser", "given": "Siegfried M." } }, { "id": "Vaca-L", "name": { "family": "Vaca", "given": "Luis" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "DNA-Photocleavage Activities of Vanadium(V)\u2212Peroxo Complexes", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1997 American Chemical Society. \n\nReceived August 1, 1996. \n\nWe gratefully acknowledge the financial support of the Hong Kong Baptist University Faculty Research Grants (FRG/93-94/II-68; to D.W.J.K.), the Hong Kong Research Grants Council (HKBC 153/95P; to D.W.J.K.), and the National Institute of General Medical Sciences, U.S. Public Health Service (GM22432; to S.I.C.). S.M.M. is a recipient of a National Research Service Predoctoral Award from the National Institute of General Medical Services.", "abstract": "The DNA-photocleavage activities (at 365 nm) of 15 vanadium(V)\u2212peroxo complexes were examined. Singlet oxygen was implicated as the species responsible for the DNA scission. The singlet oxygen was shown to be produced from the photolysis of the vanadium(V)\u2212peroxo complex using a singlet oxygen EPR spin trap, 2,2,6,6-tetramethyl-4-piperidone. A mechanism for the photolysis of the [VO(O_2)_2(bpy)]- anion at neutral pH has been proposed.", "date": "1997-03-26", "date_type": "published", "publication": "Inorganic Chemistry", "volume": "36", "number": "7", "publisher": "American Chemical Society", "pagerange": "1276-1277", "id_number": "CaltechAUTHORS:20180529-114153019", "issn": "0020-1669", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180529-114153019", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Hong Kong Baptist University", "grant_number": "FRG/93-94/II-68" }, { "agency": "Hong Kong Research Grant Council", "grant_number": "HKBC 153/95P" }, { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1021/ic960909b", "resource_type": "article", "pub_year": "1997", "author_list": "Kwong, Daniel W. J.; Chan, O. Y.; et el." }, { "id": "https://authors.library.caltech.edu/records/gpqps-4nn14", "eprint_id": 84805, "eprint_status": "archive", "datestamp": "2023-08-19 01:07:41", "lastmod": "2023-10-18 16:42:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bose-Salil", "name": { "family": "Bose", "given": "Salil" } }, { "id": "Hendler-R-W", "name": { "family": "Hendler", "given": "Richard W." } }, { "id": "Shrager-R-I", "name": { "family": "Shrager", "given": "Richard I." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Smith-P-D", "name": { "family": "Smith", "given": "Paul D." } } ] }, "title": "Multichannel Analysis of Single-Turnover Kinetics of Cytochrome aa_3 Reduction of O_2", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1997 American Chemical Society. \n\nReceived 16 July 1996. Published online 4 March 1997. \n\nAbstract published in Advance ACS Abstracts, February 1, 1997.\n\nSupplemental Material - bi2439.pdf
", "abstract": "The single-turnover kinetics of the oxidation of cytochrome aa_3 by O_2 have been studied using a new approach. Up to 1000 whole spectra covering both the Soret and \u03b1 regions were sequentially collected at room temperature from single samples with a time resolution of 10 \u03bcs. All of the spectral and time information were used in analyses based on singular value decomposition. Four spectral transitions (i.e., intermediates) were distinguished with time constants near 0.01, 0.1, 1.1, and 30 ms. Two different kinds of sequential models were evaluated, one linear and the other branched. Although past kinetic analyses have emphasized the linear sequential model, the complexity of the intramolecular electron transfer in this enzyme suggests that a branched model be considered. This is especially true in a single-turnover experiment where earlier optical and EPR studies have pointed unequivocally to a branched model [Clore et al. (1980) Biochem. J. 185, 139\u2212154; Blair et al. (1985) J. Am. Chem. Soc. 107, 7389\u22127399]. In the present study, analysis of spectral data in terms of the linear model did not reveal the formation and decay of the expected oxyferryl intermediate, whereas analysis of the branched model did. The results obtained using the branched model are consistent with all of the available evidence from a broad range of physical techniques that have been applied to examine the single-turnover kinetics of the oxidation of reduced cytochrome aa_3 by O_2.", "date": "1997-03-04", "date_type": "published", "publication": "Biochemistry", "volume": "36", "number": "9", "publisher": "American Chemical Society", "pagerange": "2439-2449", "id_number": "CaltechAUTHORS:20180213-085416151", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180213-085416151", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechAUTHORS", "doi": "10.1021/bi9617419", "primary_object": { "basename": "bi2439.pdf", "url": "https://authors.library.caltech.edu/records/gpqps-4nn14/files/bi2439.pdf" }, "resource_type": "article", "pub_year": "1997", "author_list": "Bose, Salil; Hendler, Richard W.; et el." }, { "id": "https://authors.library.caltech.edu/records/pfghj-rr893", "eprint_id": 84791, "eprint_status": "archive", "datestamp": "2023-08-19 00:59:50", "lastmod": "2023-10-18 16:41:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Musser-S-M", "name": { "family": "Musser", "given": "Siegfried M." } }, { "id": "Stowell-M-H-B", "name": { "family": "Stowell", "given": "Michael H. B." } }, { "id": "Lee-Hung-Kay", "name": { "family": "Lee", "given": "Hung Kay" } }, { "id": "Rumbley-J-N", "name": { "family": "Rumbley", "given": "Jon N." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Uncompetitive Substrate Inhibition and Noncompetitive Inhibition by 5-n-Undecyl-6-hydroxy-4,7-dioxobenzothiazole (UHDBT) and 2-n-Nonyl-4-hydroxyquinoline-N-oxide (NQNO) is Observed for the Cytochrome bo_3Complex: Implications for a Q(H_2)-Loop Proton Translocation Mechanism", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1997 American Chemical Society. \n\nReceived 15 July 1996. Published online 28 January 1997. \n\nThis work was supported by Grant GM22432 (S.I.C.) from the\nU.S. Public Health Service and by Grant DE-FG-02-87ER13716 (to Robert Gennis) from the U.S. Department of Energy. S.M.M. is the recipient of a National Research Service Predoctoral Award. \n\nSpecial thanks to M\u00e5rten Wikstr\u00f6m (Helsinki) for sharing\nmanuscripts before publication. Also, we thank Robert B.\nGennis (University of Illinois, Urbana) for his very helpful critical readings of this manuscript.", "abstract": "The cytochrome bo3 ubiquinol oxidase complex from Escherichia coli contains two binding sites for ubiquinone(ol) (UQ(H_2)). One of these binding sites, the ubiquinol oxidation site, is clearly in dynamic equilibrium with the UQ(H_2) pool in the membrane. The second site has a high affinity for ubiquinone (UQ), stabilizes a semiquinone species, and is located physically close to the low-spin heme b component of the enzyme. The UQ molecule in this site has been proposed to remain strongly bound to the enzyme during enzyme turnover and to act as a cofactor facilitating the transfer of electrons from the substrate ubiquinol to heme b [Sato-Watanabe et al. (1994) J. Biol. Chem. 269, 28908\u221228912]. In this paper, the steady-state turnover of the enzyme is examined in the presence and absence of inhibitors (UHDBT and NQNO) that appear to be recognized as ubisemiquinone analogs. It is found that the kinetics are accounted for best by a noncompetitive inhibitor binding model. Furthermore, at high concentrations, the substrates ubiquinol-1 and ubiquinol-2 inhibit turnover in an uncompetitive fashion. Together, these observations strongly suggest that there must be at least two UQ(H_2) binding sites that are in rapid equilibrium with the UQ(H_2) pool under turnover conditions. Although these data do not rule out the possibility that a strongly bound UQ molecule functions to facilitate electron transfer to heme b, they are more consistent with the behavior expected if the two UQ(H_2) binding sites were to function in a Q(H_2)-loop mechanism (similar to that of the cytochrome bc1 complex) as originally proposed by Musser and co-workers [(1993) FEBS Lett. 327, 131\u2212136]. In this model, ubiquinol is oxidized at one site and ubiquinone is reduced at the second site. While the structural similarities of the heme-copper ubiquinol and cytochrome c oxidase complexes suggest the possibility that these two families of enzymes translocate protons by similar mechanisms, the current observations indicate that the Q(H_2)-loop proton translocation mechanism for the heme-copper ubiquinol oxidase complexes should be further investigated and experimentally tested.", "date": "1997-01-28", "date_type": "published", "publication": "Biochemistry", "volume": "36", "number": "4", "publisher": "American Chemical Society", "pagerange": "894-902", "id_number": "CaltechAUTHORS:20180212-130429431", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180212-130429431", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG-02-87ER13716" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "doi": "10.1021/bi961723r", "resource_type": "article", "pub_year": "1997", "author_list": "Musser, Siegfried M.; Stowell, Michael H. B.; et el." }, { "id": "https://authors.library.caltech.edu/records/ss2yc-nfs53", "eprint_id": 6000, "eprint_status": "archive", "datestamp": "2023-08-22 11:32:03", "lastmod": "2023-10-16 20:01:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Musser-S-M", "name": { "family": "Musser", "given": "Siegfried M." } }, { "id": "Fann-Yang-Cheng", "name": { "family": "Fann", "given": "Yang-Cheng" } }, { "id": "Gurbiel-R-J", "name": { "family": "Gurbiel", "given": "Ryszard J." } }, { "id": "Hoffman-B-M", "name": { "family": "Hoffman", "given": "Brian M." }, "orcid": "0000-0002-3100-0746" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Q-band electron nuclear double resonance (ENDOR) and X-band EPR of the sulfobetaine 12 heat-treated cytochrome c oxidase complex", "ispublished": "pub", "full_text_status": "public", "keywords": "THERMUS-THERMOPHILUS; COPPER CENTER; SPECTROSCOPIC CHARACTERIZATION; PARACOCCUS-DENITRIFICANS; REDUCTASE CONTAINS; QUINOL OXIDASE; SITE; PROTEINS; SUBUNIT; DOMAIN", "note": "\u00a9 1997 by The American Society for Biochemistry and Molecular Biology, Inc. \n\nReceived for publication, July 16, 1996, and in revised form, October 10, 1996. \n\nSpecial thanks to M\u00e5rten Wikstr\u00f6m for sharing manuscripts before publication and to Michael Stowell for help in the isolation of the cytochrome bo3 complex. \n\nThis work was supported by National Institutes of Health Grants HL13531 (to B.M.H.) and GM22432 (to S.I.C.) from the United States Public Health Service. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. \n\n[S.M.M. was the] Recipient of a National Research Service Predoctoral Award.\n\nPublished - MUSjbc97.pdf
", "abstract": "Heat treatment of the bovine cytochrome c oxidase complex in the zwitterionic detergent sulfobetaine 12 (SB-12) results in loss of subunit III and the appearance of a type II copper center as characterized by electron paramagnetic resonance (EPR) spectroscopy. Previous authors (Nilsson, T., Copeland, R. A., Smith, P. A., and Chan, S. I. (1988) Biochemistry 27, 8254-8260) have interpreted this type II copper center as a modified version of the CuA site. By using electron nuclear double resonance spectroscopy, it is found that the CuA proton and nitrogen resonances remain present in the SB-12 heat-treated enzyme and that three new nitrogen resonances appear having hyperfine coupling constants consistent with histidine ligation. These hyperfine coupling constants correlate well with those recently found for the CuB histidines from the cytochrome aa3-600 quinol oxidase from Bacillus subtilis (Fann, Y. C., Ahmed, I., Blackburn, N. J., Boswell, J. S., Verkhovskaya, M. L., Hoffman, B. M., and Wikstr\u00f6m, M. (1995) Biochemistry 34, 10245-10255). In addition, the total EPR-detectable copper concentration per enzyme molecule approximately doubles upon SB-12 heat treatment. Finally, the observed type II copper EPR spectrum is virtually indistinguishable from the EPR spectrum of CuB of the as-isolated cytochrome bo3 complex from Escherichia coli. These data indicate that the type II copper species that appears results from a breaking of the strong antiferromagnetic coupling of the heme a3-CuB binuclear center.", "date": "1997-01-03", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "272", "number": "1", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "203-209", "id_number": "CaltechAUTHORS:MUSjbc97", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:MUSjbc97", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "HL13531" }, { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "primary_object": { "basename": "MUSjbc97.pdf", "url": "https://authors.library.caltech.edu/records/ss2yc-nfs53/files/MUSjbc97.pdf" }, "resource_type": "article", "pub_year": "1997", "author_list": "Musser, Siegfried M.; Fann, Yang-Cheng; et el." }, { "id": "https://authors.library.caltech.edu/records/7x8qm-cx234", "eprint_id": 54437, "eprint_status": "archive", "datestamp": "2023-08-20 07:10:19", "lastmod": "2023-10-20 16:27:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stowell-M-H-B", "name": { "family": "Stowell", "given": "Michael H. B." } }, { "id": "Rock-R-S", "name": { "family": "Rock", "given": "Ronald S." } }, { "id": "Rees-D-C", "name": { "family": "Rees", "given": "D. C." }, "orcid": "0000-0003-4073-1185" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Efficient Synthesis of Photolabile Alkoxy Benzoin Protecting Groups", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1996 Elsevier Science Ltd.\n\nReceived in USA 7 September 1995; revised 7 November 1995; accepted 10 November 1995.\n\nWe thank Prof. E. M. Carreira for helpful discussions and critical reading of this\nmanuscript. This work was supported by NIH grant GM 22432 from the National Institute of General Medical Sciences, U.S. Public Health Service. Contribution number 9139.", "abstract": "An effective implementation of the Corey-Seebach dithiane addition for the synthesis of photolabile alkoxy benzoin adducts is reported. The method allows for the facile synthesis of photolabile 3\u2032,5\u2032-dimethoxybenzoin protected compounds in near quantitative yield and is general in that it can be used for the synthesis of both symmetrical and unsymmetrical benzoins. Importantly, the dithiane intermediate reported is a versatile starting material for the synthesis of many photolabile compounds and should serve as a useful protecting group in complex synthetic schemes requiring multiple orthogonal protecting groups.", "date": "1996-01-15", "date_type": "published", "publication": "Tetrahedron Letters", "volume": "37", "number": "3", "publisher": "Elsevier", "pagerange": "307-310", "id_number": "CaltechAUTHORS:20150205-140522838", "issn": "0040-4039", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150205-140522838", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "9139", "name": "Caltech Arthur Amos Noyes Laboratory" } ] }, "doi": "10.1016/0040-4039(95)02159-0", "resource_type": "article", "pub_year": "1996", "author_list": "Stowell, Michael H. B.; Rock, Ronald S.; et el." }, { "id": "https://authors.library.caltech.edu/records/4q0me-40611", "eprint_id": 93292, "eprint_status": "archive", "datestamp": "2023-08-22 10:38:08", "lastmod": "2023-10-20 17:00:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Evans-J-S", "name": { "family": "Evans", "given": "John Spencer" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Goddard-W-A-III", "name": { "family": "Goddard", "given": "William A., III" }, "orcid": "0000-0003-0097-5716" } ] }, "title": "Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling", "ispublished": "pub", "full_text_status": "restricted", "keywords": "computational chemistry; counterion condensation; dihedral angles; internal coordinate method; Monte Carlo; peptide conformation; polyanionic sequences; protein conformation; protein folding", "note": "\u00a9 1995 The Protein Society. \n\nManuscript accepted: 11 July 1995; Manuscript received: 17 April 1995. \n\nWe thank Dr. Siddharth Dasgupta for his helpful advice during the course of this study. J.S.E. acknowledges a Postdoctoral National Research Service Award from the NIH (NIDR 1F32-DE-05445) and a fellowship award from AMGEN Pharmaceuticals. These studies were supported by a grant from DOE-AICD, using facilities supported also by NSF-CHE, NSF-GCAG, Aramco, Asahi Glass, Asahi Chemical, BP\nChemical, Chevron Petroleum Technology Co., Oronite, Vestar, Hughes Research Labs, Xerox, and Beckman Institute.", "abstract": "Many interesting proteins possess defined sequence stretches containing negatively charged amino acids. At present, experimental methods (X\u2010ray crystallography, NMR) have failed to provide structural data for many of these sequence domains. We have applied the dihedral probability grid\u2010Monte Carlo (DPG\u2010MC) conformational search algorithm to a series of N\u2010 and C\u2010capped polyelectrolyte peptides, (Glu)_(20), (Asp)_(20). (PSer)_(20), and (PSer\u2010Asp)_(10), that represent polyanionic regions in a number of important proteins, such as parathymosin, calsequestrin, the sodium channel protein, and the acidic biomineralization proteins. The atomic charges were estimated from charge equilibration and the valence and van der Waals parameters are from DREIDING. Solvation of the carboxylate and phosphate groups was treated using sodium counterions for each charged side chain (one Na^+ for COO^\u2212; two Na for CO(PO_3)^(\u22122)) plus a distance\u2010dependent (shielded) dielectric constant, \u03f5 = \u03f5_0R, to simulate solvent water. The structures of these polyelectrolyte polypeptides were obtained by the DPG\u2010MC conformational search with \u03f5_0 = 10, followed by calculation of solvation energies for the lowest energy conformers using the protein dipole\u2010Langevin dipole method of Warshel.", "date": "1995-10", "date_type": "published", "publication": "Protein Science", "volume": "4", "number": "10", "publisher": "Wiley", "pagerange": "2019-2031", "id_number": "CaltechAUTHORS:20190227-091746936", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190227-091746936", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "NIDR 1F32-DE-05445" }, { "agency": "Amgen" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NSF" }, { "agency": "Aramco" }, { "agency": "Asahi Glass" }, { "agency": "Asahi Chemical" }, { "agency": "BP Chemical" }, { "agency": "Chevron Petroleum Technology Co." }, { "agency": "Oronite" }, { "agency": "Vestar" }, { "agency": "Hughes Research Laboratories" }, { "agency": "Xerox" }, { "agency": "Caltech Beckman Institute" } ] }, "doi": "10.1002/pro.5560041007", "pmcid": "PMC2142998", "resource_type": "article", "pub_year": "1995", "author_list": "Evans, John Spencer; Chan, Sunney I.; et el." }, { "id": "https://authors.library.caltech.edu/records/5j03x-fr012", "eprint_id": 86623, "eprint_status": "archive", "datestamp": "2023-08-20 06:13:37", "lastmod": "2023-10-18 19:47:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "DiMagno-T-J", "name": { "family": "DiMagno", "given": "Theodore J." } }, { "id": "Stowell-M-H-B", "name": { "family": "Stowell", "given": "Michael H. B." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Nitrobenzene \"Caged\" Compounds as Irreversible Photoreductants: A Rational Approach to Studying Photoinduced Intermolecular Electron-Transfer Reactions in Proteins", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1995 American Chemical Society. \n\nReceived: June 8, 1995. \n\nWe would like to thank Dr. Jay Winkler for his assistance with the nanosecond transient absorption apparatus in the Beckman Institute Laser Resource Center. This work was supported by grant GM22432 from the National Institute of General Medical Sciences, U. S . Public Health Service. TJD is the recipient of a National Research Service Award from the National Institute of General Medical Sciences (GM 15647).", "abstract": "Nitrobenzene \"caged\" compounds are well-known for their use in delivering biologically active substrates to a reaction mixture after photoexcitation. We have discovered that they also behave as photoreductants from the triplet state after photoexcitation. To explore the properties of these newly discovered photoreductants, a series of substituted nitrobenzene derivatives have been synthesized. These nitrobenzene derivatives exhibit many desirable characteristics suitable for the physiological photoreduction of different proteins, and examples are shown for the photoreduction of cytochrome c and other heme proteins. The observed rate constant for photoreduction of cytochrome c, k_(obs), ranges from 300 to 36 000 s^(-1) for the various nitrobenzene derivatives. pH and ionic strength experiments are consistent with a bimolecular reaction wherein the photoreductant and the protein form an electrostatic complex prior to electron transfer. A kinetic model for this bimolecular reaction is described and simulations of the experimental data for the photoreductant 4,5-dimethoxy-2-nitrophenylacetic acid (DMNPAA) yield an inherent unimolecular electron-transfer rate constant (ket) of 14 600 s^(-1) for the photoreduction of cytochrome c at pH 6.6.", "date": "1995-08-24", "date_type": "published", "publication": "Journal of Physical Chemistry", "volume": "99", "number": "34", "publisher": "American Chemical Society", "pagerange": "13038-13047", "id_number": "CaltechAUTHORS:20180525-111314381", "issn": "0022-3654", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180525-111314381", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM15647" } ] }, "other_numbering_system": { "items": [ { "id": "9014", "name": "Division of Chemistry and Chemical Engineering" } ] }, "doi": "10.1021/j100034a052", "resource_type": "article", "pub_year": "1995", "author_list": "DiMagno, Theodore J.; Stowell, Michael H. B.; et el." }, { "id": "https://authors.library.caltech.edu/records/sp614-d7v97", "eprint_id": 83356, "eprint_status": "archive", "datestamp": "2023-08-20 06:12:06", "lastmod": "2023-10-17 23:03:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cavagnero-S", "name": { "family": "Cavagnero", "given": "Silvia" } }, { "id": "Zhou-Zhi-H", "name": { "family": "Zhou", "given": "Zhi H." } }, { "id": "Adams-M-W-W", "name": { "family": "Adams", "given": "Michael W. W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Response of Rubredoxin from Pyrococcus furiosus to Environmental Changes: Implications for the Origin of Hyperthermostability", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1995 American Chemical Society. \n\nThis work was supported by NIH Grants GM 22432 (S.I.C.) and\nGM 50736 (M.W.W.A.) from the National Institute of General Medical Sciences, U.S. Public Health Service. Contribution No. 9039 from the Arthur Amos Noyes Laboratories of Chemical Physics. \n\nWe thank Professor Pamela J. Bjorkman for the use of the program GRASP and Professor Douglas C. Rees for helpful discussion on this study.\n\nPublished - bi00031a007.pdf
", "abstract": "The bases of the hyperthermostability of rubredoxin from Pyrococcus furiosus (RdPf) have been probed by structural perturbations induced by solution pH and ionic strength changes. Comparison of the solution behavior at pH 7 and pH 2, as probed by far- and near-UV circular dichroism, Trp\nfluorescence emission, l-anilinonaphthalene-8-sulfonate (ANS) binding, and NMR spectroscopy, reveals the presence of only minimal structural variations at room temperature. At pH 2, the protein displays a surprising nearly native-like behavior at high ionic strength while, at low ionic strength, it is capable of strongly binding the hydrophobic probe ANS. All the secondary and tertiary structural features, including the environment of the hydrophobic core, appear to be intact regardless of pH and ionic strength. The apparent \"melting\" or denaturation temperature at pH 2, however, is 42 \u00b0C lower than at pH 7. This is attributed to the perturbation of many electrostatic interactions, including the disruption of all the ion pairs, which is complete at pH 2, as indicated by electrometric pH titrations. The implications of these\nfindings for the origins of the hyperthermostability of rubredoxin are discussed.", "date": "1995-08-08", "date_type": "published", "publication": "Biochemistry", "volume": "34", "number": "31", "publisher": "American Chemical Society", "pagerange": "9865-9873", "id_number": "CaltechAUTHORS:20171120-141844682", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171120-141844682", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "NIH", "grant_number": "GM 50736" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "9039", "name": "Caltech Arthur Amos Noyes Laboratories of Chemical Physics" } ] }, "doi": "10.1021/bi00031a007", "primary_object": { "basename": "bi00031a007.pdf", "url": "https://authors.library.caltech.edu/records/sp614-d7v97/files/bi00031a007.pdf" }, "resource_type": "article", "pub_year": "1995", "author_list": "Cavagnero, Silvia; Zhou, Zhi H.; et el." }, { "id": "https://authors.library.caltech.edu/records/4fssw-3ns96", "eprint_id": 93388, "eprint_status": "archive", "datestamp": "2023-08-22 10:28:10", "lastmod": "2023-10-20 17:06:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Evans-J-S", "name": { "family": "Evans", "given": "John Spencer" } }, { "id": "Mathiowetz-A-M", "name": { "family": "Mathiowetz", "given": "Alan M." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Goddard-W-A-III", "name": { "family": "Goddard", "given": "William A., III" }, "orcid": "0000-0003-0097-5716" } ] }, "title": "De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology", "ispublished": "pub", "full_text_status": "restricted", "keywords": "computational chemistry; importance sampling; Monte Carlo; peptide conformation; protein confor\u00admation; protein folding", "note": "\u00a9 1995 The Protein Society. \n\n(RECEIVED December 20, 1994; ACCEPTED March 21, 1995) \n\nWe thank Dr. Siddharth Dasgupta for helpful advice during this study. J.S.E. acknowledges a Postdoctoral National Research Service Award from the NIH (NIDR 1F32-DE-05445) and a fellowship award from AMGEN Pharmaceuticals. A.M.M. acknowledges a National Research Service Award/NIH Predoctoral Biotechnology Traineeship. These studies were supported by a grant from DOE-AICD. The facilities of the MSC are also supported by grants from the NSF (CHE91-00284 and ASC-9219368), Allied Signal, Asahi Chemical, Asahi Glass, BP America, Chevron, B.F. Goodrich, Teijin Ltd., Vestar, Xerox, Hughes Research Laboratories, and Beckman Institute. Some of these calculations were carried out on the NSF Pittsburgh Supercomputer and on the JPL Cray. This is Contribution 8949 from the Division of Chemistry and Chemical Engineering, California Institute of Technology.", "abstract": "We tested the dihedral probability grid Monte Carlo (DPG\u2010MC) methodology to determine optimal conformations of polypeptides by applying it to predict the low energy ensemble for two peptides whose solution NMR structures are known: integrin receptor peptide (YGRGDSP, Type II \u03b2\u2010turn) and S3 \u03b1\u2010helical peptide (YMSEDELKAAEAAFKRHGPT). \n\nDPG\u2010MC involves importance sampling, local random stepping in the vicinity of a current local minima, and Metropolis sampling criteria for acceptance or rejection of new structures. Internal coordinate values are based on side\u2010chain\u2010specific dihedral angle probability distributions (from analysis of high\u2010resolution protein crystal structures). Important features of DPG\u2010MC are: (1) Each DPG\u2010MC step selects the torsion angles (\u03d5, \u03c8, \u03c7) from a discrete grid that are then applied directly to the structure. The torsion angle increments can be taken as S = 60, 30, 15, 10, or 5\u00b0, depending on the application. (2) DPG\u2010MC utilizes a temperature\u2010dependent probability function (P) in conjunction with Metropolis sampling to accept or reject new structures. \n\nFor each peptide, we found close agreement with the known structure for the low energy conformational ensemble located with DPG\u2010MC. This suggests that DPG\u2010MC will be useful for predicting conformations of other polypeptides.", "date": "1995-06", "date_type": "published", "publication": "Protein Science", "volume": "4", "number": "6", "publisher": "Wiley", "pagerange": "1203-1216", "id_number": "CaltechAUTHORS:20190301-092706779", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190301-092706779", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32-DE-05445" }, { "agency": "Amgen" }, { "agency": "NIH Predoctoral Fellowship" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NSF", "grant_number": "CHE91-00284" }, { "agency": "NSF", "grant_number": "ASC-9219368" }, { "agency": "Allied-Signal" }, { "agency": "Asahi Chemical" }, { "agency": "Asahi Glass" }, { "agency": "BP America" }, { "agency": "Chevron" }, { "agency": "B. F. Goodrich" }, { "agency": "Teijin Ltd." }, { "agency": "Vestar" }, { "agency": "Xerox" }, { "agency": "Hughes Research Laboratories" }, { "agency": "Caltech Beckman Institute" } ] }, "other_numbering_system": { "items": [ { "id": "8949", "name": "Division of Chemistry and Chemical Engineering" } ] }, "doi": "10.1002/pro.5560040618", "pmcid": "PMC2143148", "resource_type": "article", "pub_year": "1995", "author_list": "Evans, John Spencer; Mathiowetz, Alan M.; et el." }, { "id": "https://authors.library.caltech.edu/records/3zqxk-mps06", "eprint_id": 84663, "eprint_status": "archive", "datestamp": "2023-08-20 05:53:32", "lastmod": "2023-10-18 16:32:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lin-Jian", "name": { "family": "Lin", "given": "Jian" } }, { "id": "Wu-Shuguang", "name": { "family": "Wu", "given": "Shuguang" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Electron Transfer from Cytochrome c to 8-azido-ATP-Modified Cytochrome c Oxidase", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1995 American Chemical Society. \n\nPublished in print 16 May 1995. \n\nThis work was supported by NIH Grant GM 22432 from the\nNational Institute of General Medical Sciences, U.S. Public Health Service. \n\nContribution No. 9015 \n\nWe are grateful to Prof. Gordon Tollin of Department of\nBiochemistry, University of Arizona, Tucson, for a gift of\n5-DRF. We also thank Dr. Jay Winkler, manager of the\nLaser Facility at the Beckman Institute of the California\nInstitute of Technology, for advice and technical assistance in the laser experiments.", "abstract": "Bovine heart cytochrome c oxidase (CcO) has been modified by 8-azido-adenosine 5'- triphosphate (8-azido-ATP), and the electron-transfer activity from ferrocytochrome c to the modified CcO under physiological ionic strengths has been studied by the laser flash photolysis technique with\n5-deazariboflavin and EDTA as the electron donor. The kinetics of intermolecular electron transfer between\nthe redox protein partners was shown to be reduced significantly. In addition, there is significant decrease\nin the binding affinity of the cytochrome c to the oxidase upon 8-azido-ATP modification. The 8-azido-ATP-modified CcO exhibited 50% of the intracomplex electron-transfer rate (k_(et)) and 56% of the association constant (K_a) normally observed between cytochrome c and native CcO under otherwise identical conditions. Since the effective electron transfer rate constant is the product of k_(et), and K_a under nonsaturation conditions, the overall electron-transfer rate has been curtailed by over a factor of 2. Similar observations have been noted with the native CcO in the presence of 3 mM ATP. In contrast, the redox potential of neither CU_A nor cytochrome a was altered upon 8-azido-ATP modification or in the presence of 3 mM ATP. Also, no gross structural changes at either the CU_A or the cytochrome a site were noted, as evidenced by a lack of any spectral perturbations in the EPR signals from both of these centers. We conclude that ATP modulates the electron transfer from cytochrome c to CcO by interacting with the CcO and altering allosterically the docking. In this manner, ATP can affect the branching of the electron input from ferrocytochrome c to cytochrome a and CU_A.", "date": "1995-05-16", "date_type": "published", "publication": "Biochemistry", "volume": "34", "number": "19", "publisher": "American Chemical Society", "pagerange": "6335-6343", "id_number": "CaltechAUTHORS:20180205-074945747", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180205-074945747", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" } ] }, "other_numbering_system": { "items": [ { "id": "9015", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "doi": "10.1021/bi00019a011", "resource_type": "article", "pub_year": "1995", "author_list": "Lin, Jian; Wu, Shuguang; et el." }, { "id": "https://authors.library.caltech.edu/records/zfk7c-v6v91", "eprint_id": 84665, "eprint_status": "archive", "datestamp": "2023-08-20 05:32:53", "lastmod": "2023-10-18 16:32:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lin-Jian", "name": { "family": "Lin", "given": "Jian" } }, { "id": "Wu-Shuguang", "name": { "family": "Wu", "given": "Shuguang" } }, { "id": "Lau-Wa-to", "name": { "family": "Lau", "given": "Wa-to" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "8-Azido-ATP Modification of Cytochrome c: Retardation of Its Electron-Transfer Activity to Cytochrome c Oxidase", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1995 American Chemical Society. \n\nPublished in print 28 February 1995. \n\nThis work was supported by NIH Grant GM 22432 from the\nNational Institute of General Medical Sciences, US. Public Health Service. \n\nContribution no. 8955. \n\nWe are grateful to Professor Gordon Tollin of the\nDepartment of Biochemistry, University of Arizona, Tucson,\nfor a gift of 5-DRF. We also thank Dr. Jay Winkler, manager\nof the laser facility at the Beckman Institute of the California Institute of Technology, for advice and technical assistance in the laser experiments. Professor Carmichael Wallace kindly provided us with a copy of a manuscript summarizing the results of related studies prior to publication. Dr. Wallace also provided a number of helpful comments on the present study.", "abstract": "Horse heart cytochrome c has been modified by 8-azido-ATP and the electron-transfer activity of the modified cytochrome c's to bovine heart cytochrome c oxidase (CcO) under physiological ionic strengths has been studied by the laser flash photolysis technique with 5-deazariboflavin and EDTA as the electron donor. The intermolecular electron transfer between the redox protein partners was shown\nto be extremely slow. The 8-azido-ATP-modified system exhibited less than 5% of the intracomplex electron-transfer rate observed between native cytochrome c and CcO under otherwise identical conditions. The binding affinity of the modified cytochrome c was greatly reduced (3 orders of magnitude) at low ionic strengths; however, it was only slightly reduced (by a factor of 2) relative to the native protein at physiological ionic strengths. Thus, the binding affinity of the ATP-cytochrome c adducts is relatively insensitive to the ionic strength compared to the native enzyme, suggesting that a different docking conformation is assumed by the ATP-cytochrome c adducts in their interaction with the oxidase. Since the redox potential of the modified cytochrome c is close to the value of its native form, we conclude that there has been a change in the docking of the cytochrome c to CcO and the electronic coupling between heme c and CUA upon 8-azido-ATP modification.", "date": "1995-02-28", "date_type": "published", "publication": "Biochemistry", "volume": "34", "number": "8", "publisher": "American Chemical Society", "pagerange": "2678-2685", "id_number": "CaltechAUTHORS:20180205-083519723", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180205-083519723", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" } ] }, "other_numbering_system": { "items": [ { "id": "8955", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "doi": "10.1021/bi00008a035", "resource_type": "article", "pub_year": "1995", "author_list": "Lin, Jian; Wu, Shuguang; et el." }, { "id": "https://authors.library.caltech.edu/records/d6q5p-khq76", "eprint_id": 54456, "eprint_status": "archive", "datestamp": "2023-08-20 02:31:46", "lastmod": "2023-10-20 16:29:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stowell-M-H-B", "name": { "family": "Stowell", "given": "Michael H. B." } }, { "id": "Larsen-R-W", "name": { "family": "Larsen", "given": "Randy W." } }, { "id": "Winkler-J-R", "name": { "family": "Winkler", "given": "Jay R." }, "orcid": "0000-0002-4453-9716" }, { "id": "Rees-D-C", "name": { "family": "Rees", "given": "Douglas C." }, "orcid": "0000-0003-4073-1185" }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Transient electron-transfer studies on the two-subunit cytochrome c oxidase from Paracoccus denitrificans", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1993 American Chemical Society.\n\nReceived: November 23, 1992.\n\nContribution No. 8722 from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA. This work was supported by Grant GM22432 from the National Institute of General Medical Science, U.S.P.H.S. Portions described at the ASBMB/Biophysical Society Joint Meeting. FASEB J. 1992, 6, A284.\n\nWe thank Siegfried M. Musser and Dr. Theodore J. DiMagno for helpful discussions and critically reviewing this manuscript. We also thank Dr. Thomas Harrold and Larry Tudor for expert assistance in the growth of P. denitrificans.", "abstract": "Intermolecular electron transfer between c-type cytochromes (equine cytochrome c_(550), P. denitrifcans c_(550), and\nP. denitrificans detergent solubilized membrane-associated c_(552)) and the two-subunit cytochrome c oxidase\nfrom P. denitrificans has been studied using a photoinitiated uroporphyrin/NADH reduction system. In the\npresence of cytochrome c oxidase, the oxidation of transiently produced soluble ferrocytochrome c_(550)'s was\nbiphasic with a fast phase k_(obs) between 80 and 90 s^(-1). The simultaneous reduction of cytochrome a occurred\nwith a k(obs) of 50 s^(-1), suggesting that cytochrome a is not the immediate electron acceptor for these soluble\ncytochromes. In contrast, the membrane-associated cytochrome c_(552) was not capable of transferring electrons\nto cytochrome c oxidase, either transiently or under steady-state conditions. It is concluded that the soluble\nand membrane-associated cytochrome c's utilize separate electron-transfer pathways into P. denitrifcans\ncytochrome c oxidase.", "date": "1993-03-25", "date_type": "published", "publication": "Journal of Physical Chemistry", "volume": "97", "number": "12", "publisher": "American Chemical Society", "pagerange": "3054-3057", "id_number": "CaltechAUTHORS:20150205-142230754", "issn": "0022-3654", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150205-142230754", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "8722", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "doi": "10.1021/j100114a036", "resource_type": "article", "pub_year": "1993", "author_list": "Stowell, Michael H. B.; Larsen, Randy W.; et el." }, { "id": "https://authors.library.caltech.edu/records/h1241-kr216", "eprint_id": 76095, "eprint_status": "archive", "datestamp": "2023-08-20 02:19:21", "lastmod": "2023-10-25 15:31:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lou-Bih-Show", "name": { "family": "Lou", "given": "Bih Show" } }, { "id": "Larsen-R-W", "name": { "family": "Larsen", "given": "Randy W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Ondrias-M-R", "name": { "family": "Ondrias", "given": "Mark R." } } ] }, "title": "Conformational dependence of carbon monoxide ligation dynamics in cytochrome c oxidase", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1993 American Chemical Society. \n\nReceived January 27, 1992. \n\nResearch supported in part by Grants GM33330 (to M.R.O.) and GM22432 (to S.I.C.) from the National Institute of General Medical Sciences, US. Public Health Service.", "abstract": "Time-resolved optical studies have recently demonstrated that ligand photolysis and rebinding in fully reduced cytochrome c oxidase (Cco) is an extremely complicated process involving structural dynamics of both the proximal and distal heme pockets of cytochrome a_3. We have expanded upon these studies by examining the corresponding ligation dynamics in mixed-valence\n(MV) Cco, which is known to exist in a conformation that is structurally and kinetically distinct from fully reduced (FR)\nCco. We report here time-resolved Raman results showing that while the promximal heme pocket dynamics of MV-Cco are\nsimilar to those of FR-Cco, the ligation dynamics of the distal pocket are affected by the protein conformational state.", "date": "1993-01-27", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "115", "number": "2", "publisher": "American Chemical Society", "pagerange": "403-407", "id_number": "CaltechAUTHORS:20170408-155639902", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170408-155639902", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM33330" }, { "agency": "NIH", "grant_number": "GM22432" } ] }, "doi": "10.1021/ja00055a006", "resource_type": "article", "pub_year": "1993", "author_list": "Lou, Bih Show; Larsen, Randy W.; et el." }, { "id": "https://authors.library.caltech.edu/records/2k4zy-jht78", "eprint_id": 88210, "eprint_status": "archive", "datestamp": "2023-08-20 01:04:54", "lastmod": "2023-10-18 21:52:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Jianling", "name": { "family": "Wang", "given": "Jianling" } }, { "id": "Larsen-R-W", "name": { "family": "Larsen", "given": "Randy W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Boldt-N-J", "name": { "family": "Boldt", "given": "Nancy J." } }, { "id": "Ondrias-M-R", "name": { "family": "Ondrias", "given": "Mark R." } } ] }, "title": "Ligand photodissociation and recombination dynamics of ferrous cytochrome c peroxidase at alkaline pH", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1992 American Chemical Society. \n\nReceived October 18, 1991. \n\nWe gratefully acknowledge the financial support of the National Institutes of Health [GM33330 (M.R.O.) and GM22432 (S.I.C.)].", "abstract": "The dynamics associated with ligand photodissociation and ligand binding provide an avenue through which information concerning conformational interactions involving the active site of heme proteins may be obtained. To date, most time-resolved spectroscopic investigations have involved exogenous \u03c0-acceptor ligands such as CO, O_2, and NO. In fact, until very recently hexacoordinate low-spin hemes with strong-field \u03c3-donor ligands were considered to be largely nonphotolabile. Magda and coworkers have, however, demonstrated that both cytochrome c and cytochrome b_5 exhibit photodissociation of nitrogenous ligands on a very fast (< 100 ps) time scale. Photodissociation of a \u03c3 ligand has also been implicated in the photodynamics of the cytochrome a_3 distal heme pocket in cytochrome c oxidase. This study characterizes the dynamics of the low-spin alkaline form of ferrous cytochrome c peroxidase (CCP) subsequent to heme photodissociation.", "date": "1992-02-12", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "114", "number": "4", "publisher": "American Chemical Society", "pagerange": "1487-1488", "id_number": "CaltechAUTHORS:20180724-152024973", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180724-152024973", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM33330" }, { "agency": "NIH", "grant_number": "GM22432" } ] }, "other_numbering_system": { "items": [ { "id": "8854", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "doi": "10.1021/ja00030a057", "resource_type": "article", "pub_year": "1992", "author_list": "Wang, Jianling; Larsen, Randy W.; et el." }, { "id": "https://authors.library.caltech.edu/records/nc66n-fca60", "eprint_id": 1068, "eprint_status": "archive", "datestamp": "2023-08-22 08:42:11", "lastmod": "2023-10-23 19:36:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Larsen-R-W", "name": { "family": "Larsen", "given": "Randy W." } }, { "id": "Pan-Lian-Ping", "name": { "family": "Pan", "given": "Lian-Ping" } }, { "id": "Musser-S-M", "name": { "family": "Musser", "given": "Siegfried M." } }, { "id": "Li-Zhuyin", "name": { "family": "Li", "given": "Zhuyin" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Could CuB be the site of redox linkage in cytochrome c oxidase?", "ispublished": "pub", "full_text_status": "public", "keywords": "proton pump, electron transfer, mitochondria, respiration, oxygen reduction, dioxygen reduction, mechanism, model, temperature, oxygen", "note": "\u00a9 1992 by the National Academy of Sciences. \n\nCommunicated by Fred Anson, August 5, 1991 (received for review May 30, 1991). \n\nThis is contribution no. 8443 from the Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology. This work was supported by Grant GM 22432 from the National Institute of General Medical Sciences, U.S. Public Health Service, and Grant PRF#19671-AC3 from the Petroleum Research Fund of the American Chemical Society. \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 - LARpnas92.pdf
", "abstract": "This paper explores the proton pumping function of cytochrome c oxidase [ferrocytochrome-c:oxygen oxidoreductase (EC 1.9.3.1)] based upon redox linkage at the \"high-potential\" CU(B) center. A model is proposed that is derived from a redox-linked ligand exchange mechanism previously described for the Cu(A) site. Qualitative analysis of this mechanism indicates that such a mechanism is feasible. However, the relatively short distance between Cu(B) and cytochrome a3 implies that the uncoupling electron transfers are quite facile. In addition, the position of the Cu(B) center with respect to the inner mitochondrial membrane argues against redox linkage at the Cu(B) site.", "date": "1992-01-15", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "89", "number": "2", "publisher": "National Academy of Sciences", "pagerange": "723-727", "id_number": "CaltechAUTHORS:LARpnas92", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:LARpnas92", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "American Chemical Society Petroleum Research Fund", "grant_number": "PRF 19671-AC3" } ] }, "other_numbering_system": { "items": [ { "id": "8443", "name": "Caltech Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "pmcid": "PMC48311", "primary_object": { "basename": "LARpnas92.pdf", "url": "https://authors.library.caltech.edu/records/nc66n-fca60/files/LARpnas92.pdf" }, "resource_type": "article", "pub_year": "1992", "author_list": "Larsen, Randy W.; Pan, Lian-Ping; et el." }, { "id": "https://authors.library.caltech.edu/records/cgme1-m0539", "eprint_id": 84797, "eprint_status": "archive", "datestamp": "2023-08-19 23:12:43", "lastmod": "2023-10-18 16:42:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Larsen-R-W", "name": { "family": "Larsen", "given": "Randy W." } }, { "id": "Li-Wei", "name": { "family": "Li", "given": "Wei" }, "orcid": "0000-0003-2543-2558" }, { "id": "Copeland-R-A", "name": { "family": "Copeland", "given": "Robert A." } }, { "id": "Witt-S-N", "name": { "family": "Witt", "given": "Stephan N." } }, { "id": "Lou-Bih-Show", "name": { "family": "Lou", "given": "Bih Show" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Ondrias-M-R", "name": { "family": "Ondrias", "given": "Mark R." } } ] }, "title": "Room temperature characterization of the dioxygen intermediates of cytochrome c oxidase by resonance Raman spectroscopy", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1990 American Chemical Society. \n\nReceived May 4, 1990; Revised Manuscript Received June 22, 1990. \n\nResearch supported in part by Grants GM 22432 (to S.I.C.) and GM 33330 (to M.R.O.) from the National Institute of General Medical Sciences, US. Public Health Service, Grant RR 08139 (to M.R.O.) from the Division of Research Resources, National Institutes of Health, and the donors of the Petroleum Research Fund, administered by the American\nChemical Society (to S.I.C.). Contribution No. 8103 from Division of Chemistry and Chemical Engineering, California Institute of Technology.", "abstract": "Resonance Raman spectroscopy was employed to investigate the heme structures of catalytic intermediates of cytochrome c oxidase at room temperature. The high-frequency resonance Raman spectra were obtained for compound C (the two-electron-reduced dioxygen intermediate), ferryl (the three-electron-reduced dioxygen intermediate), and the fully oxidized enzyme. Compound C was formed by photolyzing\nCO mixed-valence enzyme in the presence of 02. The ferryl intermediate was formed by reoxidation of\nthe fully reduced enzyme by an excess of H202. Two forms of the oxidized enzyme were prepared by\nreoxidizing the fully reduced enzyme with 02. Our data indicate that, in compound C, cyt a3 is either\nintermediate or low spin and is nonphotolabile and its oxidation state marker band, v4, appears at a higher\nfrequency than that of the resting form of the enzyme. The ferryl intermediate also displays a low-spin\ncyt u3, which is nonphotolabile, and an even higher frequency for the oxidation state marker band, v4. The\nreoxidized form of cytochrome c oxidase with a Soret absorption maximum at 420 nm has an oxidation\nstate marker band (u4) in a position similar to that of the resting form, while the spin-state region resembles\nthat of compound C. This species subsequently decays to a second oxidized form of the enzyme, which\ndisplays a high-frequency resonance Raman spectrum identical with that of the original resting enzyme.", "date": "1990-10-30", "date_type": "published", "publication": "Biochemistry", "volume": "29", "number": "43", "publisher": "American Chemical Society", "pagerange": "10135-10140", "id_number": "CaltechAUTHORS:20180212-143012991", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180212-143012991", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "NIH", "grant_number": "GM 33330" }, { "agency": "NIH", "grant_number": "RR 08139" }, { "agency": "American Chemical Society Petroleum Research Fund" } ] }, "other_numbering_system": { "items": [ { "id": "8103", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "doi": "10.1021/bi00495a018", "resource_type": "article", "pub_year": "1990", "author_list": "Larsen, Randy W.; Li, Wei; et el." }, { "id": "https://authors.library.caltech.edu/records/6fj1k-nt237", "eprint_id": 84796, "eprint_status": "archive", "datestamp": "2023-08-19 22:55:36", "lastmod": "2023-10-18 16:42:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Watnick-P-I", "name": { "family": "Watnick", "given": "Paula I." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Dea-Phoebe", "name": { "family": "Dea", "given": "Phoebe" } } ] }, "title": "Hydrophobic mismatch in gramicidin A'/Lecithin systems", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1990 American Chemical Society. \n\nPublished in print 3 July 1990. \n\nContribution No. 8343 of the Division of Chemistry and Chemical Engineering, California Institute of Technology. \n\nThis work was supported by Grants GM-22432 (S.I.C.), GM-36132 (P.D.), and RR-08101 (P.D.) from the National Institutes of General Medical Sciences, US. Public Health Service, and by the donors of the Petroleum Research Fund, administered by the American Chemical Society. P.I.W. was a recipient of a National Research Service Award (T32 GM07616) from the National Institutes of General Medical Sciences. \n\nAccess to the Southern California Regional NMR Facility\nat Caltech, supported by National Science Foundation Grant\nCHE84-40137, for the NMR experiments is gratefully acknowledged. We thank Drs. T. Handel, A. Nayeem, H. Eckert, and J. Yesinowski for helpful discussions and assistance.", "abstract": "Gramicidin A' (GA') has been added to three lipid systems of varying hydrophobic thicknesses: dimyristoyllecithin (DML), dipalmitoyllecithin (DPL), and distearoyllecithin (DSL). The similarity in length between the hydrophobic portion of GA' and the hydrocarbon chains of the lipid bilayers has been studied by using ^(31)P and ^2H NMR. Hydrophobic mismatch has been found to be most severe in the DML bilayer system and minimal in the case of DSL. In addition, the effects of hydrophobic mismatch on the cooperative properties of the bilayer have been obtained from ^2H NMR relaxation measurements. The results indicate\nthat incorporation of the peptide into the bilayer disrupts the cooperative director fluctuations characteristic\nof pure multilamellar lipid dispersions. Finally, the GA'llecithin ratio at which the well-known transformation\nfrom bilayer to reverse hexagonal (H_(II)) phase occurs (Van Echteld et al., 1982; Chupin et al., 1987) is shown\nto depend on the acyl chain length of the phospholipid. A rationale is proposed for this chain length dependence.", "date": "1990-07-03", "date_type": "published", "publication": "Biochemistry", "volume": "29", "number": "26", "publisher": "American Chemical Society", "pagerange": "6215-6221", "id_number": "CaltechAUTHORS:20180212-141345237", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180212-141345237", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NIH", "grant_number": "GM-36132" }, { "agency": "NIH", "grant_number": "RR-08101" }, { "agency": "American Chemical Society Petroleum Research Fund" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM07616" }, { "agency": "NSF", "grant_number": "CHE84-40137" } ] }, "other_numbering_system": { "items": [ { "id": "8343", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "doi": "10.1021/bi00478a015", "resource_type": "article", "pub_year": "1990", "author_list": "Watnick, Paula I.; Chan, Sunney I.; et el." }, { "id": "https://authors.library.caltech.edu/records/ge0mt-rcw10", "eprint_id": 1108, "eprint_status": "archive", "datestamp": "2023-08-22 07:11:22", "lastmod": "2023-10-23 17:37:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Watnick-P-I", "name": { "family": "Watnick", "given": "Paula I." } }, { "id": "Dea-Phoebe", "name": { "family": "Dea", "given": "Phoebe" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Characterization of the transverse relaxation rates in lipid bilayers", "ispublished": "pub", "full_text_status": "public", "keywords": "deuterium NMR, bilayer membrane, director fluctuations", "note": "\u00a9 1990 by the National Academy of Sciences. \n\nCommunicated by Harden M. McConnell, December 26, 1989. \n\nWe are indebted to M. Dea, H. Eckert, T. Handel, A. Nayeem, and J. Yesinowski for helpful discussions and assistance. This work was supported by Grants GM-22432 (to S.I.C.), GM-36132 (to P.D.), and RR-08101 (to P.D.) from the National Institutes of General Medical Sciences, U.S. Public Health Service; and Petroleum Research Fund Grant 20212-B4 (to P.D.) administered by the American Chemical Society. P.I.W. was a recipient of National Research Service Award T32 GM07616 from the National Institutes of General Medical Sciences. Access to the Southern California Regional NMR Facility at Caltech, supported by Grant CHE84-40137 from the National Science Foundation, for the NMR experiments is gratefully acknowledged. This is contribution 7974 from the Division of Chemistry and Chemical Engineering. \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 - WATpnas90.pdf
", "abstract": "The 2H NMR transverse relaxation rates of a deuterated phospholipid bilayer reflect slow motions in the bilayer membrane. A study of dimyristoyl lecithin specifically deuterated at several positions of the hydrocarbon chains indicates that these motions are cooperative and are confined to the hydrocarbon chains of the lipid bilayer. However, lipid head group interactions do play an important role in modulating the properties of the cooperative fluctuations of the hydrocarbon chains (director fluctuations), as evidenced by the effects of various lipid additives on the 2H NMR transverse relaxation rates of the dimyristoyl lecithin bilayer.", "date": "1990-03-15", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "87", "number": "6", "publisher": "National Academy of Sciences", "pagerange": "2082-2086", "id_number": "CaltechAUTHORS:WATpnas90", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:WATpnas90", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NIH", "grant_number": "GM-36132" }, { "agency": "NIH", "grant_number": "RR-08101" }, { "agency": "National Institute of General Medical Sciences" }, { "agency": "American Chemical Society Petroleum Research Fund", "grant_number": "20212-B4" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM07616" }, { "agency": "NSF", "grant_number": "CHE84-40137" } ] }, "other_numbering_system": { "items": [ { "id": "7974", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "pmcid": "PMC53630", "primary_object": { "basename": "WATpnas90.pdf", "url": "https://authors.library.caltech.edu/records/ge0mt-rcw10/files/WATpnas90.pdf" }, "resource_type": "article", "pub_year": "1990", "author_list": "Watnick, Paula I.; Dea, Phoebe; et el." }, { "id": "https://authors.library.caltech.edu/records/kc43t-g0h14", "eprint_id": 83042, "eprint_status": "archive", "datestamp": "2023-08-19 22:25:21", "lastmod": "2023-10-17 22:52:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Li-Peter-Mark", "name": { "family": "Li", "given": "Peter Mark" } } ] }, "title": "Cytochrome c oxidase: understanding nature's design of a proton pump", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1990 American Chemical Society. \n\nReceived June 16, 1989; Revised Manuscript Received July 17, 1989. \n\nThis work was supported by Grant GM 22432 from the National Institute of General Medical Sciences, U.S. Public Health Service. Acknowledgement is made to the donors of the Petroleum Research Fund, administered by the American Chemical Society, for partial support.", "abstract": "It has been estimated that nearly 90% of the O_2 consumed\nby aerobic organisms participates in the dioxygen chemistry\nof cytochrome c oxidase and becomes reduced to water in the\nterminal step of respiration. Cytochrome oxidases of the aa_3\ntype (having two a-type cytochromes) are found in a wide\nvariety of aerobic organisms including bacteria, fungi, single-\ncelled eukaryotes, plants, and animals. It is an integral\nmembrane protein complex comprised of 2 or 3 subunits in\nthe simplest bacterial systems and as many as 13 dissimilar\nsubunits in mammals [for a review, see Wikstr\u00f6m et al.\n(1981)].", "date": "1990-01-09", "date_type": "published", "publication": "Biochemistry", "volume": "29", "number": "1", "publisher": "American Chemical Society", "pagerange": "1-12", "id_number": "CaltechAUTHORS:20171107-152051230", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171107-152051230", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "American Chemical Society Petroleum Research Fund" } ] }, "other_numbering_system": { "items": [ { "id": "7961", "name": "Caltech Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "doi": "10.1021/bi00453a001", "resource_type": "article", "pub_year": "1990", "author_list": "Chan, Sunney I. and Li, Peter Mark" }, { "id": "https://authors.library.caltech.edu/records/8qjk1-ss476", "eprint_id": 11624, "eprint_status": "archive", "datestamp": "2023-08-22 06:52:43", "lastmod": "2023-10-17 15:15:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Copeland-R-A", "name": { "family": "Copeland", "given": "Robert A." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Proton translocation in proteins", "ispublished": "pub", "full_text_status": "public", "note": "\"Reprinted, with permission, from the Annual Review of Physical Chemistry, Volume 40 copyright 1989 by Annual Reviews, www.annualreviews.org\" \n\nWe wish to thank the many collaborators who have contributed to the work reported here. In particular we wish to thank P. M. Li, P. A. Smith, J. Gelles, D. F. Blair, S. N. Witt, J. Morgan, N. E. Gabriel, T. Nilsson, W. R. Ellis, Jr., H. B. Gray, H. Wang, M. Ma, R. Larsen, M. Ondrias, T. G. Spiro, and C. Martin. We also gratefully acknowledge helpful discussions with W. Woodruff, G. Babcock, B. Malmstr\u00f6m, M. Wikstr\u00f6m, M. Brunori, and P. Sarti. The work reported here from our laboratory was supported by grant GM22432 from the National Institute of General Medical Sciences, US Public Health Service to S.I.C. R.A.C. acknowledges support from a Chaim Weizmann Research Fellowship.\n\nPublished - COParpc89.pdf
", "abstract": "The active transport of protons across the low dielectric barrier imposed by biological membranes is accomplished by a plethora of proteins that span the ca. 40 \u00c5 of the phospholipid bilayer. The free energy derived from the proton electrochemical potential established by the translocation of these protons can subsequently be used to drive vital chemical reactions of the cell, such as ATP synthesis and cell locomotion. Membrane-bound proton translocating proteins have now been found for a variety of organisms and tissues (1). The driving force for proton pumping in these proteins is supplied by numerous mechanisms, including light absorption (e.g. bacteriorhodopsin) (2a,b), ligand binding (e.g. ATPase) (3), and electrochemistry (e.g. electron transfer through cytochrome c oxidase) (4). Thus nature has devised a variety of methods for supplying the energy required for proton pumping by these proteins. Such diversity notwithstanding, the proteins most likely share some common elements of structure and mechanism that allow them to function as proton pumps. A number of theoretical mechanisms have been put forth for both general proton translocation (5-7) and for energy coupling in specific proton pumps. However, despite almost three decades of intensive research, the details of the mechanism(s) and structural requirements for proton pumping remain largely unresolved. To some extent this is the result of the paucity of structural information available for integral membrane proteins. This situation may soon improve as a result of advances in protein methodologies that have allowed several integral membrane proteins to be successfully crystalized (8), and the increased use of genetic engineering to obtain recombinant proton translocating proteins that will offer an opportunity to assess the importance of specific amino acids for the proton translocation process (9).", "date": "1989-10", "date_type": "published", "publication": "Annual Review of Physical Chemistry", "volume": "40", "publisher": "Annual Reviews, Inc.", "pagerange": "671-698", "id_number": "CaltechAUTHORS:COParpc89", "issn": "0066-426X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:COParpc89", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM22432" }, { "agency": "National Institute of General Medical Sciences" }, { "agency": "Chaim Weizmann Research Fellowship" } ] }, "doi": "10.1146/annurev.pc.40.100189.003323", "primary_object": { "basename": "COParpc89.pdf", "url": "https://authors.library.caltech.edu/records/8qjk1-ss476/files/COParpc89.pdf" }, "resource_type": "article", "pub_year": "1989", "author_list": "Copeland, Robert A. and Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/gfccg-xv525", "eprint_id": 1515, "eprint_status": "archive", "datestamp": "2023-08-22 04:50:19", "lastmod": "2023-10-23 16:17:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Jin-Feng", "name": { "family": "Wang", "given": "Jin-Feng" } }, { "id": "Falke-J-J", "name": { "family": "Falke", "given": "Joseph J." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "A proton NMR study of the mechanism of the erythrocyte glucose transporter", "ispublished": "pub", "full_text_status": "public", "keywords": "membrane; binding sites; sugar transport; sliding-barrier model", "note": "\u00a9 1986 by the National Academy of Sciences. \n\nCommunicated by John D. Baldeschwieler, January 7, 1986. \n\nThis work was supported in part by Grant GM 22432 from the National Institute of General Medical Sciences. We acknowledge use of the Southern California Regional High Field Nuclear Magnetic Resonance Facility funded by Grants CHE-7916324 and CHE-8314759 from the National Science Foundation. J.J.F. was a National Science Foundation Predoctoral Fellow. This is contribution no. 7222 from the Arthur Amos Noyes Laboratory of Chemical Physics. \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 - WANpnas86.pdf
", "abstract": "A generalizable 1H NMR technique is developed and used to monitor \u00df-D-glucose binding to glucose transport sites on erythrocyte membranes. This technique provides resolution of \u00df-D-glucose binding sites on opposite sides of the membrane, thereby enabling study of recruitment of transport sites from one side of the membrane to the other. Cytochalasin B, which competitively and specifically inhibits glucose binding to the inward-facing glucose transport site, recruits all glucose transport sites on both sides of the membrane to the inward-facing conformation. This result strongly supports a one-site model in which a single transport site alternates between distinct inward- and outward-facing conformations. The rate-limiting step in the transport process is translocation of the transport site between the two conformations, since the \u00df-D-glucose binding and dissociation events at both the inward- and outward-facing transport sites are shown to be fast compared to the known turnover rate of the glucose transport cycle. A model is presented for the transport machinery in which the glucose molecule binds in a cleft between channel-forming transmembrane helices, and during the transport event a sliding barrier moves past the transport site, thereby exposing the site to the opposite solution compartment.", "date": "1986-05-15", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "83", "number": "10", "publisher": "National Academy of Sciences", "pagerange": "3277-3281", "id_number": "CaltechAUTHORS:WANpnas86", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:WANpnas86", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM 22432" }, { "agency": "NSF", "grant_number": "CHE-7916324" }, { "agency": "NSF", "grant_number": "CHE-8314759" }, { "agency": "NSF Predoctoral Fellowship" } ] }, "other_numbering_system": { "items": [ { "id": "7222", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "pmcid": "PMC323496", "primary_object": { "basename": "WANpnas86.pdf", "url": "https://authors.library.caltech.edu/records/gfccg-xv525/files/WANpnas86.pdf" }, "resource_type": "article", "pub_year": "1986", "author_list": "Wang, Jin-Feng; Falke, Joseph J.; et el." }, { "id": "https://authors.library.caltech.edu/records/9ccj7-egp22", "eprint_id": 12092, "eprint_status": "archive", "datestamp": "2023-08-22 04:31:48", "lastmod": "2023-10-17 16:31:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Falke-J-J", "name": { "family": "Falke", "given": "Joseph J." } }, { "id": "Kanes-K-J", "name": { "family": "Kanes", "given": "Katherine J." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "The minimal structure containing the band 3 anion transport site. A 35Cl NMR study", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1985 by the American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, March 22,1985) \n\nThis work was supported by National Institute of General Medical Sciences Grant GM-22432 (to S.I.C.) and by a National Science Foundation predoctoral fellowship (to J.J.F.). This is contribution 7096 from the Arthur Amos Noyes Laboratory of Chemical Physics. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.\n\nPublished - FALjbc85c.pdf
", "abstract": "35Cl NMR, which enables observation of chloride binding to the anion transport site on band 3, is used in the present study to determine the minimal structure containing the intact transport site. Removal of cytoskeletal and other nonintegral membrane proteins, or removal of the 40-kDa cytoskeletal domain of band 3, each leave the transport site intact. Similarly, cleavage of the 52-kDa transport domain into 17- and 35-kDa fragments by chymotrypsin leaves the transport site intact. Extensive proteolysis by papain reduces the integral red cell membrane proteins to their transmembrane segments. Papain treatment removes approximately 60% of the extramembrane portion of the transport domain and produces small fragments primarily in the range 3-7 kDa, with 5 kDa being most predominant. Papain treatment damages, but does not destroy, chloride binding to the transport site; thus, the minimal structure containing the transport site is composed solely of transmembrane segments. In short, the results are completely consistent with a picture in which the transport site is buried in the membrane where it is protected from proteolysis; the transmembrane segments that surround the transport site are held together by strong attractive forces within the bilayer; and the transport site is accessed by solution chloride via an anion channel leading from the transport site to the solution.", "date": "1985-10-25", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "260", "number": "24", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "13294-13303", "id_number": "CaltechAUTHORS:FALjbc85c", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:FALjbc85c", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NSF Predoctoral Fellowship" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "7096", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "FALjbc85c.pdf", "url": "https://authors.library.caltech.edu/records/9ccj7-egp22/files/FALjbc85c.pdf" }, "resource_type": "article", "pub_year": "1985", "author_list": "Falke, Joseph J.; Kanes, Katherine J.; et el." }, { "id": "https://authors.library.caltech.edu/records/wfjsd-6nq41", "eprint_id": 13003, "eprint_status": "archive", "datestamp": "2023-08-19 17:57:44", "lastmod": "2023-10-17 21:42:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Falke-J-J", "name": { "family": "Falke", "given": "Joseph J." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Evidence that anion transport by band 3 proceeds via a ping-pong mechanism involving a single transport site. A 35 Cl NMR study", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1985 by the American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, August 20, 1984) \n\nThis work was supported by National Institute of General Medical Sciences Grant GM-22432 (to S.I.C.) and by a National Science Foundation predoctoral fellowship (to J.J.F.). Contribution 7068 from the Arthur Amos Noyes Laboratory of Chemical Physics. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.\n\nPublished - FALjbc85b.pdf
", "abstract": "Band 3 catalyzes the one-for-one exchange of monovalent anions across the red cell membrane. At least two anion binding sites have been postulated to exist on the transport unit: 1) a transport site that has been observed by saturation kinetics and by 35 Cl NMR studies of chloride binding, and 2) a 35Cl NMR-invisible inhibitory site that has been proposed to explain the inhibition of anion exchange at large anion concentrations. A number of independent studies have indicated that the transport site is alternately exposed to different sides of the membrane during the transport cycle. Yet the role, if any, of the postulated inhibitory site in the transport cycle is not known. Here it is shown that: 1) when the [Cl-], [Br-], or pH is varied, the band 3 transport sites on both sides of the membrane behave like a homogeneous population of simple anion binding sites in 35Cl NMR experiments, and 2) when the [Cl-] is varied, the outward-facing transport site behaves like a simple anion binding site. These results indicate that the postulated inhibitory site has no effect on chloride binding to the transport site. Instead, the results are quantitatively consistent with the ping-pong model (Gunn, R. B., and Frolich, O. (1979) J. Gen. Physiol. 74, 351-374), which states that the transport site is the only site involved in the transport cycle. Expressions are derived for the macroscopically observed characteristics of a ping-pong transporter: these characteristics are shown to be weighted averages of the microscopic properties of the inward- and outward-facing conformations of the transport site. \n\nIn addition to supporting the simplicity of the transport mechanism, the high pH titration curve for chloride binding to the transport site provides insight into the structure of the site. The macroscopically observed pKA = 11.1 \u00b1 0.1 in the leaky ghost system indicates that an arginine must provide the essential positive charge in the inward- or outward-facing conformation of the transport site, or in both conformations.", "date": "1985-08-15", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "260", "number": "17", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "9537-9544", "id_number": "CaltechAUTHORS:FALjbc85b", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:FALjbc85b", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NSF Predoctoral Fellowship" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "7068", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "FALjbc85b.pdf", "url": "https://authors.library.caltech.edu/records/wfjsd-6nq41/files/FALjbc85b.pdf" }, "resource_type": "article", "pub_year": "1985", "author_list": "Falke, Joseph J. and Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/p6s99-wf839", "eprint_id": 13001, "eprint_status": "archive", "datestamp": "2023-08-19 17:57:40", "lastmod": "2023-10-17 21:42:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Falke-J-J", "name": { "family": "Falke", "given": "Joseph J." } }, { "id": "Kanes-K-J", "name": { "family": "Kanes", "given": "Katherine J." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "The kinetic equation for the chloride transport cycle of band 3. A 35Cl and 37Cl NMR study", "ispublished": "pub", "full_text_status": "public", "note": "Copyright \u00a9 1985 by the American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, August 30, 1984) \n\nThis work was supported by National Institute of General Medical Sciences Grant GM-22432 (to S.I.C.) and by a National Science Foundation predoctoral fellowship (to J.J.F.). Contribution 7081 from the Arthur Amos Noyes Laboratory. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.\n\nPublished - FALjbc85a.pdf
", "abstract": "The nature of a transmembrane transport process depends largely on the identity of the reaction that is rate-limiting in the transport cycle. The one-for-one exchange of two chloride ions across the red cell membrane by band 3 can be decomposed into two component reactions: 1) the binding and dissociation of chloride at the transport site, and 2) the translocation of bound chloride across the membrane. The present work utilizes 35 Cl NMR and 37 Cl NMR to set lower limits on the rates of chloride binding and dissociation at the saturated inward- and outward-facing band 3 transport sites (\u226510^(5) events site^-1 s^-1 in all cases). At both 0-3 and 37 degrees C, the NMR data specify that chloride binding and dissociation a the saturated transport sites are not rate-limiting, indicating that translocation of bound chloride across the membrane is the slowest step in the overall transport cycle. \n\nUsing these results, it is now possible to describe many features of the kinetic equation for the ping-pong transport cycle of band 3. This transport cycle can be decomposed into two half-reactions associated with the transport of two chloride ions in opposite directions across the membrane, where each half-reaction is composed of sequential binding, translocation, and dissociation events. One half-reaction contains the rate-limiting translocation event that controls the turnover of the transport cycle; in this half-reaction, translocation must be slower than binding and dissociation. The other half-reaction contains the non-rate-limiting translocation event that in principle could be faster than binding or dissociation. However, when the following sufficient (but not necessary) condition is satisfied, both translocation events are slower than binding and dissociation: if the non-rate-limiting translocation rate is within a factor of 10^(2) (0-3 degrees C) or 2 (37 degrees C) of the overall turnover rate, then translocation is rate-limiting in each saturated half-reaction. Thus, even though chloride appears to migrate through a channel that leads from the transport site to solution, the results support a picture in which the binding, dissociation, and channel migration events are rapid compared to the translocation of bound chloride across the membrane. In this case, chloride binding to the transport site can be described by a simple dissociation constant (KD = kappa OFF/kappa ON) rather than by a Michaelis-Menten constant (KM = (kappa OFF + kappa TRANSLOCATION)/KAPPA ON).", "date": "1985-08-15", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "260", "number": "17", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "9545-9551", "id_number": "CaltechAUTHORS:FALjbc85a", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:FALjbc85a", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NSF Predoctoral Fellowship" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "7081", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "FALjbc85a.pdf", "url": "https://authors.library.caltech.edu/records/p6s99-wf839/files/FALjbc85a.pdf" }, "resource_type": "article", "pub_year": "1985", "author_list": "Falke, Joseph J.; Kanes, Katherine J.; et el." }, { "id": "https://authors.library.caltech.edu/records/c1tbq-zh179", "eprint_id": 12108, "eprint_status": "archive", "datestamp": "2023-08-22 04:19:10", "lastmod": "2023-10-17 16:31:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Martin-C-T", "name": { "family": "Martin", "given": "Craig T." } }, { "id": "Scholes-C-P", "name": { "family": "Scholes", "given": "Charles P." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "The identification of histidine ligands to cytochrome a in cytochrome c oxidase", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1985 American Society of Biological Chemists. \n\nReceived for publication, August 17, 1984. \n\nThis paper is Contribution 7078 from the Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. \n\n[C.T.M. was the] [r]ecipient of National Research Service Award 5T32GM-07616 from the National Institute of General Medical Sciences. \n\n[C.P.S. was the] [r]ecipient of Grant AM-18884 from the National Institute of Arthritis, Metabolism, and Digestive Diseases, United States Public Health Service and Grant RR07122 from the Biomedical Research Support Grant Program, Division of Research Resources, National Institutes of Health. \n\n[S.I.C. was the] [r]ecipient of Grant GM-22432 from the National Institute of General Medical Sciences and Biomedical Research Support Grant RR07003.\n\nPublished - MARjbc85.pdf
", "abstract": "A histidine auxotroph of Saccharomyces cerevisiae has been used to metabolically incorporate [1,3-15N2] histidine into yeast cytochrome c oxidase. Electron nuclear double resonance (ENDOR) spectroscopy of cytochrome a in the [15N]histidine-substituted enzyme reveals an ENDOR signal which can be assigned to hyperfine coupling of a histidine 15N with the low-spin heme, thereby unambiguously identifying histidine as an axial ligand to this cytochrome. Comparison of this result with similar ENDOR data obtained on two 15N-substituted bisimidazole model compounds, metmyoglobin-[15N]imidazole and bis[15N]imidazole tetraphenyl porphyrin, provides strong evidence for bisimidazole coordination in cytochrome a.", "date": "1985-03-10", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "260", "number": "5", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "2857-2861", "id_number": "CaltechAUTHORS:MARjbc85", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:MARjbc85", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32GM-07616" }, { "agency": "NIH", "grant_number": "AM-18884" }, { "agency": "NIH", "grant_number": "RR07122" }, { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NIH", "grant_number": "RR07003" }, { "agency": "National Institute of General Medical Sciences" }, { "agency": "National Institute of Arthritis, Metabolism, and Digestive Diseases" } ] }, "other_numbering_system": { "items": [ { "id": "7078", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "MARjbc85.pdf", "url": "https://authors.library.caltech.edu/records/c1tbq-zh179/files/MARjbc85.pdf" }, "resource_type": "article", "pub_year": "1985", "author_list": "Martin, Craig T.; Scholes, Charles P.; et el." }, { "id": "https://authors.library.caltech.edu/records/ymwgp-51628", "eprint_id": 32199, "eprint_status": "archive", "datestamp": "2023-08-19 17:09:16", "lastmod": "2023-10-17 23:02:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Brudvig-G-W", "name": { "family": "Brudvig", "given": "Gary W." } }, { "id": "Blair-D-F", "name": { "family": "Blair", "given": "David F." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Electron Spin Relaxation of Cu_A and Cytochrome a in Cytochrome c Oxidase. Comparison to heme, copper, and sulfur radical complexes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1984 American Society for Biochemistry and Molecular Biology.\n\nReceived for publication, April 3, 1984.\n\nRecipient of National Research Service Award 5T32GM-07616\nfrom the National Institute of General Medical Sciences.\nRecipient of National Research Service Award 5T32GM-07616\nfrom the National Institute of General Medical Science.\nRecipient of Grant GM-22432 from the National Institute of\nGeneral Medical Sciences and Biomedical Research Support Grant RR 07003.\n\nWe are grateful to Craig T. Martin, Jeff Gelles, and Joel Morgan for technical assistance and helpful discussions.\n\nThis paper is Contribution 6823 from the Arthur Amos Noyes\nLaboratory of Chemical Physics, California Institute of Technology,\nPasadena, CA 91125. The costs of publication of this article were\ndefrayed in part by the payment of page charges. This article must\ntherefore be hereby marked \"advertisement\" in accordance with 18\nU.S.C. Section 1734 solely to indicate this fact.\n\nPublished - BRUjbc84.pdf
", "abstract": "The method of continuous saturation has been used to measure the electron spin relaxation parameter T_(1)T_(2) at temperatures between 10 and 50 K for a variety of S = 1/2 species including: Cu_A and cytochrome a of cytochrome c oxidase, the type 1 copper in several blue copper proteins, the type 2 copper in laccase, inorganic Cu(II) complexes, sulfur radicals, and low spin heme proteins. The temperature dependence and the magnitude of T_(1)T_(2) for all of the species examined are accounted for by assuming that the Van Vleck Raman process dominates the electron spin-lattice relaxation. Over the entire temperature range examined, the relaxation of the type 1 coppers in six to seven times faster than that of type 2 copper, inorganic copper, and sulfur radicals, in spite of the similar g-anisotropies of these species. This result may indicate that the coupling of the phonon bath to the spin center is more effective in type 1 coppers than in the other complexes studied. The relaxation of Cu_A of cytochrome oxidase exhibits an unusual temperature dependence relative to the other copper complexes studied, suggesting that the protein environment of this center is different from that of the other copper centers studied and/or that Cu_A is influenced by a magnetic dipolar interaction with another, faster-relaxing paramagnetic site in the enzyme. A comparison of the saturation characteristics of the Cu_A EPR signal in native and partially reduced CO complexes of the enzyme also suggests the existence of such an interaction. The implications of these results with respect to the disposition of the metal centers in cytochrome oxidase are discussed", "date": "1984-09-10", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "259", "number": "17", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "11001-11009", "id_number": "CaltechAUTHORS:20120629-110323859", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120629-110323859", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32GM-07616" }, { "agency": "NIH", "grant_number": "RR 07003" }, { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "6823", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "BRUjbc84.pdf", "url": "https://authors.library.caltech.edu/records/ymwgp-51628/files/BRUjbc84.pdf" }, "resource_type": "article", "pub_year": "1984", "author_list": "Brudvig, Gary W.; Blair, David F.; et el." }, { "id": "https://authors.library.caltech.edu/records/3dj2v-y2s66", "eprint_id": 11372, "eprint_status": "archive", "datestamp": "2023-08-22 03:56:25", "lastmod": "2023-10-16 23:45:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Falke-J-J", "name": { "family": "Falke", "given": "Joseph J." } }, { "id": "Pace-R-J", "name": { "family": "Pace", "given": "R. J." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Chloride binding to the anion transport binding sites of band 3. A 35Cl NMR study", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1984 by the American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, September 13, 1983) \n\nThis work was supported by National Institute of General Medical Sciences Grant GM-22432. Contribution 6887 from the Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. \n\n[J.J.F. was] [s]upported by a National Science Foundation Predoctoral Fellowship. \n\nAppendices I-III (including Figs. A1 and A2) are presented in miniprint at the end of this paper. Miniprint is easily read with the aid of a standard magnifying glass\n\nPublished - FALjbc84b.pdf
", "abstract": "Band 3 is an integral membrane protein that exchanges anions across the red cell membrane. Due to the abundance and the high turnover rate of the band 3 transport unit, the band 3 system is the most heavily used ion-transport system in a typical vertebrate organism. Here we show that 35Cl NMR enables direct and specific observation of substrate Cl- binding to band 3 transport sites, which are identified by a variety of criteria: (a) the sites are inhibited by 4,4'- dinitrostilbene -2,2'- disulfonate, which is known to inhibit competitively Cl- binding to band 3 transport sites; (b) the sites have affinities for 4,4'- dinitrostilbene -2,2'-disulfonate and Cl- that are quantitatively similar to the known affinities of band 3 transport sites for these anions; and (c) the sites have relative affinities for Cl-, HCO-3, F-, and I- that are quantitatively similar to the known relative affinities of band 3 transport sites for these anions. The 35Cl NMR assay also reveals a class of low affinity Cl- binding sites (KD much greater than 0.5 M) that are not affected by 4,4'- dinitrostilbene -2,2'- disulfonate. These low affinity sites may be responsible for the inhibition of band 3 catalyzed anion exchange that has been previously observed at high [Cl-]. In the following paper the 35Cl NMR assay is used to resolve the band 3 transport sites on opposite sides of the membrane, thereby enabling direct observation of the transmembrane recruitment of transport sites.", "date": "1984-05-25", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "259", "number": "10", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "6472-6480", "id_number": "CaltechAUTHORS:FALjbc84b", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:FALjbc84b", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NSF Predoctoral Fellowship" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "6887", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "FALjbc84b.pdf", "url": "https://authors.library.caltech.edu/records/3dj2v-y2s66/files/FALjbc84b.pdf" }, "resource_type": "article", "pub_year": "1984", "author_list": "Falke, Joseph J.; Pace, R. J.; et el." }, { "id": "https://authors.library.caltech.edu/records/fpjd4-6cv83", "eprint_id": 13002, "eprint_status": "archive", "datestamp": "2023-08-19 16:45:03", "lastmod": "2023-10-17 21:42:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Falke-J-J", "name": { "family": "Falke", "given": "Joseph J." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Steiner-M", "name": { "family": "Steiner", "given": "Michael" } }, { "id": "Osterhelt-D", "name": { "family": "Oesterhelt", "given": "Dieter" } }, { "id": "Towner-P", "name": { "family": "Towner", "given": "Paul" } }, { "id": "Lanyi-J-K", "name": { "family": "Lanyi", "given": "Janos K." } } ] }, "title": "Halide binding by the purified halorhodopsin chromoprotein. II. New chloride-binding sites revealed by 35Cl NMR", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1984 by the American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, September 26, 1983) \n\nThis work is Contribution 6908 from the Arthur Amos Noyes Laboratory of Chemical Physics. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. \n\n[J.J.F. was] [s]upported by a National Science Foundation predoctoral fellowship. \n\n[S.I.C. was] [s]upported by National Institute of General Medical Sciences Grant GM-22432\n\nPublished - FALjbc84a.pdf
", "abstract": "Halorhodopsin is a light-driven chloride pump in the cell membrane of Halobacterium halobium. Recently, a polypeptide of apparent Mr = 20,000 has been purified that contains the halorhodopsin chromophore. Here we use 35Cl NMR to show that the purified chromoprotein possesses two previously unknown classes of chloride-binding sites. One class exhibits a low affinity (KD much greater than 1 M) for chloride and bromide. The second class exhibits a higher affinity (KD = 110 \u00b1 50 mM) for chloride and also binds other anions according to the affinity series I-, SCN- greater than Br-, NO-3 greater than Cl- greater than F- , citrate. Both classes of NMR site remain intact at pH 11, indicating that the essential positive charges are provided by arginine. Also, both classes are unaffected by bleaching, suggesting that the sites are not in the immediate vicinity of the halorhodopsin chromophore. Although the chromoprotein also appears to contain the chloride- transport site (Steiner, M., Oesterhelt, D., Ariki, M., and Lanyi, J. K. (1984) J. Biol. Chem. 259, 2179-2184), this site was not detected by 35Cl NMR, suggesting that the transport site is in the interior of the protein where it is sampled slowly by chloride in the medium. It is proposed that the purified chromoprotein possesses a channel leading from the medium to the transport site and that the channel contains the high affinity NMR site which facilitates the migration of chloride between the medium and the transport site. \n\nWe have also used 35Cl NMR to study chloride binding to purified monomeric bacteriorhodopsin; however, this protein contains no detectable chloride-binding sites.", "date": "1984-02-25", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "259", "number": "4", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "2185-2189", "id_number": "CaltechAUTHORS:FALjbc84a", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:FALjbc84a", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Predoctoral Fellowship" }, { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "6908", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "FALjbc84a.pdf", "url": "https://authors.library.caltech.edu/records/fpjd4-6cv83/files/FALjbc84a.pdf" }, "resource_type": "article", "pub_year": "1984", "author_list": "Falke, Joseph J.; Chan, Sunney I.; et el." }, { "id": "https://authors.library.caltech.edu/records/sxr15-7je06", "eprint_id": 12366, "eprint_status": "archive", "datestamp": "2023-08-22 03:14:01", "lastmod": "2023-10-17 16:42:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stevens-T-H", "name": { "family": "Stevens", "given": "Tom H." } }, { "id": "Martin-C-T", "name": { "family": "Martin", "given": "Craig T." } }, { "id": "Wang-Hsin", "name": { "family": "Wang", "given": "Hsin" } }, { "id": "Brudvig-G-W", "name": { "family": "Brudvig", "given": "Gary W." } }, { "id": "Scholes-C-P", "name": { "family": "Scholes", "given": "Charles P." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "The nature of CuA in cytochrome c oxidase", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1982 by the American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, February 18, 1982) \n\nWe are grateful to Drs. Hal Beilan and Doug Brown for their technical assistance in the synthesis of labeled cysteine in the early stages of this work. We are indebted to Dr. Savely Goldin for assistance in performing the ENDOR measurements and to Dr. Randall Morse for helpful discussions. \n\nThis paper is Contribution 6444 from the Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. \n\n[T.H.S. was the] [r]ecipient of National Research Service Award 5T32GM-07616 from the National Institute of General Medical Sciences. \n\n[C.P.S. was the] [r]ecipient of Grant AM-17884 from the National Institute of Arthritis, Metabolism, and Digestive Diseases, United States Public Health Service, Grant RR07122 from the Biomedical Research Support Grant Program, Division of Research Resources, National Institutes of Health, and National Institutes of Health Research Career Development Award 1K04 AM-00274. \n\n[S.I.C. was the] [r]ecipient of Grant GM-22432 from the National Institutes of General Medical Sciences and Biomedical Research Support Grant RR07003.\n\nPublished - STEjbc82.pdf
", "abstract": "The isolation and purification of yeast cytochrome c oxidase is described. Characterization of the purified protein indicates that it is spectroscopically identical with cytochrome c oxidase isolated from beef heart. Preparations of isotopically substituted yeast cytochrome c oxidase are obtained incorporating [1,3-15N2]histidine or [beta,beta- 2H2]cysteine. Electron paramagnetic resonance and electron nuclear double resonance spectra of the isotopically substituted proteins identify unambiguously at least 1 cysteine and 1 histidine as ligands to CuA and suggest that substantial spin density is delocalized onto a cysteine sulfur in the oxidized protein to render the site Cu(I)-S.", "date": "1982-10-25", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "257", "number": "20", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "12106-10113", "id_number": "CaltechAUTHORS:STEjbc82", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:STEjbc82", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "5T32GM-07616" }, { "agency": "NIH", "grant_number": "AM-17884" }, { "agency": "NIH", "grant_number": "RR07122" }, { "agency": "NIH", "grant_number": "1K04 AM-00274" }, { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NIH", "grant_number": "RR07003" }, { "agency": "National Institute of General Medical Sciences" }, { "agency": "National Institute of Arthritis, Metabolism, and Digestive Diseases" } ] }, "other_numbering_system": { "items": [ { "id": "6444", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "STEjbc82.pdf", "url": "https://authors.library.caltech.edu/records/sxr15-7je06/files/STEjbc82.pdf" }, "resource_type": "article", "pub_year": "1982", "author_list": "Stevens, Tom H.; Martin, Craig T.; et el." }, { "id": "https://authors.library.caltech.edu/records/aewr9-8ce72", "eprint_id": 11604, "eprint_status": "archive", "datestamp": "2023-08-22 02:37:51", "lastmod": "2023-10-17 15:09:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stevens-T-H", "name": { "family": "Stevens", "given": "Tom H." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Histidine is the axial ligand to cytochrome alpha 3 in cytochrome c oxidase", "ispublished": "pub", "full_text_status": "public", "note": "Copyright \u00a9 1981 by the American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, October 30, 1980) \n\nThis work was supported by Grant GM-22432 from the National Institute of General Medical Sciences, United States Public Health Service, by BRSG Grant RR07003 awarded by the Biomedical Research Support Grant Program, Division of Research Resources, National Institutes of Health, and by National Research Service Award 1T32 GM-07616 from the National Institute of General Medical Sciences. Contribution No. 6334 from the Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, Calif. 91125. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.\n\nPublished - STEjbc81.pdf
", "abstract": "The nitric oxide-bound complexes of reduced yeast cytochrome c oxidase incorporated with [1,3-15N2]histidine have been investigated by EPR spectroscopy. The results of this study have allowed the unambiguous identification of histidine as the endogenous axial ligand to cytochrome alpha 3.", "date": "1981-02-10", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "256", "number": "3", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "1069-1071", "id_number": "CaltechAUTHORS:STEjbc81", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:STEjbc81", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NIH", "grant_number": "BRSG RR07003" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "1T32 GM-0761" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "6334", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "primary_object": { "basename": "STEjbc81.pdf", "url": "https://authors.library.caltech.edu/records/aewr9-8ce72/files/STEjbc81.pdf" }, "resource_type": "article", "pub_year": "1981", "author_list": "Stevens, Tom H. and Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/4w75b-zne42", "eprint_id": 69623, "eprint_status": "archive", "datestamp": "2023-08-19 12:42:48", "lastmod": "2023-10-20 20:15:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bocian-D-F", "name": { "family": "Bocian", "given": "David F." } }, { "id": "Lemley-A-T", "name": { "family": "Lemley", "given": "Ann T." } }, { "id": "Petersen-N-O", "name": { "family": "Petersen", "given": "Nils O." } }, { "id": "Brudvig-G-W", "name": { "family": "Brudvig", "given": "Gary W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Resonance Raman Spectra of Cytochrome c Oxidase. Excitation in the 600-nm Region", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1979 American Chemical Society. \n\nReceived December 1, 1978. \n\nContribution No. 5906 from the Arthur Amos Noyes Laboratory of Chemical Physics (D.F.B., G. W.B., and S.J.C.)D.F.B., G.W.B., and S.I.C. were supported by Grant GM22432 from the National Institute of General Medical Sciences, U.S. Public Health Service, and by BRSG Grant RR07003 awarded by the Biomedical Research Support Grant Program, Division of Research Resources, National Institutes of Health. G.W.B. is a recipient of a National Institutes of Health predoctoral traineeship. A.T.L. was supported by Grant EY01377 awarded to Aaron Lewis by the National Eye Institute, U.S. Public Health Service. \n\nThe resonance Raman studies reported here were undertaken in the laboratory of Professor Aaron Lewis, whom we gratefully acknowledge. The authors also thank William Lambert for aiding in the studies of laser-induced photo reduction and Professor Ahmed Zewail for the use of the facilities in his laboratory.", "abstract": "The resonance Raman (RR) spectra of oxidized, reduced, and oxidized cyanide-bound cytochrome c oxidase with excitation at several wavelengths in the 600-nm region are presented. No evidence is found for laser-induced photoreduction of the oxidized protein with irradiation at \u03bb ~600 nm at 195 K, in contrast to the predominance of this process upon irradiation in the Soret region at this temperature. The Raman spectra of all three protein species are very similar, and there are no Raman bands which are readily assignable to either cytochrome a or cytochrome a3, exclusively. The Raman spectra of the three protein species do, however, exhibit a number of bands not observed in the RR spectra of other hemoproteins upon excitation in their visible absorption bands. In particular, strong Raman bands are observed in the lowf-requency region of the RR spectra ( <500 cm^-1). The frequencies of these bands are similar to those of the copper-ligand vibrations observed in the RR spectra of type 1 copper proteins upon excitation in the 600-nm absorption band characteristic of these proteins. In cytochrome c oxidase, these bands do not disappear upon reduction of the protein and, therefore, cannot be attributed to copper-ligand vibrations. Thus, all the observed RR bands are associated with the two heme A moieties in the enzyme.", "date": "1979-10", "date_type": "published", "publication": "Biochemistry", "volume": "18", "number": "20", "publisher": "American Chemical Society", "pagerange": "4396-4402", "id_number": "CaltechAUTHORS:20160815-122514293", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160815-122514293", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute of General Medical Sciences", "grant_number": "GM22432" }, { "agency": "NIH", "grant_number": "RR07003" }, { "agency": "NIH Predoctoral Fellowship" }, { "agency": "National Eye Institute", "grant_number": "EY01377" } ] }, "other_numbering_system": { "items": [ { "id": "5906", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "doi": "10.1021/bi00587a020", "resource_type": "article", "pub_year": "1979", "author_list": "Bocian, David F.; Lemley, Ann T.; et el." }, { "id": "https://authors.library.caltech.edu/records/274rg-pnz74", "eprint_id": 1498, "eprint_status": "archive", "datestamp": "2023-08-22 02:02:52", "lastmod": "2023-10-23 16:11:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stevens-T-H", "name": { "family": "Stevens", "given": "Tom H." } }, { "id": "Brudvig-G-W", "name": { "family": "Brudvig", "given": "Gary W." } }, { "id": "Bocian-D-F", "name": { "family": "Bocian", "given": "David F." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Structure of cytochrome a3-Cua3 couple in cytochrome c oxidase as revealed by nitric oxide binding studies", "ispublished": "pub", "full_text_status": "public", "keywords": "electron paramagnetic resonance; antiferromagnetic coupling; heme proteins; copper proteins; ferroheme-NO", "note": "\u00a9 1979 by the National Academy of Sciences. \n\nCommunicated by Harry B. Gray, April 23, 1979. \n\nWe thank Dr. Helmut Beinert for critical reviews of this manuscript and several useful discussions on its content. This work was partially supported by Grant GM 22432 from the National Institute of General Medical Sciences, U.S. Public Health Service, and by Grant RR07003 awarded by the Biomedical Research Support Grant Program, Division of Research Resources, National Institutes of Health. T.H.S. and G.W.B. are recipients of National Institutes of Health Predoctoral Traineeships. This is contribution no. 5918 from the Division of Chemistry and Chemical Engineering. \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 - STEpnas79.pdf
", "abstract": "The addition of NO to oxidized cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) causes the appearance of a high-spin heme electron paramagnetic resonance (EPR) signal due to cytochrome a3. This suggests that NO coordinates to Cu{a3}+2 and breaks the antiferromagnetic couple by forming a cytochrome a3+3-Cu{a3}+2-NO complex. The intensity of the high-spin cytochrome a3 signal depends on the method of preparation of the enzyme and maximally accounts for 58% of one heme. The effect of N3- on the cytochrome a3+3-Cu{a3}+2-NO complex is to reduce cytochrome a3 to the ferrous state, and this is followed by formation of a new complex that exhibits EPR signals characteristic of a triplet species. On the basis of optical and EPR results, a NO bridge between cytochrome a3+2 and Cu{a3}+2 is proposed-i.e., cytochrome a3+2-NO-Cu{a3}+2. The half-field transition observed at g = 4.34 in the EPR spectrum of this triplet species exhibits resolved copper hyperfine splittings with |A{}| = 0.020 cm-1, indicating that the Cu{a3}+2 in the cytochrome a3+2-NO-Cu{a3}+2 complex is similar to a type 2 copper site.", "date": "1979-07", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "76", "number": "7", "publisher": "National Academy of Sciences", "pagerange": "3320-3324", "id_number": "CaltechAUTHORS:STEpnas79", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:STEpnas79", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NIH", "grant_number": "RR07003" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "other_numbering_system": { "items": [ { "id": "5918", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "pmcid": "PMC383817", "primary_object": { "basename": "STEpnas79.pdf", "url": "https://authors.library.caltech.edu/records/274rg-pnz74/files/STEpnas79.pdf" }, "resource_type": "article", "pub_year": "1979", "author_list": "Stevens, Tom H.; Brudvig, Gary W.; et el." }, { "id": "https://authors.library.caltech.edu/records/zw8a5-xt896", "eprint_id": 11623, "eprint_status": "archive", "datestamp": "2023-08-22 01:51:07", "lastmod": "2023-10-17 15:15:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bocian-D-F", "name": { "family": "Bocian", "given": "David F." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "NMR studies of membrane structure and dynamics", "ispublished": "pub", "full_text_status": "public", "note": "\"Reprinted, with permission, from the Annual Review of Physical Chemistry, Volume 29 copyright 1978 by Annual Reviews, www.annualreviews.org\" \n\nThe authors gratefully acknowledge support by Grant No. 22432 from the National Institute of General Medical Sciences, US Public Health Service. This is contribution No. 5724 from the Division of Chemistry and Chemical Engineering.\n\nPublished - BOCarpc78.pdf
", "abstract": "Over the past decade, there has been considerable interest in the motional state of the phospholipid bilayer membrane. The motivation underlying these efforts has been the contention that the phospholipid bilayer is the basic matrix in which membrane proteins are embedded to form the biological membrane, and that the permeability and mechanical properties of the membrane, as well as the enzymatic activity of membrane proteins, are dependent upon the fluidity of the bilayer, especially the motional state of the hydrocarbon chains.", "date": "1978-10", "date_type": "published", "publication": "Annual Review of Physical Chemistry", "volume": "29", "publisher": "Annual Reviews", "pagerange": "307-335", "id_number": "CaltechAUTHORS:BOCarpc78", "issn": "0066-426X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:BOCarpc78", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "National Institute of General Medical Sciences" } ] }, "other_numbering_system": { "items": [ { "id": "5724", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "doi": "10.1146/annurev.pc.29.100178.001515", "primary_object": { "basename": "BOCarpc78.pdf", "url": "https://authors.library.caltech.edu/records/zw8a5-xt896/files/BOCarpc78.pdf" }, "resource_type": "article", "pub_year": "1978", "author_list": "Bocian, David F. and Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/8xc9m-3en80", "eprint_id": 1493, "eprint_status": "archive", "datestamp": "2023-08-22 01:32:07", "lastmod": "2023-10-23 16:10:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Valerie-W", "name": { "family": "Hu", "given": "Valerie W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Brown-G-S", "name": { "family": "Brown", "given": "George S." } } ] }, "title": "X-ray absorption edge studies on oxidized and reduced cytochrome c oxidase", "ispublished": "pub", "full_text_status": "public", "keywords": "copper oxidation states; absorption edge fine structure; model copper compounds; core electronic transitions; synchrotron radiation", "note": "\u00a9 1977 by the National Academy of Sciences. \n\nCommunicated by Harry B. Gray, June 23, 1977. \n\nThis research would not have been possible without the overwhelming generosity of several people. Drs. Tsoo E. King, Chang-An Yu, and Linda Yu of the State University of New York at Albany generously supplied us with purified and concentrated cytochrome c oxidase. Drs. Robert Gagne and Harry Gray and Mr. Dave Dooley provided us with many of the model compounds referred to in this paper. Dr. William Blumberg made available to us his data on several model compounds prior to publication. To all these individuals, we are extremely grateful. We would also like to thank Drs. W. E. Blumberg, R. Gamble, H. B. Gray, and R. G. Shulman for many stimulating discussions and their continued interest and encouragement throughout this work. This work was partially supported by Grant 22432 from the National Institute of General Medical Sciences, U.S. Public Health Service, and by National Science Foundation Grant DMR73-07692, in cooperation with the Stanford Linear Accelerator Center and the U.S. Energy Research and Development Administration. V.W.H. is a recipient of a National Institutes of Health predoctoral traineeship. This is Contribution no. 5551 from the Division of Chemistry and Chemical Engineering. \n\nThe costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U. S. C. \u00a71734 solely to indicate this fact.\n\nPublished - HUVpnas77.pdf
", "abstract": "The x-ray absorption edge spectra of the Cu and Fe centers in oxidized and reduced cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase; EC 1.9.3.1) have been obtained using synchrotron radiation from the SPEAR storage ring at the Stanford Linear Accelerator Center. In addition, oxidized and reduced plastocyanin as well as a number of model copper compounds in various oxidation states were also examined. A comparison of the absorption edge fine structure of cytochrome oxidase with those of the models indicates that one of the two coppers in the oxidized protein is in the + 1 oxidation state. Upon reduction of the protein with dithionite, the second copper becomes Cu(I). The shift in the Fe K-edge of cytochrome oxidase upon reduction is small (about 2 eV or 3 x 10(-19) J) and is comparable to that previously observed for the reduction of the heme iron of cytochrome c.", "date": "1977-09", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "74", "number": "9", "publisher": "National Academy of Sciences", "pagerange": "3821-3825", "id_number": "CaltechAUTHORS:HUVpnas77", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HUVpnas77", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-22432" }, { "agency": "NSF", "grant_number": "DMR73-07692" }, { "agency": "Energy Research and Development Administration (ERDA)" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "other_numbering_system": { "items": [ { "id": "5551", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "pmcid": "PMC431745", "primary_object": { "basename": "HUVpnas77.pdf", "url": "https://authors.library.caltech.edu/records/8xc9m-3en80/files/HUVpnas77.pdf" }, "resource_type": "article", "pub_year": "1977", "author_list": "Hu, Valerie W.; Chan, Sunney I.; et el." }, { "id": "https://authors.library.caltech.edu/records/jawx3-8aj13", "eprint_id": 1126, "eprint_status": "archive", "datestamp": "2023-08-22 00:49:36", "lastmod": "2023-10-23 16:04:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lau-Arthur-L-Y", "name": { "family": "Lau", "given": "Arthur L. Y." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "Alamethicin-mediated fusion of lecithin vesicles", "ispublished": "pub", "full_text_status": "public", "keywords": "nuclear magnetic resonance, model membranes, antibiotics, ion transport across membranes, voltage gateable ion channels", "note": "\u00a9 1975 by the National Academy of Sciences. \n\nCommunicated by John D. Baldeschwieler, March 19, 1975. \n\nWe thank Dr. G. B. Whitfield, Jr., of the Upjohn Co., Kalamazoo, Mich., for his generous gift of two 25-mg samples of alamethicin which made this and other related studies possible. This work was supported by Grant no. GM-14523-09 from the National Institute of General Medical Sciences, U.S. Public Health Service. A.L.Y.L. is a Danforth Predoctoral Fellow, 1971-1975. This is Contribution no. 5049.\n\nPublished - LAUpnas75.pdf
", "abstract": "It was recently shown that alamethicin greatly facilitates the fusion of small, sonicated, lecithin bilayer vesicles. In the present work the details of this fusion process have been followed by monitoring the inner and outer choline methyl signals separately by proton magnetic resonance spectroscopy. It is shown that during the alamethicin-induced fusion some of the antibiotic molecules become translocated from the extravesicular aqueous medium into the enclosed intravesicular space, and these alamethicin molecules were found to affect the choline methyl signals from the inner half of the bilayer only. No evidence was obtained for transmembrane coupling of the two halves of the bilayer in the presence of alamethicin or for any effects that might be construed as due to incorporation of alamethicin molecules into the hydrophobic core of the bilayer.", "date": "1975-06", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "72", "number": "6", "publisher": "National Academy of Sciences", "pagerange": "2170-2174", "id_number": "CaltechAUTHORS:LAUpnas75", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:LAUpnas75", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-14523-09" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "other_numbering_system": { "items": [ { "id": "5049", "name": "Caltech Division of Chemistry and Chemical Engineering" } ] }, "pmcid": "PMC432718", "primary_object": { "basename": "LAUpnas75.pdf", "url": "https://authors.library.caltech.edu/records/jawx3-8aj13/files/LAUpnas75.pdf" }, "resource_type": "article", "pub_year": "1975", "author_list": "Lau, Arthur L. Y. and Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/hxqas-ryv07", "eprint_id": 59045, "eprint_status": "archive", "datestamp": "2023-08-19 07:48:51", "lastmod": "2023-10-23 20:00:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dea-Phoebe", "name": { "family": "Dea", "given": "Phoebe" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Dea-F-J", "name": { "family": "Dea", "given": "Frank J." } } ] }, "title": "High-Resolution Proton Magnetic Resonance Spectra of a Rabbit Sciatic Nerve", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1972 American Association for the Advancement of Science.\n\nReceived 23 August 1971.\n\nSupported in part by grant GM-14523 from the U.S. Public Health Service and grant GP-8540 from the National Science Foundation. \n\nContribution No. 4315 from the Noyes Laboratory of Chemical Physics.", "abstract": "Proton magnetic resonance spectra (220-megahertz field) of an isolated rabbit sciatic nerve in its native state have been observed and assigned to the extracellular water, intracellular water, and phospholipids of the nerve. This study indicates that the nerve fibers contain fluid-like hydrophobic regions, in agreement with the results of recent electron spin resonance spin-labeled studies of excitable membranes of nerve and muscle.", "date": "1972-01-14", "date_type": "published", "publication": "Science", "volume": "175", "number": "4018", "publisher": "American Association for the Advancement of Science", "pagerange": "206-209", "id_number": "CaltechAUTHORS:20150728-154738893", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150728-154738893", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-14523" }, { "agency": "NSF", "grant_number": "GP-8540" } ] }, "other_numbering_system": { "items": [ { "id": "4315", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "doi": "10.1126/science.175.4018.206", "resource_type": "article", "pub_year": "1972", "author_list": "Dea, Phoebe; Chan, Sunney I.; et el." }, { "id": "https://authors.library.caltech.edu/records/pgbs8-k0b57", "eprint_id": 1225, "eprint_status": "archive", "datestamp": "2023-08-21 23:55:52", "lastmod": "2023-10-23 15:56:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Lin-L", "name": { "family": "Lin", "given": "L." } }, { "id": "Clutter-D", "name": { "family": "Clutter", "given": "Dale" } }, { "id": "Dea-Phoebe", "name": { "family": "Dea", "given": "Phoebe" } } ] }, "title": "The anomalous deuterium isotope effect on the chemical shift of the bridge hydrogen in the enol tautomer of 2,4-pentanedione", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1970 by the National Academy of Sciences. \n\nCommunicated by John D. Roberts, January 29, 1970. \n\nWe wish to gratefully acknowledge the financial support of this research by the U.S. Public Health Service (grant GM-13212) and the National Science Foundation (grant GP-8540).\n\nPublished - CHApnas70.pdf
", "abstract": "The nature of the intramolecular hydrogen bond in the enol tautomer of 2,4-pentanedione has been investigated by high resolution proton and deuteron magnetic resonance spectroscopy. An unusually large deuterium isotope effect on the chemical shift of the bridge hydrogen has been observed. This unexpected result, together with the observation of a pronounced temperature dependence for both the proton and deuteron resonances, suggests that two states with different chemical shifts for the bridge hydrogen are involved in rapid equilibrium and that the anomalous deuterium isotope effect has its origin in the effect of deuterium substitution on the energy separation between these states. It is proposed that these states correspond to the symmetrical and asymmetrical structures of the intramolecular hydrogen bond.", "date": "1970-04", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "65", "number": "4", "publisher": "National Academy of Sciences", "pagerange": "816-822", "id_number": "CaltechAUTHORS:CHApnas70", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHApnas70", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-13212" }, { "agency": "NSF", "grant_number": "GP-8540" } ] }, "pmcid": "PMC282988", "primary_object": { "basename": "CHApnas70.pdf", "url": "https://authors.library.caltech.edu/records/pgbs8-k0b57/files/CHApnas70.pdf" }, "resource_type": "article", "pub_year": "1970", "author_list": "Chan, Sunney I.; Lin, L.; et el." }, { "id": "https://authors.library.caltech.edu/records/zrahm-1f790", "eprint_id": 8966, "eprint_status": "archive", "datestamp": "2023-08-21 23:55:20", "lastmod": "2023-10-23 15:55:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Glaser-M", "name": { "family": "Glaser", "given": "Michael" } }, { "id": "Simpkins-H", "name": { "family": "Simpkins", "given": "Henry" } }, { "id": "Singer-S-J", "name": { "family": "Singer", "given": "S. J." } }, { "id": "Sheetz-M", "name": { "family": "Sheetz", "given": "Michael" } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "On the interactions of lipids and proteins in the red blood cell membrane", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1970 by the National Academy of Sciences. \n\nCommunicated December 12, 1969. \n\nThis work was supported in part by U.S.P.H.S. grant GM-15971 to S.J. Singer and U.S.P.H.S. grant GM-14523 and NSF grant GP-8540 to S.I. Chan (Caltech). \n\n[M.S. was a] National Institute of Health Predoctoral Trainee, 1969-1970. \n\nA.A. Noyes Laboratory of Chemical Physics, Contribution No. 3977.\n\nPublished - GLApnas70.pdf
", "abstract": "The effects of temperature and of the action of a purified phospholipase C enzyme preparation on human red blood cell membranes has been investigated by chemical analyses, circular dichroism, and proton magnetic resonance measurements. The results indicate that a substantial fraction of the phospholipids and the proteins of the membranes can change structure independently of one another, suggesting a mosaic pattern for the organization of the lipids and proteins in membranes.", "date": "1970-03", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "65", "number": "3", "publisher": "National Academy of Sciences", "pagerange": "721-728", "id_number": "CaltechAUTHORS:GLApnas70", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:GLApnas70", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship" }, { "agency": "NIH", "grant_number": "GM-15971" }, { "agency": "NIH", "grant_number": "GM-14523" }, { "agency": "NSF", "grant_number": "GP-8540" } ] }, "other_numbering_system": { "items": [ { "id": "3977", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "pmcid": "PMC282966", "primary_object": { "basename": "GLApnas70.pdf", "url": "https://authors.library.caltech.edu/records/zrahm-1f790/files/GLApnas70.pdf" }, "resource_type": "article", "pub_year": "1970", "author_list": "Glaser, Michael; Simpkins, Henry; et el." }, { "id": "https://authors.library.caltech.edu/records/70kbr-19m67", "eprint_id": 54721, "eprint_status": "archive", "datestamp": "2023-08-19 07:00:09", "lastmod": "2023-10-20 20:08:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Manatt-S", "name": { "family": "Manatt", "given": "Stanley" } }, { "id": "Elleman-D-D", "name": { "family": "Elleman", "given": "Daniel D." } }, { "id": "Vaughan-R-W", "name": { "family": "Vaughan", "given": "Robert W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Tsay-Fun-Dow", "name": { "family": "Tsay", "given": "Fun-Dow" } }, { "id": "Huntress-W-T-Jr", "name": { "family": "Huntress", "given": "Wesley T., Jr." } } ] }, "title": "Magnetic Resonance Studies of Lunar Samples", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1970 American Association for the Advancement of Science.\n\n4 January 1970.\n\nWe thank D. B. Nash, M. M. Neugebauer, E. M. Bollin, P. C. Lauterbur for their many helpful discussions. I his paper is contribution No. 3998 from the Division of Chemistry and Chemical Engineering, California Institute of Technology. Sponsored under NASA contract No. NAS 7-100.", "abstract": "Electron spin resonance searches at 9.5 gigahertz on several fines samples and portions of several rocks have yielded signals whose lineshapes and temperature dependences show that the samples are principally ferromagnetic in nature. Proton magnetic resonance searches at 60 megahertz of these samples have not revealed any signals ascribable to water or any other types of hydrogen in concentrations greater than 0.0001 percent by weight contained in narrow lines (5 oersteds wide or less) and 0.01 percent by weight in wide lines (as wide as 100 oersteds).", "date": "1970-01-30", "date_type": "published", "publication": "Science", "volume": "167", "number": "3918", "publisher": "American Association for the Advancement of Science", "pagerange": "709-711", "id_number": "CaltechAUTHORS:20150211-111941293", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150211-111941293", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NASA", "grant_number": "NAS 7-100" } ] }, "other_numbering_system": { "items": [ { "id": "3998", "name": "Caltech DIvision of Chemistry and Chemical Engineering" } ] }, "doi": "10.1126/science.167.3918.709", "resource_type": "article", "pub_year": "1970", "author_list": "Manatt, Stanley; Elleman, Daniel D.; et el." }, { "id": "https://authors.library.caltech.edu/records/demyy-dq489", "eprint_id": 9403, "eprint_status": "archive", "datestamp": "2023-08-21 23:44:18", "lastmod": "2023-10-16 22:11:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Raftery-M-A", "name": { "family": "Raftery", "given": "M. A." } }, { "id": "Dahlquist-F-W", "name": { "family": "Dahlquist", "given": "F. W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "S. I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Parsons-S-M", "name": { "family": "Parsons", "given": "S. M." } } ] }, "title": "A Proton Magnetic Resonance Study of the Association of Lysozyme with Monosaccharide Inhibitors", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1968 by the American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, February 2, 1968) \n\nContribution 3645 from the Gates and Crellin Laboratories of Chemistry, California Institute of Technology. This research was supported by United States Public Health Service Grants GM-14452-01 and GM-14523-02. \n\n[F.W.D. and S.M.P. were] National Institutes of Health Trainee[s] 1967-1968. \n\n[S.I.C. was an] Alfred P. Sloan Fellow. \n\nA preliminary account of the work described here was presented at the Gordon Research Conference on Proteins, New Hampton School, New Hampshire, June 27, 1966.\n\nPublished - RAFjbc68.pdf
", "abstract": "It has been shown that the acetamido methyl protons of N-acetyl-d-glucosamine undergo a chemical shift to higher fields in their proton magnetic resonance spectrum when the inhibitor is bound to lysozyme. The observed chemical shift in the presence of the enzyme is different for the agr- and \u00df-anomeric forms of 2-acetamido-2-deoxy-d-glucopyranose indicating either a difference in the affinity of the anomeric forms for lysozyme or different magnetic environments for the methyl protons in their enzyme-bound state. That the agr- and \u00df-anomeric forms of GlcAc bind to lysozyme in a competitive fashion was indicated by observing the proton magnetic resonance spectra in the presence of 2-acetamido-d3-2-deoxy-agr-d-glucopyranose. The methyl glycosides, methyl-agr-GlcAc and methyl-\u00df-GlcAc, were also shown to bind competitively with both anomers of GlcAc. Quantitative analysis of the chemical shift data observed for the association of GlcAc with lysozyme was complicated by the mutarotation of GlcAc between its agr- and \u00df-anomeric forms. However, in the case of the methyl glucosides, where the conformation of each anomer is frozen, it was possible to analyze the chemical shift data in a straightforward manner, and the dissociation constant as well as the chemical shift of the acetamido methyl protons of the enzyme-inhibitor complex was determined for both anomers. The results indicate that the two anomers of methyl-GlcAc bind to lysozyme with slightly different affinities but that the acetamido methyl groups of both anomers experience identical magnetic environments in the enzyme-inhibitor complex.", "date": "1968-08-25", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "243", "number": "16", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "4175-4180", "id_number": "CaltechAUTHORS:RAFjbc68", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:RAFjbc68", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-14452-01" }, { "agency": "NIH", "grant_number": "GM-14523-02" }, { "agency": "NIH Predoctoral Fellowship" } ] }, "other_numbering_system": { "items": [ { "id": "3645", "name": "Gates and Crellin Laboratories of Chemistry" } ] }, "primary_object": { "basename": "RAFjbc68.pdf", "url": "https://authors.library.caltech.edu/records/demyy-dq489/files/RAFjbc68.pdf" }, "resource_type": "article", "pub_year": "1968", "author_list": "Raftery, M. A.; Dahlquist, F. W.; et el." }, { "id": "https://authors.library.caltech.edu/records/62nvm-x8f60", "eprint_id": 723, "eprint_status": "archive", "datestamp": "2023-08-21 23:44:13", "lastmod": "2023-10-23 15:58:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bangerter-B-W", "name": { "family": "Bangerter", "given": "Benedict W." } }, { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" } ] }, "title": "A Proton Magnetic Resonance Study of The Interaction of Adenosine with Polyuridylic Acid: Evidence for Both Adenine-Uracil Base-Stacking and Base-Pairing", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1968 by the National Academy of Sciences \n\nCommunicated by Norman Davidson, May 15, 1968 \n\nThis work was supported in part by grant GM-14523-02, U.S. Public Health Service. \n\nNoyes Laboratory of Chemical Physics, Contribution no. 3676.\n\nPublished - BANpnas68.pdf
", "abstract": "We report here a proton magnetic resonance (pmr) study of the interaction of adenosine with polyuridylic acid in aqueous solution. The results of this study indicate that the mode of interaction is adenosine intercalation and adenine-uracil base-stacking above 26[degrees]C, and verifies that a triple-stranded complex which is stabilized by both adenine-uracil hydrogen-bonding and adenine-adenine base-stacking is formed below this temperature. Some information regarding the dynamics of these processes has also been obtained.", "date": "1968-08-15", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "60", "number": "4", "publisher": "National Academy of Sciences", "pagerange": "1144-1151", "id_number": "CaltechAUTHORS:BANpnas68", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:BANpnas68", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-14523-02" } ] }, "other_numbering_system": { "items": [ { "id": "3676", "name": "Arthur Amos Noyes Laboratory of Chemical Physics" } ] }, "pmcid": "PMC224893", "primary_object": { "basename": "BANpnas68.pdf", "url": "https://authors.library.caltech.edu/records/62nvm-x8f60/files/BANpnas68.pdf" }, "resource_type": "article", "pub_year": "1968", "author_list": "Bangerter, Benedict W. and Chan, Sunney I." }, { "id": "https://authors.library.caltech.edu/records/swpw1-eqv66", "eprint_id": 949, "eprint_status": "archive", "datestamp": "2023-08-21 23:29:41", "lastmod": "2023-10-23 15:58:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chan-S-I", "name": { "family": "Chan", "given": "Sunney I." }, "orcid": "0000-0002-5348-2723" }, { "id": "Bangerter-B-W", "name": { "family": "Bangerter", "given": "Benedict W." } }, { "id": "Peter-H-H", "name": { "family": "Peter", "given": "Heinrich H." } } ] }, "title": "Purine binding to dinucleotides: Evidence for base stacking and insertion", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1966 by the National Academy of Sciences. \n\nCommunicated by John D. Roberts, February 24, 1966.\n \nGates and Crellin Laboratories of Chemistry, Contribution no. 3321\n\nPublished - CHApnas66.pdf
", "abstract": "In an effort to understand the factors which may contribute to the stabilization of nucleic acids as well as the basic mechanism of the recognition process involved in the enzymatic replication of nucleic acids in vitro, we have embarked upon a systematic study of the interaction of biological bases and nucleosides with simple oligonucleotides by proton magnetic resonance. We wish to report here results which we have obtained on the interaction of purine with the following 3' --> 5'-dinucleotides: TpT, TpdU, and dUpT (T = thymidine, dU = 2'-deoxyuridine).", "date": "1966-04-15", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "55", "number": "4", "publisher": "National Academy of Sciences", "pagerange": "720-727", "id_number": "CaltechAUTHORS:CHApnas66", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:CHApnas66", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "other_numbering_system": { "items": [ { "id": "3321", "name": "Gates and Crellin Laboratories of Chemistry" } ] }, "pmcid": "PMC224219", "primary_object": { "basename": "CHApnas66.pdf", "url": "https://authors.library.caltech.edu/records/swpw1-eqv66/files/CHApnas66.pdf" }, "resource_type": "article", "pub_year": "1966", "author_list": "Chan, Sunney I.; Bangerter, Benedict W.; et el." } ]