1
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Murali R, Pace LA, Sanford RA, Ward LM, Lynes MM, Hatzenpichler R, Lingappa UF, Fischer WW, Gennis RB, Hemp J. Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proc Natl Acad Sci U S A 2024; 121:e2316422121. [PMID: 38900790 PMCID: PMC11214002 DOI: 10.1073/pnas.2316422121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/24/2024] [Indexed: 06/22/2024] Open
Abstract
Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.
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Affiliation(s)
- Ranjani Murali
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV89154
| | - Laura A. Pace
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
- meliora.bio, Salt Lake City, UT84103
| | - Robert A. Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - L. M. Ward
- Department of Geosciences, Smith College, Northampton, MA01063
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Mackenzie M. Lynes
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT59717
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT59717
| | - Usha F. Lingappa
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720
| | - Woodward W. Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
| | - James Hemp
- meliora.bio, Salt Lake City, UT84103
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
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2
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Noodleman L, Götz AW, Han Du WG, Hunsicker-Wang L. Reaction pathways, proton transfer, and proton pumping in ba3 class cytochrome c oxidase: perspectives from DFT quantum chemistry and molecular dynamics. Front Chem 2023; 11:1186022. [PMID: 38188931 PMCID: PMC10766771 DOI: 10.3389/fchem.2023.1186022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
After drawing comparisons between the reaction pathways of cytochrome c oxidase (CcO, Complex 4) and the preceding complex cytochrome bc1 (Complex 3), both being proton pumping complexes along the electron transport chain, we provide an analysis of the reaction pathways in bacterial ba3 class CcO, comparing spectroscopic results and kinetics observations with results from DFT calculations. For an important arc of the catalytic cycle in CcO, we can trace the energy pathways for the chemical protons and show how these pathways drive proton pumping of the vectorial protons. We then explore the proton loading network above the Fe heme a3-CuB catalytic center, showing how protons are loaded in and then released by combining DFT-based reaction energies with molecular dynamics simulations over states of that cycle. We also propose some additional reaction pathways for the chemical and vector protons based on our recent work with spectroscopic support.
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Affiliation(s)
- Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, United States
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
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3
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Safari C, Ghosh S, Andersson R, Johannesson J, Båth P, Uwangue O, Dahl P, Zoric D, Sandelin E, Vallejos A, Nango E, Tanaka R, Bosman R, Börjesson P, Dunevall E, Hammarin G, Ortolani G, Panman M, Tanaka T, Yamashita A, Arima T, Sugahara M, Suzuki M, Masuda T, Takeda H, Yamagiwa R, Oda K, Fukuda M, Tosha T, Naitow H, Owada S, Tono K, Nureki O, Iwata S, Neutze R, Brändén G. Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. SCIENCE ADVANCES 2023; 9:eadh4179. [PMID: 38064560 PMCID: PMC10708180 DOI: 10.1126/sciadv.adh4179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.
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Affiliation(s)
- Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Jonatan Johannesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Owens Uwangue
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Doris Zoric
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Emil Sandelin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Per Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Matthijs Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Toshi Arima
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mamoru Suzuki
- Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Japan
| | - Hanae Takeda
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Raika Yamagiwa
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kazumasa Oda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
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Shimada A, Baba J, Nagao S, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S. Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons. J Biol Chem 2023; 299:105277. [PMID: 37742916 PMCID: PMC10598403 DOI: 10.1016/j.jbc.2023.105277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
Cytochrome c oxidase (CcO) reduces O2 in the O2-reduction site by sequential four-electron donations through the low-potential metal sites (CuA and Fea). Redox-coupled X-ray crystal structural changes have been identified at five distinct sites including Asp51, Arg438, Glu198, the hydroxyfarnesyl ethyl group of heme a, and Ser382, respectively. These sites interact with the putative proton-pumping H-pathway. However, the metal sites responsible for each structural change have not been identified, since these changes were detected as structural differences between the fully reduced and fully oxidized CcOs. Thus, the roles of these structural changes in the CcO function are yet to be revealed. X-ray crystal structures of cyanide-bound CcOs under various oxidation states showed that the O2-reduction site controlled only the Ser382-including site, while the low-potential metal sites induced the other changes. This finding indicates that these low-potential site-inducible structural changes are triggered by sequential electron-extraction from the low-potential sites by the O2-reduction site and that each structural change is insensitive to the oxidation and ligand-binding states of the O2-reduction site. Because the proton/electron coupling efficiency is constant (1:1), regardless of the reaction progress in the O2-reduction site, the structural changes induced by the low-potential sites are assignable to those critically involved in the proton pumping, suggesting that the H-pathway, facilitating these low-potential site-inducible structural changes, pumps protons. Furthermore, a cyanide-bound CcO structure suggests that a hypoxia-inducible activator, Higd1a, activates the O2-reduction site without influencing the electron transfer mechanism through the low-potential sites, kinetically confirming that the low-potential sites facilitate proton pump.
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Affiliation(s)
- Atsuhiro Shimada
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Jumpei Baba
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Shuhei Nagao
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Kyoko Shinzawa-Itoh
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kazumasa Muramoto
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan.
| | - Tomitake Tsukihara
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
| | - Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan.
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5
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Yang X, Liu S, Yin Z, Chen M, Song J, Li P, Yang L. New insights into the proton pumping mechanism of ba 3 cytochrome c oxidase: the functions of key residues and water. Phys Chem Chem Phys 2023; 25:25105-25115. [PMID: 37461851 DOI: 10.1039/d3cp01334k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
As the terminal oxidase of cell respiration in mitochondria and aerobic bacteria, the proton pumping mechanism of ba3-type cytochrome c oxidase (CcO) of Thermus thermophiles is still not fully understood. Especially, the functions of key residues which were considered as the possible proton loading sites (PLSs) above the catalytic center, as well as water located above and within the catalytic center, remain unclear. In this work, molecular dynamic simulations were performed on a set of designed mutants of key residues (Asp287, Asp372, His376, and Glu126II). The results showed that Asp287 may not be a PLS, but it could modulate the ability of the proton transfer pathway to transfer protons through its salt bridge with Arg225. Maintaining the closed state of the water pool above the catalytic center is necessary for the participation of inside water molecules in proton transfer. Water molecules inside the water pool can form hydrogen bond chains with PLS to facilitate proton transfer. Additional quantum cluster models of the Fe-Cu metal catalytic center are established, indicating that when the proton is transferred from Tyr237, it is more likely to reach the OCu atom directly through only one water molecule. This work provides a more profound understanding of the functions of important residues and specific water molecules in the proton pumping mechanism of CcO.
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Affiliation(s)
- Xiaoyue Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
| | - Shaohui Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
| | - Zhili Yin
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
| | - Mengguo Chen
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
| | - Jinshuai Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Henan 450001, China
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, Illinois 60660, USA
| | - Longhua Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
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6
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Flynn AJ, Antonyuk SV, Eady RR, Muench SP, Hasnain SS. A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Nat Commun 2023; 14:3416. [PMID: 37296134 PMCID: PMC10256718 DOI: 10.1038/s41467-023-39140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.
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Affiliation(s)
- Alex J Flynn
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Robert R Eady
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England.
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7
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Zatloukalova M, Poltorak L, Bilewicz R, Vacek J. Lipid-based liquid crystalline materials in electrochemical sensing and nanocarrier technology. Mikrochim Acta 2023; 190:187. [PMID: 37071228 PMCID: PMC10113356 DOI: 10.1007/s00604-023-05727-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/02/2023] [Indexed: 04/19/2023]
Abstract
Some biologically active substances are unstable and poorly soluble in aqueous media, at the same time exhibiting low bioavailability. The incorporation of these biologically active compounds into the structure of a lipid-based lyotropic liquid crystalline phase or nanoparticles can increase or improve their stability and transport properties, subsequent bioavailability, and applicability in general. The aim of this short overview is (1) to clarify the principle of self-assembly of lipidic amphiphilic molecules in an aqueous environment and (2) to present lipidic bicontinuous cubic and hexagonal phases and their current biosensing (with a focus on electrochemical protocols) and biomedical applications.
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Affiliation(s)
- Martina Zatloukalova
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15, Olomouc, Czech Republic.
| | - Lukasz Poltorak
- Electrochemistry@Soft Interfaces Team, Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, 91-403, Lodz, Poland
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15, Olomouc, Czech Republic.
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Muramoto K, Shinzawa-Itoh K. Calcium-bound structure of bovine cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148956. [PMID: 36708913 DOI: 10.1016/j.bbabio.2023.148956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
The crystal structure of bovine cytochrome c oxidase (CcO) shows a sodium ion (Na+) bound to the surface of subunit I. Changes in the absorption spectrum of heme a caused by calcium ions (Ca2+) are detected as small red shifts, and inhibition of enzymatic activity under low turnover conditions is observed by addition of Ca2+ in a competitive manner with Na+. In this study, we determined the crystal structure of Ca2+-bound bovine CcO in the oxidized and reduced states at 1.7 Å resolution. Although Ca2+ and Na+ bound to the same site of oxidized and reduced CcO, they led to different coordination geometries. Replacement of Na+ with Ca2+ caused a small structural change in the loop segments near the heme a propionate and formyl groups, resulting in spectral changes in heme a. Redox-coupled structural changes observed in the Ca2+-bound form were the same as those previously observed in the Na+-bound form, suggesting that binding of Ca2+ does not severely affect enzymatic function, which depends on these structural changes. The relation between the Ca2+ binding and the inhibitory effect during slow turnover, as well as the possible role of bound Ca2+ are discussed.
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Affiliation(s)
- Kazumasa Muramoto
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.
| | - Kyoko Shinzawa-Itoh
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.
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9
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Structures of the intermediates in the catalytic cycle of mitochondrial cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148933. [PMID: 36403794 DOI: 10.1016/j.bbabio.2022.148933] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
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10
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Azarkina NV, Borisov VB, Oleynikov IP, Sudakov RV, Vygodina TV. Interaction of Terminal Oxidases with Amphipathic Molecules. Int J Mol Sci 2023; 24:ijms24076428. [PMID: 37047401 PMCID: PMC10095113 DOI: 10.3390/ijms24076428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
The review focuses on recent advances regarding the effects of natural and artificial amphipathic compounds on terminal oxidases. Terminal oxidases are fascinating biomolecular devices which couple the oxidation of respiratory substrates with generation of a proton motive force used by the cell for ATP production and other needs. The role of endogenous lipids in the enzyme structure and function is highlighted. The main regularities of the interaction between the most popular detergents and terminal oxidases of various types are described. A hypothesis about the physiological regulation of mitochondrial-type enzymes by lipid-soluble ligands is considered.
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Affiliation(s)
- Natalia V Azarkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
| | - Vitaliy B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
| | - Ilya P Oleynikov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
| | - Roman V Sudakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
| | - Tatiana V Vygodina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld. 40, 119992 Moscow, Russia
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11
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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12
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Ishigami I, Russi S, Cohen A, Yeh SR, Rousseau DL. Temperature-dependent structural transition following X-ray-induced metal center reduction in oxidized cytochrome c oxidase. J Biol Chem 2022; 298:101799. [PMID: 35257742 PMCID: PMC8971940 DOI: 10.1016/j.jbc.2022.101799] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022] Open
Abstract
Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain in the inner membrane of mitochondria. It contains four metal redox centers, two of which, CuB and heme a3, form the binuclear center (BNC), where dioxygen is reduced to water. Crystal structures of CcO in various forms have been reported, from which ligand-binding states of the BNC and conformations of the protein matrix surrounding it have been deduced to elucidate the mechanism by which the oxygen reduction chemistry is coupled to proton translocation. However, metal centers in proteins can be susceptible to X-ray-induced radiation damage, raising questions about the reliability of conclusions drawn from these studies. Here, we used microspectroscopy-coupled X-ray crystallography to interrogate how the structural integrity of bovine CcO in the fully oxidized state (O) is modulated by synchrotron radiation. Spectroscopic data showed that, upon X-ray exposure, O was converted to a hybrid O∗ state where all the four metal centers were reduced, but the protein matrix was trapped in the genuine O conformation and the ligands in the BNC remained intact. Annealing the O∗ crystal above the glass transition temperature induced relaxation of the O∗ structure to a new R∗ structure, wherein the protein matrix converted to the fully reduced R conformation with the exception of helix X, which partly remained in the O conformation because of incomplete dissociation of the ligands from the BNC. We conclude from these data that reevaluation of reported CcO structures obtained with synchrotron light sources is merited.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Silvia Russi
- Structural Molecular Biology, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA
| | - Aina Cohen
- Structural Molecular Biology, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
| | - Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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13
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Du WGH, Götz AW, Noodleman L. Mössbauer Property Calculations on Fea33+∙∙∙H2O∙∙∙CuB2+ Dinuclear Center Models of the Resting Oxidized as-Isolated Cytochrome c Oxidase. Chemphyschem 2022; 23:e202100831. [PMID: 35142420 PMCID: PMC9054037 DOI: 10.1002/cphc.202100831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/03/2022] [Indexed: 11/24/2022]
Abstract
Mössbauer isomer shift and quadrupole splitting properties have been calculated using the OLYP‐D3(BJ) density functional method on previously obtained (W.‐G. Han Du, et al., Inorg Chem. 2020, 59, 8906–8915) geometry optimized Fea33+−H2O−CuB2+ dinuclear center (DNC) clusters of the resting oxidized (O state) “as‐isolated” cytochrome c oxidase (CcO). The calculated results are highly consistent with the available experimental observations. The calculations have also shown that the structural heterogeneities of the O state DNCs implicated by the Mössbauer experiments are likely consequences of various factors, particularly the variable positions of the central H2O molecule between the Fea33+ and CuB2+ sites in different DNCs, whether or not this central H2O molecule has H‐bonding interaction with another H2O molecule, the different spin states having similar energies for the Fea33+ sites, and whether the Fea33+ and CuB2+ sites are ferromagnetically or antiferromagnetically spin‐coupled.
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Affiliation(s)
- Wen-Ge Han Du
- The Scripps Research Institute, Integrative Structural and Computational Biology, UNITED STATES
| | | | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, Hz112, 10550 North Torrey Pines Road, 92037, La Jolla, UNITED STATES
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14
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Methods of Measuring Mitochondrial Potassium Channels: A Critical Assessment. Int J Mol Sci 2022; 23:ijms23031210. [PMID: 35163132 PMCID: PMC8835872 DOI: 10.3390/ijms23031210] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/22/2022] Open
Abstract
In this paper, the techniques used to study the function of mitochondrial potassium channels are critically reviewed. The majority of these techniques have been known for many years as a result of research on plasma membrane ion channels. Hence, in this review, we focus on the critical evaluation of techniques used in the studies of mitochondrial potassium channels, describing their advantages and limitations. Functional analysis of mitochondrial potassium channels in comparison to that of plasmalemmal channels presents additional experimental challenges. The reliability of functional studies of mitochondrial potassium channels is often affected by the need to isolate mitochondria and by functional properties of mitochondria such as respiration, metabolic activity, swelling capacity, or high electrical potential. Three types of techniques are critically evaluated: electrophysiological techniques, potassium flux measurements, and biochemical techniques related to potassium flux measurements. Finally, new possible approaches to the study of the function of mitochondrial potassium channels are presented. We hope that this review will assist researchers in selecting reliable methods for studying, e.g., the effects of drugs on mitochondrial potassium channel function. Additionally, this review should aid in the critical evaluation of the results reported in various articles on mitochondrial potassium channels.
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15
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Cryo-EM structures of intermediates suggest an alternative catalytic reaction cycle for cytochrome c oxidase. Nat Commun 2021; 12:6903. [PMID: 34824221 PMCID: PMC8617209 DOI: 10.1038/s41467-021-27174-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/29/2021] [Indexed: 11/08/2022] Open
Abstract
Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion. Thus, the enzyme's catalytic cycle may have to be turned by 180 degrees.
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16
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Dragelj J, Mroginski MA, Knapp EW. Beating Heart of Cytochrome c Oxidase: The Shared Proton of Heme a3 Propionates. J Phys Chem B 2021; 125:9668-9677. [PMID: 34427096 DOI: 10.1021/acs.jpcb.1c03619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cytochrome c oxidase (CcO) pumps protons from the N-side to the P-side and consumes electrons from the P-side of the mitochondrial membrane driven by energy gained from reduction of dioxygen to water. ATP synthesis uses the resulting proton gradient and electrostatic potential difference. Since the distance a proton travels through CcO is too large for a one-step transfer process, proton-loading sites (PLS) that can carry protons transiently are necessary. One specific pump-active PLS couples to the redox reaction, thus energizing the proton to move across the membrane against electric potential and proton gradient. The PLS should also prevent proton backflow. Therefore, the propionates of the two redox-active hemes in CcO were suggested as PLS candidates although, according to CcO crystal structures, none of the four propionates can be protonated on account of strong H-bonds. Here, we show that modeling the local structure around heme a3 propionates enhances significantly their capability of carrying a proton jointly. This was not possible for the propionates of heme a. The modeled structures are stable in molecular dynamics simulations (MDS) and are energetically similar to the crystal structure. Precise electrostatic energy computations of MDS data are used to estimate the pKA values of all titratable residues in CcO. For the modeled structures, the heme a3 propionates have pKA values high enough to host a proton transiently but not too high to fix the proton permanently. The change in pKA throughout the redox reaction is sufficient to push the proton to the P-side of the membrane and to provide the protons with the necessary amount of energy for ATP synthesis.
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Affiliation(s)
- Jovan Dragelj
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Fabeckstrasse 36a, 14195 Berlin, Germany.,Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Ernst Walter Knapp
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Fabeckstrasse 36a, 14195 Berlin, Germany
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17
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Zhu G, Zeng H, Zhang S, Juli J, Tai L, Zhang D, Pang X, Zhang Y, Lam SM, Zhu Y, Peng G, Michel H, Sun F. The Unusual Homodimer of a Heme‐Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Guoliang Zhu
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Hui Zeng
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Shuangbo Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Jana Juli
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Linhua Tai
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Danyang Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiaoyun Pang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Yan Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Sin Man Lam
- LipidALL Technologies Company Limited Changzhou 213022 Jiangsu Province China
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences No.1 West Beichen Road, Chaoyang District Beijing 100101 China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Guohong Peng
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Fei Sun
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
- Center for Biological Imaging Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
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18
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Zhu G, Zeng H, Zhang S, Juli J, Tai L, Zhang D, Pang X, Zhang Y, Lam SM, Zhu Y, Peng G, Michel H, Sun F. The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew Chem Int Ed Engl 2021; 60:13323-13330. [PMID: 33665933 PMCID: PMC8251803 DOI: 10.1002/anie.202016785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 02/03/2023]
Abstract
The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family cytochrome c oxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome c and naphthoquinol as electron donors. Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 Å resolution electron cryo-microscopic structure and discovered a novel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add a new conceptual understanding of structural variation of cytochrome c oxidases in different species.
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Affiliation(s)
- Guoliang Zhu
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Hui Zeng
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Shuangbo Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Jana Juli
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Linhua Tai
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Danyang Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xiaoyun Pang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Yan Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Sin Man Lam
- LipidALL Technologies Company LimitedChangzhou213022Jiangsu ProvinceChina
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesNo.1 West Beichen Road, Chaoyang DistrictBeijing100101China
| | - Yun Zhu
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Guohong Peng
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Hartmut Michel
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Fei Sun
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- Center for Biological ImagingInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
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19
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Specific inhibition of proton pumping by the T315V mutation in the K channel of cytochrome ba 3 from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148450. [PMID: 34022199 DOI: 10.1016/j.bbabio.2021.148450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/06/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022]
Abstract
Cytochrome ba3 from Thermus thermophilus belongs to the B family of heme-copper oxidases and pumps protons across the membrane with an as yet unknown mechanism. The K channel of the A family heme-copper oxidases provides delivery of a substrate proton from the internal water phase to the binuclear heme-copper center (BNC) during the reductive phase of the catalytic cycle, while the D channel is responsible for transferring both substrate and pumped protons. By contrast, in the B family oxidases there is no D-channel and the structural equivalent of the K channel seems to be responsible for the transfer of both categories of protons. Here we have studied the effect of the T315V substitution in the K channel on the kinetics of membrane potential generation coupled to the oxidative half-reaction of the catalytic cycle of cytochrome ba3. The results suggest that the mutated enzyme does not pump protons during the reaction of the fully reduced form with molecular oxygen in a single turnover. Specific inhibition of proton pumping in the T315V mutant appears to be a consequence of inability to provide rapid (τ ~ 100 μs) reprotonation of the internal transient proton donor(s) of the K channel. In contrast to the A family, the K channel of the B-type oxidases is necessary for the electrogenic transfer of both pumped and substrate protons during the oxidative half-reaction of the catalytic cycle.
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20
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Abstract
Bacteria power their energy metabolism using membrane-bound respiratory enzymes that capture chemical energy and transduce it by pumping protons or Na+ ions across their cell membranes. Recent breakthroughs in molecular bioenergetics have elucidated the architecture and function of many bacterial respiratory enzymes, although key mechanistic principles remain debated. In this Review, we present an overview of the structure, function and bioenergetic principles of modular bacterial respiratory chains and discuss their differences from the eukaryotic counterparts. We also discuss bacterial supercomplexes, which provide central energy transduction systems in several bacteria, including important pathogens, and which could open up possible avenues for treatment of disease.
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21
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Noodleman L, Han Du WG, McRee D, Chen Y, Goh T, Götz AW. Coupled transport of electrons and protons in a bacterial cytochrome c oxidase-DFT calculated properties compared to structures and spectroscopies. Phys Chem Chem Phys 2021; 22:26652-26668. [PMID: 33231596 DOI: 10.1039/d0cp04848h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After a general introduction to the features and mechanisms of cytochrome c oxidases (CcOs) in mitochondria and aerobic bacteria, we present DFT calculated physical and spectroscopic properties for the catalytic reaction cycle compared with experimental observations in bacterial ba3 type CcO, also with comparisons/contrasts to aa3 type CcOs. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a3 Fe center and a near lying Cu center (called CuB) where by successive reduction and protonation, molecular O2 is transformed to two H2O molecules, and protons are pumped from an inner region across the membrane to an outer region by transit through the CcO integral membrane protein. Structures, energies and vibrational frequencies for Fe-O and O-O modes are calculated by DFT over the catalytic cycle. The calculated DFT frequencies in the DNC of CcO are compared with measured frequencies from Resonance Raman spectroscopy to clarify the composition, geometry, and electronic structures of different intermediates through the reaction cycle, and to trace reaction pathways. X-ray structures of the resting oxidized state are analyzed with reference to the known experimental reaction chemistry and using DFT calculated structures in fitting observed electron density maps. Our calculations lead to a new proposed reaction pathway for coupling the PR → F → OH (ferryl-oxo → ferric-hydroxo) pathway to proton pumping by a water shift mechanism. Through this arc of the catalytic cycle, major shifts in pKa's of the special tyrosine and a histidine near the upper water pool activate proton transfer. Additional mechanisms for proton pumping are explored, and the role of the CuB+ (cuprous state) in controlling access to the dinuclear reaction site is proposed.
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Affiliation(s)
- Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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22
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Shilova A, Lebrette H, Aurelius O, Nan J, Welin M, Kovacic R, Ghosh S, Safari C, Friel RJ, Milas M, Matej Z, Högbom M, Brändén G, Kloos M, Shoeman RL, Doak B, Ursby T, Håkansson M, Logan DT, Mueller U. Current status and future opportunities for serial crystallography at MAX IV Laboratory. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1095-1102. [PMID: 32876583 PMCID: PMC7467353 DOI: 10.1107/s1600577520008735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Over the last decade, serial crystallography, a method to collect complete diffraction datasets from a large number of microcrystals delivered and exposed to an X-ray beam in random orientations at room temperature, has been successfully implemented at X-ray free-electron lasers and synchrotron radiation facility beamlines. This development relies on a growing variety of sample presentation methods, including different fixed target supports, injection methods using gas-dynamic virtual-nozzle injectors and high-viscosity extrusion injectors, and acoustic levitation of droplets, each with unique requirements. In comparison with X-ray free-electron lasers, increased beam time availability makes synchrotron facilities very attractive to perform serial synchrotron X-ray crystallography (SSX) experiments. Within this work, the possibilities to perform SSX at BioMAX, the first macromolecular crystallography beamline at MAX IV Laboratory in Lund, Sweden, are described, together with case studies from the SSX user program: an implementation of a high-viscosity extrusion injector to perform room temperature serial crystallography at BioMAX using two solid supports - silicon nitride membranes (Silson, UK) and XtalTool (Jena Bioscience, Germany). Future perspectives for the dedicated serial crystallography beamline MicroMAX at MAX IV Laboratory, which will provide parallel and intense micrometre-sized X-ray beams, are discussed.
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Affiliation(s)
- Anastasya Shilova
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm 10691, Sweden
| | - Oskar Aurelius
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Martin Welin
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Rebeka Kovacic
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Ross J. Friel
- School of Information Technology, Halmstad University, Halmstad 30118, Sweden
| | - Mirko Milas
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Zdenek Matej
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm 10691, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas Ursby
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Derek T. Logan
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Uwe Mueller
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
- Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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23
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Han Du WG, McRee D, Götz AW, Noodleman L. A Water Molecule Residing in the Fe a33+···Cu B2+ Dinuclear Center of the Resting Oxidized as-Isolated Cytochrome c Oxidase: A Density Functional Study. Inorg Chem 2020; 59:8906-8915. [PMID: 32525689 PMCID: PMC8114904 DOI: 10.1021/acs.inorgchem.0c00724] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Indexed: 11/30/2022]
Abstract
Although the dinuclear center (DNC) of the resting oxidized "as-isolated" cytochrome c oxidase (CcO) is not a catalytically active state, its detailed structure, especially the nature of the bridging species between the Fea33+ and CuB2+ metal sites, is still both relevant and unsolved. Recent crystallographic work has shown an extended electron density for a peroxide type dioxygen species (O1-O2) bridging the Fea3 and CuB centers. In this paper, our density functional theory (DFT) calculations show that the observed peroxide type electron density between the two metal centers is most likely a mistaken analysis due to overlap of the electron density of a water molecule located at different positions between apparent O1 and O2 sites in DNCs of different CcO molecules with almost the same energy. Because the diffraction pattern and the resulting electron density map represent the effective long-range order averaged over many molecules and unit cells in the X-ray structure, this averaging can lead to an apparent observed superposition of different water positions between the Fea33+ and CuB2+ metal sites.
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Affiliation(s)
- Wen-Ge Han Du
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Duncan McRee
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of
California San Diego, 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Louis Noodleman
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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24
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Cai X, Son CY, Mao J, Kaur D, Zhang Y, Khaniya U, Cui Q, Gunner MR. Identifying the proton loading site cluster in the ba 3 cytochrome c oxidase that loads and traps protons. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148239. [PMID: 32531221 DOI: 10.1016/j.bbabio.2020.148239] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/05/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022]
Abstract
Cytochrome c Oxidase (CcO) is the terminal electron acceptor in aerobic respiratory chain, reducing O2 to water. The released free energy is stored by pumping protons through the protein, maintaining the transmembrane electrochemical gradient. Protons are held transiently in a proton loading site (PLS) that binds and releases protons driven by the electron transfer reaction cycle. Multi-Conformation Continuum Electrostatics (MCCE) was applied to crystal structures and Molecular Dynamics snapshots of the B-type Thermus thermophilus CcO. Six residues are identified as the PLS, binding and releasing protons as the charges on heme b and the binuclear center are changed: the heme a3 propionic acids, Asp287, Asp372, His376 and Glu126B. The unloaded state has one proton and the loaded state two protons on these six residues. Different input structures, modifying the PLS conformation, show different proton distributions and result in different proton pumping behaviors. One loaded and one unloaded protonation states have the loaded/unloaded states close in energy so the PLS binds and releases a proton through the reaction cycle. The alternative proton distributions have state energies too far apart to be shifted by the electron transfers so are locked in loaded or unloaded states. Here the protein can use active states to load and unload protons, but has nearby trapped states, which stabilize PLS protonation state, providing new ideas about the CcO proton pumping mechanism. The distance between the PLS residues Asp287 and His376 correlates with the energy difference between loaded and unloaded states.
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Affiliation(s)
- Xiuhong Cai
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Chang Yun Son
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Junjun Mao
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Chemistry, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Yingying Zhang
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Qiang Cui
- Department of Chemistry & Department of Biomedical Engineering & Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - M R Gunner
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA; Department of Chemistry, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
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25
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Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase. J Mol Biol 2020; 432:5104-5123. [PMID: 32113953 DOI: 10.1016/j.jmb.2020.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
The lipid cubic phase (LCP) has been used extensively as a medium for crystallizing membrane proteins. It is an attractive environment in which to perform such studies because it incorporates a lipid bilayer. It is therefore considered a useful and a faithful biomembrane mimetic. Here, we bring together evidence that supports this view. Biophysical characterizations are described demonstrating that the cubic phase is a porous medium into and out of which water-soluble molecules can diffuse for binding to and reaction with reconstituted proteins. The proteins themselves are shown to be functionally reconstituted into and to have full mobility in the bilayered membrane, a prerequisite for LCP crystallogenesis. Spectroscopic methods have been used to characterize the conformation and disposition of proteins in the mesophase. Procedures for performing activity assays on enzymes directly in the cubic phase have been reported. Specific examples described here include a kinase and two transferases, where quantitative kinetics and mechanism-defining measurements were performed directly or via a coupled assay system. Finally, ligand-binding assays are described, where binding to proteins in the mesophase membrane was monitored directly by eye and indirectly by fluorescence quenching, enabling binding constant determinations for targets with affinity values in the micromolar and nanomolar range. These results make a convincing case that the lipid bilayer of the cubic mesophase is an excellent membrane mimetic and a suitable medium in which to perform not only crystallogenesis but also biochemical and biophysical characterizations of membrane proteins.
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26
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Structure of the cytochrome aa 3 -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site. Proc Natl Acad Sci U S A 2019; 117:872-876. [PMID: 31888984 DOI: 10.1073/pnas.1915013117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Virtually all proton-pumping terminal respiratory oxygen reductases are members of the heme-copper oxidoreductase superfamily. Most of these enzymes use reduced cytochrome c as a source of electrons, but a group of enzymes have evolved to directly oxidize membrane-bound quinols, usually menaquinol or ubiquinol. All of the quinol oxidases have an additional transmembrane helix (TM0) in subunit I that is not present in the related cytochrome c oxidases. The current work reports the 3.6-Å-resolution X-ray structure of the cytochrome aa 3 -600 menaquinol oxidase from Bacillus subtilis containing 1 equivalent of menaquinone. The structure shows that TM0 forms part of a cleft to accommodate the menaquinol-7 substrate. Crystals which have been soaked with the quinol-analog inhibitor HQNO (N-oxo-2-heptyl-4-hydroxyquinoline) or 3-iodo-HQNO reveal a single binding site where the inhibitor forms hydrogen bonds to amino acid residues shown previously by spectroscopic methods to interact with the semiquinone state of menaquinone, a catalytic intermediate.
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27
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Szundi I, Funatogawa C, Soulimane T, Einarsdóttir Ó. The Reactions of O 2 and NO with Mixed-Valence ba 3 Cytochrome c Oxidase from Thermus thermophilus. Biophys J 2019; 118:386-395. [PMID: 31870538 DOI: 10.1016/j.bpj.2019.11.3390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Earlier CO flow-flash experiments on the fully reduced Thermus thermophilus ba3 (Tt ba3) cytochrome oxidase revealed that O2 binding was slowed down by a factor of 10 in the presence of CO (Szundi et al., 2010, PNAS 107, 21010-21015). The goal of the current study is to explore whether the long apparent lifetime (∼50 ms) of the CuB+-CO complex generated upon photolysis of the CO-bound mixed-valence Tt ba3 (Koutsoupakis et al., 2019, Acc. Chem. Res. 52, 1380-1390) affects O2 and NO binding and the ability of CuB to act as an electron donor during O-O bond splitting. The CO recombination, NO binding, and the reaction of mixed-valence Tt ba3 with O2 were investigated by time-resolved optical absorption spectroscopy using the CO flow-flash approach and photolabile O2 and NO carriers. No electron backflow was detected after photolysis of the mixed-valence CO-bound Tt ba3. The rate of O2 and NO binding was two times slower than in the fully reduced enzyme in the presence of CO and 20 times slower than in the absence of CO. The purported long-lived CuB+-CO complex did not prevent O-O bond splitting and the resulting PM formation, which was significantly faster (5-10 times) than in the bovine heart enzyme. We propose that O2 binding to heme a3 in Tt ba3 causes CO to dissociate from CuB+ in a concerted manner through steric and/or electronic effects, thus allowing CuB+ to act as an electron donor in the mixed-valence enzyme. The significantly faster O2 binding and O-O bond cleavage in Tt ba3 compared to analogous steps in the aa3 oxidases could reflect evolutionary adaptation of the enzyme to the microaerobic conditions of the T. thermophilus HB8 species.
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Affiliation(s)
- Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California
| | - Chie Funatogawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California
| | - Tewfik Soulimane
- Deparment of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Ólőf Einarsdóttir
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California.
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28
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Han Du WG, Götz AW, Noodleman L. DFT Fe a3-O/O-O Vibrational Frequency Calculations over Catalytic Reaction Cycle States in the Dinuclear Center of Cytochrome c Oxidase. Inorg Chem 2019; 58:13933-13944. [PMID: 31566371 PMCID: PMC6839913 DOI: 10.1021/acs.inorgchem.9b01840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional vibrational frequency calculations have been performed on eight geometry optimized cytochrome c oxidase (CcO) dinuclear center (DNC) reaction cycle intermediates and on the oxymyoglobin (oxyMb) active site. The calculated Fe-O and O-O stretching modes and their frequency shifts along the reaction cycle have been compared with the available resonance Raman (rR) measurements. The calculations support the proposal that in state A[Fea33+-O2-•···CuB+] of CcO, O2 binds with Fea32+ in a similar bent end-on geometry to that in oxyMb. The calculations show that the observed 20 cm-1 shift of the Fea3-O stretching mode from the PR to F state is caused by the protonation of the OH- ligand on CuB2+ (PR[Fea34+═O2-···HO--CuB2+] → F[Fea34+═O2-···H2O-CuB2+]), and that the H2O ligand is still on the CuB2+ site in the rR identified F[Fea34+═O2-···H2O-CuB2+] state. Further, the observed rR band at 356 cm-1 between states PR and F is likely an O-Fea3-porphyrin bending mode. The observed 450 cm-1 low Fea3-O frequency mode for the OH active oxidized state has been reproduced by our calculations on a nearly symmetrically bridged Fea33+-OH-CuB2+ structure with a relatively long Fea3-O distance near 2 Å. Based on Badger's rule, the calculated Fea3-O distances correlate well with the calculated νFe-O-2/3 (νFe-O is the Fea3-O stretching frequency) with correlation coefficient R = 0.973.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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29
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Andersson R, Safari C, Båth P, Bosman R, Shilova A, Dahl P, Ghosh S, Dunge A, Kjeldsen-Jensen R, Nan J, Shoeman RL, Kloos M, Doak RB, Mueller U, Neutze R, Brändén G. Well-based crystallization of lipidic cubic phase microcrystals for serial X-ray crystallography experiments. Acta Crystallogr D Struct Biol 2019; 75:937-946. [PMID: 31588925 PMCID: PMC6779076 DOI: 10.1107/s2059798319012695] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022] Open
Abstract
Serial crystallography is having an increasing impact on structural biology. This emerging technique opens up new possibilities for studying protein structures at room temperature and investigating structural dynamics using time-resolved X-ray diffraction. A limitation of the method is the intrinsic need for large quantities of well ordered micrometre-sized crystals. Here, a method is presented to screen for conditions that produce microcrystals of membrane proteins in the lipidic cubic phase using a well-based crystallization approach. A key advantage over earlier approaches is that the progress of crystal formation can be easily monitored without interrupting the crystallization process. In addition, the protocol can be scaled up to efficiently produce large quantities of crystals for serial crystallography experiments. Using the well-based crystallization methodology, novel conditions for the growth of showers of microcrystals of three different membrane proteins have been developed. Diffraction data are also presented from the first user serial crystallography experiment performed at MAX IV Laboratory.
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Affiliation(s)
- Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | | | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Andreas Dunge
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, SE-431 50 Gothenburg, Sweden
| | - Rasmus Kjeldsen-Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark
| | - Jie Nan
- MAX IV Laboratory, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Robert L. Shoeman
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marco Kloos
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Uwe Mueller
- MAX IV Laboratory, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
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30
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Abstract
X-ray crystallographic analyses of mitochondrial cytochrome c oxidase (CcO) have been based on its dimeric form. Recent cryo-electron microscopy structures revealed that CcO exists in its monomeric form in the respiratory supercomplex. This study, using amphipol-stabilized CcO, shows that the activity of monomer is higher than that of the dimer. The crystal structure of monomer determined here shows that the local structure of one of the proton transfer pathways differs from that in the dimer. The crystal structure also shows that cardiolipins are located at the interface region in the supercomplex. Taken together, these results suggest that CcO in the monomeric state, dimeric state, and supercomplex state depending on cardiolipins are involved in regulation of respiratory electron transport. Cytochrome c oxidase (CcO), a membrane enzyme in the respiratory chain, catalyzes oxygen reduction by coupling electron and proton transfer through the enzyme with a proton pump across the membrane. In all crystals reported to date, bovine CcO exists as a dimer with the same intermonomer contacts, whereas CcOs and related enzymes from prokaryotes exist as monomers. Recent structural analyses of the mitochondrial respiratory supercomplex revealed that CcO monomer associates with complex I and complex III, indicating that the monomeric state is functionally important. In this study, we prepared monomeric and dimeric bovine CcO, stabilized using amphipol, and showed that the monomer had high activity. In addition, using a newly synthesized detergent, we determined the oxidized and reduced structures of monomer with resolutions of 1.85 and 1.95 Å, respectively. Structural comparison of the monomer and dimer revealed that a hydrogen bond network of water molecules is formed at the entry surface of the proton transfer pathway, termed the K-pathway, in monomeric CcO, whereas this network is altered in dimeric CcO. Based on these results, we propose that the monomer is the activated form, whereas the dimer can be regarded as a physiological standby form in the mitochondrial membrane. We also determined phospholipid structures based on electron density together with the anomalous scattering effect of phosphorus atoms. Two cardiolipins are found at the interface region of the supercomplex. We discuss formation of the monomeric CcO, dimeric CcO, and supercomplex, as well as their role in regulation of CcO activity.
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31
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Interfaces Between Alpha-helical Integral Membrane Proteins: Characterization, Prediction, and Docking. Comput Struct Biotechnol J 2019; 17:699-711. [PMID: 31303974 PMCID: PMC6603304 DOI: 10.1016/j.csbj.2019.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 11/28/2022] Open
Abstract
Protein-protein interaction (PPI) is an essential mechanism by which proteins perform their biological functions. For globular proteins, the molecular characteristics of such interactions have been well analyzed, and many computational tools are available for predicting PPI sites and constructing structural models of the complex. In contrast, little is known about the molecular features of the interaction between integral membrane proteins (IMPs) and few methods exist for constructing structural models of their complexes. Here, we analyze the interfaces from a non-redundant set of complexes of α-helical IMPs whose structures have been determined to a high resolution. We find that the interface is not significantly different from the rest of the surface in terms of average hydrophobicity. However, the interface is significantly better conserved and, on average, inter-subunit contacting residue pairs correlate more strongly than non-contacting pairs, especially in obligate complexes. We also develop a neural network-based method, with an area under the receiver operating characteristic curve of 0.75 and a Pearson correlation coefficient of 0.70, for predicting interface residues and their weighted contact numbers (WCNs). We further show that predicted interface residues and their WCNs can be used as restraints to reconstruct the structure α-helical IMP dimers through docking for fourteen out of a benchmark set of sixteen complexes. The RMSD100 values of the best-docked ligand subunit to its native structure are <2.5 Å for these fourteen cases. The structural analysis conducted in this work provides molecular details about the interface between α-helical IMPs and the WCN restraints represent an efficient means to score α-helical IMP docking candidates.
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Key Words
- AUC, Area under the ROC curve
- IMP, Integral membrane protein
- MAE, Mean absolute error
- MSA, Multiple sequence alignment
- Membrane protein docking
- Membrane protein interfaces
- Neural networks
- OPM, Orientations of proteins in membranes
- PCC, Pearson correlation coefficient
- PDB, Protein data bank
- PPI, Protein-protein interaction
- PPM, Positioning of proteins in membrane.
- PPV, Positive predictive value
- PSSM, Position-specific scoring matrix
- RMSD, Root-mean-square distance
- ROC, Receiver operating characteristic curve
- RSA, Relative solvent accessibility
- TNR, True negative rate
- TPR, True positive rate
- WCN, Weighted contact number
- Weighted contact numbers
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32
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Koutsoupakis C, Soulimane T, Varotsis C. Discrete Ligand Binding and Electron Transfer Properties of ba 3-Cytochrome c Oxidase from Thermus thermophilus: Evolutionary Adaption to Low Oxygen and High Temperature Environments. Acc Chem Res 2019; 52:1380-1390. [PMID: 31021078 DOI: 10.1021/acs.accounts.9b00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (C cO) couples the oxidation of cytochrome c to the reduction of molecular oxygen to water and links these electron transfers to proton translocation. The redox-driven C cO conserves part of the released free energy generating a proton motive force that leads to the synthesis of the main biological energy source ATP. Cytochrome ba3 oxidase is a B-type oxidase from the extremely thermophilic eubacterium Thermus thermophilus with high O2 affinity, expressed under elevated temperatures and limited oxygen supply and possessing discrete structural, ligand binding, and electron transfer properties. The origin and the cause of the peculiar, as compared to other C cOs, thermodynamic and kinetic properties remain unknown. Fourier transform infrared (FTIR) and time-resolved step-scan FTIR (TRS2-FTIR) spectroscopies have been employed to investigate the origin of the binding and electron transfer properties of cytochrome ba3 oxidase in both the fully reduced (FR) and mixed valence (MV) forms. Several independent and not easily separated factors leading to increased thermostability and high O2 affinity have been determined. These include (i) the increased hydrophobicity of the active center, (ii) the existence of a ligand input channel, (iii) the high affinity of CuB for exogenous ligands, (iv) the optimized electron transfer (ET) pathways, (v) the effective proton-input channel and water-exit pathway as well the proton-loading/exit sites, (vi) the specifically engineered protein structure, and (vii) the subtle thermodynamic and kinetic regulation. We correlate the unique ligand binding and electron transfer properties of cytochrome ba3 oxidase with the existence of an adaption mechanism which is necessary for efficient function. These results suggest that a cascade of structural factors have been optimized by evolution, through protein architecture, to ensure the conversion of cytochrome ba3 oxidase into a high O2-affinity enzyme that functions effectively in its extreme native environment. The present results show that ba3-cytochrome c oxidase uses a unique structural pattern of energy conversion that has taken into account all the extreme environmental factors that affect the function of the enzyme and is assembled in such a way that its exclusive functions are secured. Based on the available data of CcOs, we propose possible factors including the rigidity and nonpolar hydrophobic interactions that contribute to the behavior observed in cytochrome ba3 oxidase.
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Affiliation(s)
- Constantinos Koutsoupakis
- Department of Environmental Science and Technology, Cyprus University of Technology, P.O. Box 50329, 3603 Lemesos, Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Science Department and Materials & Surface Science Institute (MSSI), University of Limerick, Limerick, Ireland
| | - Constantinos Varotsis
- Department of Environmental Science and Technology, Cyprus University of Technology, P.O. Box 50329, 3603 Lemesos, Cyprus
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33
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Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
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Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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34
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Mahinthichaichan P, Gennis RB, Tajkhorshid E. Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:712-724. [PMID: 29883591 DOI: 10.1016/j.bbabio.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/05/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
The superfamily of heme‑copper oxidoreductases (HCOs) include both NO and O2 reductases. Nitric oxide reductases (NORs) are bacterial membrane enzymes that catalyze an intermediate step of denitrification by reducing nitric oxide (NO) to nitrous oxide (N2O). They are structurally similar to heme‑copper oxygen reductases (HCOs), which reduce O2 to water. The experimentally observed apparent bimolecular rate constant of NO delivery to the deeply buried catalytic site of NORs was previously reported to approach the diffusion-controlled limit (108-109 M-1 s-1). Using the crystal structure of cytochrome-c dependent NOR (cNOR) from Pseudomonas aeruginosa, we employed several protocols of molecular dynamics (MD) simulation, which include flooding simulations of NO molecules, implicit ligand sampling and umbrella sampling simulations, to elucidate how NO in solution accesses the catalytic site of this cNOR. The results show that NO partitions into the membrane, enters the enzyme from the lipid bilayer and diffuses to the catalytic site via a hydrophobic tunnel that is resolved in the crystal structures. This is similar to what has been found for O2 diffusion through the closely related O2 reductases. The apparent second order rate constant approximated using the simulation data is ~5 × 108 M-1 s-1, which is optimized by the dynamics of the amino acid side chains lining in the tunnel. It is concluded that both NO and O2 reductases utilize well defined hydrophobic tunnels to assure that substrate diffusion to the buried catalytic sites is not rate limiting under physiological conditions.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
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35
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Mahinthichaichan P, Gennis RB, Tajkhorshid E. Cytochrome aa 3 Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O 2 for Catalysis. Biochemistry 2018; 57:2150-2161. [PMID: 29546752 DOI: 10.1021/acs.biochem.7b01194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cytochrome aa3 is the terminal respiratory enzyme of all eukaryotes and many bacteria and archaea, reducing O2 to water and harnessing the free energy from the reaction to generate the transmembrane electrochemical potential. The diffusion of O2 to the heme-copper catalytic site, which is buried deep inside the enzyme, is the initiation step of the reaction chemistry. Our previous molecular dynamics (MD) study with cytochrome ba3, a homologous enzyme of cytochrome aa3 in Thermus thermophilus, demonstrated that O2 diffuses from the lipid bilayer to its reduction site through a 25 Å long tunnel inferred by Xe binding sites detected by X-ray crystallography [Mahinthichaichan, P., Gennis, R., and Tajkhorshid, E. (2016) Biochemistry 55, 1265-1278]. Although a similar tunnel is observed in cytochrome aa3, this putative pathway appears partially occluded between the entrances and the reduction site. Also, the experimentally determined second-order rate constant for O2 delivery in cytochrome aa3 (∼108 M-1 s-1) is 10 times slower than that in cytochrome ba3 (∼109 M-1 s-1). A question to be addressed is whether cytochrome aa3 utilizes this X-ray-inferred tunnel as the primary pathway for O2 delivery. Using complementary computational methods, including multiple independent flooding MD simulations and implicit ligand sampling calculations, we probe the O2 delivery pathways in cytochrome aa3 of Rhodobacter sphaeroides. All of the O2 molecules that arrived in the reduction site during the simulations were found to diffuse through the X-ray-observed tunnel, despite its apparent constriction, supporting its role as the main O2 delivery pathway in cytochrome aa3. The rate constant for O2 delivery in cytochrome aa3, approximated using the simulation results, is 10 times slower than in cytochrome ba3, in agreement with the experimentally determined rate constants.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Robert B Gennis
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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36
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Wikström M, Krab K, Sharma V. Oxygen Activation and Energy Conservation by Cytochrome c Oxidase. Chem Rev 2018; 118:2469-2490. [PMID: 29350917 PMCID: PMC6203177 DOI: 10.1021/acs.chemrev.7b00664] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
This review focuses on the type
A cytochrome c oxidases (CcO), which
are found in all mitochondria
and also in several aerobic bacteria. CcO catalyzes
the respiratory reduction of dioxygen (O2) to water by
an intriguing mechanism, the details of which are fairly well understood
today as a result of research for over four decades. Perhaps even
more intriguingly, the membrane-bound CcO couples
the O2 reduction chemistry to translocation of protons
across the membrane, thus contributing to generation of the electrochemical
proton gradient that is used to drive the synthesis of ATP as catalyzed
by the rotary ATP synthase in the same membrane. After reviewing the
structure of the core subunits of CcO, the active
site, and the transfer paths of electrons, protons, oxygen, and water,
we describe the states of the catalytic cycle and point out the few
remaining uncertainties. Finally, we discuss the mechanism of proton
translocation and the controversies in that area that still prevail.
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Affiliation(s)
- Mårten Wikström
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland
| | - Klaas Krab
- Department of Molecular Cell Physiology , Vrije Universiteit , P.O. Box 7161 , Amsterdam 1007 MC , The Netherlands
| | - Vivek Sharma
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland.,Department of Physics , University of Helsinki , P.O. Box 64 , Helsinki FI-00014 , Finland
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37
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Han Du WG, Götz AW, Noodleman L. A Water Dimer Shift Activates a Proton Pumping Pathway in the P R → F Transition of ba 3 Cytochrome c Oxidase. Inorg Chem 2018; 57:1048-1059. [PMID: 29308889 DOI: 10.1021/acs.inorgchem.7b02461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Broken-symmetry density functional calculations have been performed on the [Fea34+,CuB2+] state of the dinuclear center (DNC) for the PR → F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+, which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea34+,CuB2+] state (state F) is of the form Fea34+═O2-···CuB2+, in which the H2O ligand that resulted from protonation of the OH- ligand in the PR state is dissociated from the CuB2+ site. The calculated Fea34+═O2- distance in F (1.68 Å) is 0.03 Å longer than that in PR (1.65 Å), which can explain the different Fea34+═O2- stretching modes in P (804 cm-1) and F (785 cm-1) identified by resonance Raman experiments. In this F state, the CuB2+···O2- (ferryl-oxygen) distance is only around 2.4 Å. Hence, the subsequent OH state [Fea33+-OH--CuB2+] with a μ-hydroxo bridge can be easily formed, as shown by our calculations.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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38
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Zatloukalová M, Nazaruk E, Novák D, Vacek J, Bilewicz R. Lipidic liquid crystalline cubic phases for preparation of ATP-hydrolysing enzyme electrodes. Biosens Bioelectron 2017; 100:437-444. [PMID: 28961546 DOI: 10.1016/j.bios.2017.09.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 09/17/2017] [Accepted: 09/18/2017] [Indexed: 11/26/2022]
Abstract
The lipidic liquid-crystalline cubic phase (LCP) is a membrane-mimetic material useful for the stabilization and structural analysis of membrane proteins. Here, we focused on the incorporation of the membrane ATP-hydrolysing sodium/potassium transporter Na+/K+-ATPase (NKA) into a monoolein-derived LCP. Small-angle X-ray scattering was employed for the determination of the LCP structure, which was of Pn3m symmetry for all the formulations studied. The fully characterized NKA-LCP material was immobilized onto a glassy carbon electrode, forming a highly stable enzyme electrode and a novel sensing platform. A typical NKA voltammetric signature was monitored via the anodic reaction of tyrosine and tryptophan residues. The in situ enzyme activity evaluation was based on the ability of NKA to transform ATP to ADP and free phosphate, the latter reacting with ammonium molybdate to form the ammonium phosphomolybdate complex under acidic conditions. The square-wave voltammetric detection of phosphomolybdate was performed and complemented with spectrophotometric measurement at 710nm. The anodic voltammetric response, corresponding to the catalytic ATP-hydrolysing function of NKA incorporated into the LCP, was monitored at around + 0.2V vs. Ag/AgCl in the presence or absence of ouabain, a specific NKA inhibitor. NKA incorporated into the LCP retained its ATP-hydrolysing activity for 7 days, while the solubilized protein became practically inactive. The novelty of this work is the first incorporation of NKA into a lipidic cubic phase with consequent enzyme functionality and stability evaluation using voltammetric detection. The application of LCPs could also be important in the further development of new membrane protein electrochemical sensors and enzyme electrodes.
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Affiliation(s)
- Martina Zatloukalová
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 775 15 Olomouc, Czech Republic
| | - Ewa Nazaruk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - David Novák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 775 15 Olomouc, Czech Republic
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 775 15 Olomouc, Czech Republic.
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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39
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Mitochondrial cytochrome c oxidase: catalysis, coupling and controversies. Biochem Soc Trans 2017; 45:813-829. [PMID: 28620043 DOI: 10.1042/bst20160139] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 01/04/2023]
Abstract
Mitochondrial cytochrome c oxidase is a member of a diverse superfamily of haem-copper oxidases. Its mechanism of oxygen reduction is reviewed in terms of the cycle of catalytic intermediates and their likely chemical structures. This reaction cycle is coupled to the translocation of protons across the inner mitochondrial membrane in which it is located. The likely mechanism by which this occurs, derived in significant part from studies of bacterial homologues, is presented. These mechanisms of catalysis and coupling, together with current alternative proposals of underlying mechanisms, are critically reviewed.
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40
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Andersson R, Safari C, Dods R, Nango E, Tanaka R, Yamashita A, Nakane T, Tono K, Joti Y, Båth P, Dunevall E, Bosman R, Nureki O, Iwata S, Neutze R, Brändén G. Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature. Sci Rep 2017; 7:4518. [PMID: 28674417 PMCID: PMC5495810 DOI: 10.1038/s41598-017-04817-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/19/2017] [Indexed: 11/11/2022] Open
Abstract
Cytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba3-type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2.3 Å resolution from data collected at an X-ray Free Electron Laser. We find overall agreement with earlier X-ray structures solved from diffraction data collected at cryogenic temperature. Previous structures solved from synchrotron radiation data, however, have shown conflicting results regarding the identity of the active-site ligand. Our room-temperature structure, which is free from the effects of radiation damage, reveals that a single-oxygen species in the form of a water molecule or hydroxide ion is bound in the active site. Structural differences between the ba3-type and aa3-type cytochrome c oxidases around the proton-loading site are also described.
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Affiliation(s)
- Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden
| | - Eriko Nango
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Rie Tanaka
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Ayumi Yamashita
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - So Iwata
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden.
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41
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Poiana F, von Ballmoos C, Gonska N, Blomberg MRA, Ädelroth P, Brzezinski P. Splitting of the O-O bond at the heme-copper catalytic site of respiratory oxidases. SCIENCE ADVANCES 2017; 3:e1700279. [PMID: 28630929 PMCID: PMC5473675 DOI: 10.1126/sciadv.1700279] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/20/2017] [Indexed: 05/30/2023]
Abstract
Heme-copper oxidases catalyze the four-electron reduction of O2 to H2O at a catalytic site that is composed of a heme group, a copper ion (CuB), and a tyrosine residue. Results from earlier experimental studies have shown that the O-O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (PR ; Fe4+=O2-, CuB2+-OH-). We show that with the Thermus thermophilus ba3 oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the PR ferryl (τ ≅110 μs), which indicates that O2 is reduced before the splitting of the O-O bond. Application of density functional theory indicates that the electron acceptor at the catalytic site is a high-energy peroxy state [Fe3+-O--O-(H+)], which is formed before the PR ferryl. The rates of heme b oxidation and PR ferryl formation were more similar at pH 10, indicating that the formation of the high-energy peroxy state involves proton transfer within the catalytic site, consistent with theory. The combined experimental and theoretical data suggest a general mechanism for O2 reduction by heme-copper oxidases.
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Affiliation(s)
- Federica Poiana
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | - Nathalie Gonska
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Margareta R. A. Blomberg
- Department of Organic Chemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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42
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Funatogawa C, Li Y, Chen Y, McDonald W, Szundi I, Fee JA, Stout CD, Einarsdóttir Ó. Role of the Conserved Valine 236 in Access of Ligands to the Active Site of Thermus thermophilus ba3 Cytochrome Oxidase. Biochemistry 2016; 56:107-119. [DOI: 10.1021/acs.biochem.6b00590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chie Funatogawa
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Yang Li
- Department
of Molecular Biology, The Scripps Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Chen
- Department
of Molecular Biology, The Scripps Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - William McDonald
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Istvan Szundi
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - James A. Fee
- Department
of Molecular Biology, The Scripps Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - C. David Stout
- Department
of Molecular Biology, The Scripps Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ólöf Einarsdóttir
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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43
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Mayne CG, Arcario MJ, Mahinthichaichan P, Baylon JL, Vermaas JV, Navidpour L, Wen PC, Thangapandian S, Tajkhorshid E. The cellular membrane as a mediator for small molecule interaction with membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:2290-2304. [PMID: 27163493 PMCID: PMC4983535 DOI: 10.1016/j.bbamem.2016.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 01/05/2023]
Abstract
The cellular membrane constitutes the first element that encounters a wide variety of molecular species to which a cell might be exposed. Hosting a large number of structurally and functionally diverse proteins associated with this key metabolic compartment, the membrane not only directly controls the traffic of various molecules in and out of the cell, it also participates in such diverse and important processes as signal transduction and chemical processing of incoming molecular species. In this article, we present a number of cases where details of interaction of small molecular species such as drugs with the membrane, which are often experimentally inaccessible, have been studied using advanced molecular simulation techniques. We have selected systems in which partitioning of the small molecule with the membrane constitutes a key step for its final biological function, often binding to and interacting with a protein associated with the membrane. These examples demonstrate that membrane partitioning is not only important for the overall distribution of drugs and other small molecules into different compartments of the body, it may also play a key role in determining the efficiency and the mode of interaction of the drug with its target protein. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Christopher G Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Mark J Arcario
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
| | - Paween Mahinthichaichan
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Javier L Baylon
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Josh V Vermaas
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Latifeh Navidpour
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Po-Chao Wen
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Sundarapandian Thangapandian
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
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44
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Sengupta K, Chatterjee S, Dey A. In Situ Mechanistic Investigation of O2 Reduction by Iron Porphyrin Electrocatalysts Using Surface-Enhanced Resonance Raman Spectroscopy Coupled to Rotating Disk Electrode (SERRS-RDE) Setup. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01122] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Kushal Sengupta
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sudipta Chatterjee
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Abhishek Dey
- Department
of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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45
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Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:1594-1606. [PMID: 27317965 PMCID: PMC4995112 DOI: 10.1016/j.bbabio.2016.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/21/2016] [Accepted: 06/14/2016] [Indexed: 01/22/2023]
Abstract
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.
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Affiliation(s)
- Longhua Yang
- Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA
| | - Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA.
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Shelar A, Bansal M. Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2804-2817. [PMID: 27521749 DOI: 10.1016/j.bbamem.2016.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 08/07/2016] [Indexed: 12/11/2022]
Abstract
Transmembrane (TM) helices in integral membrane proteins are primarily α-helical in structure. Here we analyze 1134 TM helices in 90 high resolution membrane proteins and find that apart from the widely prevalent α-helices, TM regions also contain stretches of 310 (3 to 8 residues) and π-helices (5 to 19 residues) with distinct sequence signatures. The various helix perturbations in TM regions comprise of helices with kinked geometry, as well as those with an interspersed 310/π-helical fragment and show high occurrence in a few membrane proteins. Proline is frequently present at sites of these perturbations, but it is neither a necessary nor a sufficient requirement. Helix perturbations are also conserved within a family of membrane proteins despite low sequence identity in the perturbed region. Furthermore, a perturbation influences the geometry of the TM helix, mediates inter-helical interactions within and across protein chains and avoids hydrophobic mismatch of the helix termini with the bilayer. An analysis of π-helices in the TM regions of the heme copper oxidase superfamily shows that interspersed π-helices can vary in length from 6 to 19 amino acids or be entirely absent, depending upon the protein function. The results presented here would be helpful for prediction of 310 and π-helices in TM regions and can assist the computational design of membrane proteins.
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Affiliation(s)
- Ashish Shelar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field. Data Brief 2016; 8:1209-14. [PMID: 27547799 PMCID: PMC4979044 DOI: 10.1016/j.dib.2016.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/01/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8 Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F), we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.
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Affiliation(s)
- Longhua Yang
- Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Hanazono Y, Takeda K, Miki K. Characterization of the Nqo5 subunit of bacterial complex I in the isolated state. FEBS Open Bio 2016; 6:687-95. [PMID: 27398308 PMCID: PMC4932448 DOI: 10.1002/2211-5463.12070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 11/09/2022] Open
Abstract
The subunits that comprise bacterial complex I (NADH:ubiquinone oxidoreductase) are also found in more complicated mitochondrial enzymes in eukaryotic organisms. Although the Nqo5 subunit is one of these conserved components and important for the formation of complex, it has been little studied. Here, we report structure analyses of isolated Nqo5 from Thermus thermophilus. Biochemical studies indicated that the C-terminal region following the 30-Kd subunit motif is disordered in the isolated state, while the remaining portion is already folded. Crystallographic studies of a trypsin-resistant fragment revealed detailed structural differences in the folded domain between the isolated and complexed states.
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Affiliation(s)
- Yuya Hanazono
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto Japan
| | - Kazuki Takeda
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto Japan; RIKEN SPring-8 Center at Harima Institute Sayo Hyogo Japan
| | - Kunio Miki
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto Japan; RIKEN SPring-8 Center at Harima Institute Sayo Hyogo Japan
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49
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Han Du WG, Götz AW, Yang L, Walker RC, Noodleman L. A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus. Phys Chem Chem Phys 2016; 18:21162-71. [PMID: 27094074 DOI: 10.1039/c6cp00349d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Broken-symmetry density functional calculations have been performed on the [Fea3, CuB] dinuclear center (DNC) of ba3 cytochrome c oxidase from Thermus thermophilus in the states of [Fea3(3+)-(HO2)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], using both PW91-D3 and OLYP-D3 functionals. Tyr237 is a special tyrosine cross-linked to His233, a ligand of CuB. The calculations have shown that the DNC in these states strongly favors the protonation of His376, which is above propionate-A, but not of the carboxylate group of propionate-A. The energies of the structures obtained by constrained geometry optimizations along the O-O bond cleavage pathway between [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] have also been calculated. The transition of [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] → [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] shows a very small barrier, which is less than 3.0/2.0 kcal mol(-1) in PW91-D3/OLYP-D3 calculations. The protonation state of His376 does not affect this O-O cleavage barrier. The rate limiting step of the transition from state A (in which O2 binds to Fea3(2+)) to state PM ([Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], where the O-O bond is cleaved) in the catalytic cycle is, therefore, the proton transfer originating from Tyr237 to O-O to form the hydroperoxo [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] state. The importance of His376 in proton uptake and the function of propionate-A/neutral-Asp372 as a gate to prevent the proton from back-flowing to the DNC are also shown.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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50
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Li B, Mendenhall J, Nguyen ED, Weiner BE, Fischer AW, Meiler J. Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. J Chem Inf Model 2016; 56:423-34. [PMID: 26804342 PMCID: PMC5537626 DOI: 10.1021/acs.jcim.5b00517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prediction of the three-dimensional (3D) structures of proteins by computational methods is acknowledged as an unsolved problem. Accurate prediction of important structural characteristics such as contact number is expected to accelerate the otherwise slow progress being made in the prediction of 3D structure of proteins. Here, we present a dropout neural network-based method, TMH-Expo, for predicting the contact number of transmembrane helix (TMH) residues from sequence. Neuronal dropout is a strategy where certain neurons of the network are excluded from back-propagation to prevent co-adaptation of hidden-layer neurons. By using neuronal dropout, overfitting was significantly reduced and performance was noticeably improved. For multi-spanning helical membrane proteins, TMH-Expo achieved a remarkable Pearson correlation coefficient of 0.69 between predicted and experimental values and a mean absolute error of only 1.68. In addition, among those membrane protein-membrane protein interface residues, 76.8% were correctly predicted. Mapping of predicted contact numbers onto structures indicates that contact numbers predicted by TMH-Expo reflect the exposure patterns of TMHs and reveal membrane protein-membrane protein interfaces, reinforcing the potential of predicted contact numbers to be used as restraints for 3D structure prediction and protein-protein docking. TMH-Expo can be accessed via a Web server at www.meilerlab.org .
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Affiliation(s)
- Bian Li
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeffrey Mendenhall
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Elizabeth Dong Nguyen
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Brian E. Weiner
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Axel W. Fischer
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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