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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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2
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Gorriz RF, Volkenandt S, Imhof P. Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase. Int J Mol Sci 2023; 24:10464. [PMID: 37445646 DOI: 10.3390/ijms241310464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Cytochrome c Oxidase (CcO), a membrane protein of the respiratory chain, pumps protons against an electrochemical gradient by using the energy of oxygen reduction to water. The ("chemical") protons required for this reaction and those pumped are taken up via two distinct channels, named D-channel and K-channel, in a step-wise and highly regulated fashion. In the reductive phase of the catalytic cycle, both channels transport protons so that the pumped proton passes the D-channel before the "chemical" proton has crossed the K-channel. By performing molecular dynamics simulations of CcO in the O→E redox state (after the arrival of the first reducing electron) with various combinations of protonation states of the D- and K-channels, we analysed the effect of protonation on the two channels. In agreement with previous work, the amount of water observed in the D-channel was significantly higher when the terminal residue E286 was not (yet) protonated than when the proton arrived at this end of the D-channel and E286 was neutral. Since a sufficient number of water molecules in the channel is necessary for proton transport, this can be understood as E286 facilitating its own protonation. K-channel hydration shows an even higher dependence on the location of the excess proton in the K-channel. Also in agreement with previous work, the K-channel exhibits a very low hydration level that likely hinders proton transfer when the excess proton is located in the lower part of the K-channel, that is, on the N-side of S365. Once the proton has passed S365 (towards the reaction site, the bi-nuclear centre (BNC)), the amount of water in the K-channel provides hydrogen-bond connectivity that renders proton transfer up to Y288 at the BNC feasible. No significant direct effect of the protonation state of one channel on the hydration level, hydrogen-bond connectivity, or interactions between protein residues in the other channel could be observed, rendering proton conductivity in the two channels independent of each other. Regulation of the order of proton uptake and proton passage in the two channels such that the "chemical" proton leaves its channel last must, therefore, be achieved by other means of communication, such as the location of the reducing electron.
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Affiliation(s)
- Rene F Gorriz
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Senta Volkenandt
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Petra Imhof
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
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3
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Blomberg MRA. The Redox-Active Tyrosine Is Essential for Proton Pumping in Cytochrome c Oxidase. Front Chem 2021; 9:640155. [PMID: 33937193 PMCID: PMC8079940 DOI: 10.3389/fchem.2021.640155] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
Cellular respiration involves electron transport via a number of enzyme complexes to the terminal Cytochrome c oxidase (CcO), in which molecular oxygen is reduced to water. The free energy released in the reduction process is used to establish a transmembrane electrochemical gradient, via two processes, both corresponding to charge transport across the membrane in which the enzymes are embedded. First, the reduction chemistry occurring in the active site of CcO is electrogenic, which means that the electrons and protons are delivered from opposite sides of the membrane. Second, the exergonic chemistry is coupled to translocation of protons across the entire membrane, referred to as proton pumping. In the largest subfamily of the CcO enzymes, the A-family, one proton is pumped for every electron needed for the chemistry, making the energy conservation particularly efficient. In the present study, hybrid density functional calculations are performed on a model of the A-family CcOs. The calculations show that the redox-active tyrosine, conserved in all types of CcOs, plays an essential role for the energy conservation. Based on the calculations a reaction mechanism is suggested involving a tyrosyl radical (possibly mixed with tyrosinate character) in all reduction steps. The result is that the free energy released in each reduction step is large enough to allow proton pumping in all reduction steps without prohibitively high barriers when the gradient is present. Furthermore, the unprotonated tyrosine provides a mechanism for coupling the uptake of two protons per electron in every reduction step, i.e. for a secure proton pumping.
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Affiliation(s)
- Margareta R A Blomberg
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
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4
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Cai X, Haider K, Lu J, Radic S, Son CY, Cui Q, Gunner M. Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:997-1005. [DOI: 10.1016/j.bbabio.2018.05.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/11/2018] [Accepted: 05/16/2018] [Indexed: 11/25/2022]
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5
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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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Samudio BM, Couch V, Stuchebrukhov AA. Monte Carlo Simulations of Glu-242 in Cytochrome c Oxidase. J Phys Chem B 2016; 120:2095-105. [PMID: 26865374 DOI: 10.1021/acs.jpcb.5b10998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Monte Carlo (MC) simulations of conformational changes and protonation of Glu-242, a key residue that shuttles protons in cytochrome c oxidase (CcO), are reported. Previous studies suggest that this residue may play a role of the valve of the enzyme proton pump. Here we examine how sensitive the results of simulations are to the computational method used. We applied both molecular mechanic (MM) and hybrid quantum mechanic:molecular mechanic (QM:MM) methods and find that the results are qualitatively different. The results indicate that the mechanism for proton gating in CcO is still an open issue.
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Affiliation(s)
- Benjamin M Samudio
- Department of Chemistry , University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Vernon Couch
- Department of Chemistry , University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Alexei A Stuchebrukhov
- Department of Chemistry , University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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7
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Blomberg MRA, Siegbahn PEM. Protonation of the binuclear active site in cytochrome c oxidase decreases the reduction potential of CuB. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1173-80. [PMID: 26072193 DOI: 10.1016/j.bbabio.2015.06.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/22/2015] [Accepted: 06/07/2015] [Indexed: 12/14/2022]
Abstract
One of the remaining mysteries regarding the respiratory enzyme cytochrome c oxidase is how proton pumping can occur in all reduction steps in spite of the low reduction potentials observed in equilibrium titration experiments for two of the active site cofactors, CuB(II) and Fea3(III). It has been speculated that, at least the copper cofactor can acquire two different states, one metastable activated state occurring during enzyme turnover, and one relaxed state with lower energy, reached only when the supply of electrons stops. The activated state should have a transiently increased CuB(II) reduction potential, allowing proton pumping. The relaxed state should have a lower reduction potential, as measured in the titration experiments. However, the structures of these two states are not known. Quantum mechanical calculations show that the proton coupled reduction potential for CuB is inherently high in the active site as it appears after reaction with oxygen, which explains the observed proton pumping. It is suggested here that, when the flow of electrons ceases, a relaxed resting state is formed by the uptake of one extra proton, on top of the charge compensating protons delivered in each reduction step. The extra proton in the active site decreases the proton coupled reduction potential for CuB by almost half a volt, leading to agreement with titration experiments. Furthermore, the structure for the resting state with an extra proton is found to have a hydroxo-bridge between CuB(II) and Fea3(III), yielding a magnetic coupling that can explain the experimentally observed EPR silence.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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8
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Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pKA and conformation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1837:1998-2003. [PMID: 25149865 DOI: 10.1016/j.bbabio.2014.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/09/2014] [Accepted: 08/12/2014] [Indexed: 11/21/2022]
Abstract
The metabolism of aerobic life uses the conversion of molecular oxygen to water as an energy source. This reaction is catalyzed by cytochrome e oxidase (CeO) consuming four electrons and four protons, which move along specific routes. While all four electrons are transferred via the same cofactors to the binuclear reaction center (BNC), the protons take two different routes in the A-type CeO, i.e., two of the four chemical protons consumed in the reaction arrive via the D-channel in the oxidative first half starting after oxygen binding. The other two chemical protons enter via the K-channel in the reductive second half of the reaction cycle. To date, the mechanism behind these separate proton transport pathways has not been understood. In this study, we propose a model that can explain the reaction-step specific opening and closing of the K-channel by conformational and pKA changes of its central lysine 362. Molecular dynamics simulations reveal an upward movement of Lys362 towards the BNC, which had already been supposed by several experimental studies. Redox state-dependent pKA calculations provide evidence that Lys362 may protonate transiently, thereby opening the K-channel only in the reductive second half of the reaction cycle. From our results, we develop a model that assigns a key role to Lys362 in the proton gating between the two proton input channels of the A-type CeO.
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9
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Wikström M, Sharma V, Kaila VRI, Hosler JP, Hummer G. New Perspectives on Proton Pumping in Cellular Respiration. Chem Rev 2015; 115:2196-221. [DOI: 10.1021/cr500448t] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mårten Wikström
- Institute
of Biotechnology, University of Helsinki, Biocenter 3 (Viikinkaari 1), PB
65, Helsinki 00014, Finland
| | - Vivek Sharma
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, Tampere 33720, Finland
| | - Ville R. I. Kaila
- Department
Chemie, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching, Germany
| | - Jonathan P. Hosler
- Department
of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße
3, 60438 Frankfurt
am Main, Germany
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10
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How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradient. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:364-376. [PMID: 25529353 DOI: 10.1016/j.bbabio.2014.12.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 11/18/2014] [Accepted: 12/10/2014] [Indexed: 12/12/2022]
Abstract
Experiments have shown that the A-family cytochrome c oxidases pump four protons per oxygen molecule, also at a high electrochemical gradient. This has been considered a puzzle, since two of the reduction potentials involved, Cu(II) and Fe(III), were estimated from experiments to be too low to afford proton pumping at a high gradient. The present quantum mechanical study (using hybrid density functional theory) suggests a solution to this puzzle. First, the calculations show that the charge compensated Cu(II) potential for CuB is actually much higher than estimated from experiment, of the same order as the reduction potentials for the tyrosyl radical and the ferryl group, which are also involved in the catalytic cycle. The reason for the discrepancy between theory and experiment is the very large uncertainty in the experimental observations used to estimate the equilibrium potentials, mainly caused by the lack of methods for direct determination of reduced CuB. Second, the calculations show that a high energy metastable state, labeled EH, is involved during catalytic turnover. The EH state mixes the low reduction potential of Fe(III) in heme a3 with another, higher potential, here suggested to be that of the tyrosyl radical, resulting in enough exergonicity to allow proton pumping at a high gradient. In contrast, the corresponding metastable oxidized state, OH, is not significantly higher in energy than the resting state, O. Finally, to secure the involvement of the high energy EH state it is suggested that only one proton is taken up via the K-channel during catalytic turnover.
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11
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Blomberg MRA, Siegbahn PEM. Proton pumping in cytochrome c oxidase: energetic requirements and the role of two proton channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1165-77. [PMID: 24418352 DOI: 10.1016/j.bbabio.2014.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/02/2014] [Accepted: 01/06/2014] [Indexed: 12/15/2022]
Abstract
Cytochrome c oxidase is a superfamily of membrane bound enzymes catalyzing the exergonic reduction of molecular oxygen to water, producing an electrochemical gradient across the membrane. The gradient is formed both by the electrogenic chemistry, taking electrons and protons from opposite sides of the membrane, and by proton pumping across the entire membrane. In the most efficient subfamily, the A-family of oxidases, one proton is pumped in each reduction step, which is surprising considering the fact that two of the reduction steps most likely are only weakly exergonic. Based on a combination of quantum chemical calculations and experimental information, it is here shown that from both a thermodynamic and a kinetic point of view, it should be possible to pump one proton per electron also with such an uneven distribution of the free energy release over the reduction steps, at least up to half the maximum gradient. A previously suggested pumping mechanism is developed further to suggest a reason for the use of two proton transfer channels in the A-family. Since the rate of proton transfer to the binuclear center through the D-channel is redox dependent, it might become too slow for the steps with low exergonicity. Therefore, a second channel, the K-channel, where the rate is redox-independent is needed. A redox-dependent leakage possibility is also suggested, which might be important for efficient energy conservation at a high gradient. A mechanism for the variation in proton pumping stoichiometry over the different subfamilies of cytochrome oxidase is also suggested. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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von Ballmoos C, Lachmann P, Gennis RB, Ädelroth P, Brzezinski P. Timing of Electron and Proton Transfer in the ba3 Cytochrome c Oxidase from Thermus thermophilus. Biochemistry 2012; 51:4507-17. [DOI: 10.1021/bi300132t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christoph von Ballmoos
- Department of Biochemistry and
Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Lachmann
- Department of Biochemistry and
Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, United
States
| | - Pia Ädelroth
- Department of Biochemistry and
Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and
Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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Lee HJ, Reimann J, Huang Y, Ädelroth P. Functional proton transfer pathways in the heme–copper oxidase superfamily. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:537-44. [DOI: 10.1016/j.bbabio.2011.10.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 10/19/2011] [Accepted: 10/21/2011] [Indexed: 12/21/2022]
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Proton transfer in ba3 cytochrome c oxidase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:650-7. [DOI: 10.1016/j.bbabio.2011.11.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/15/2011] [Accepted: 11/16/2011] [Indexed: 11/23/2022]
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Varanasi L, Hosler JP. Subunit III-depleted cytochrome c oxidase provides insight into the process of proton uptake by proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:545-51. [PMID: 22023935 DOI: 10.1016/j.bbabio.2011.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/10/2011] [Accepted: 10/10/2011] [Indexed: 11/30/2022]
Abstract
We review studies of subunit III-depleted cytochrome c oxidase (CcO III (-)) that elucidate the structural basis of steady-state proton uptake from solvent into an internal proton transfer pathway. The removal of subunit III from R. sphaeroides CcO makes proton uptake into the D pathway a rate-determining step, such that measurements of the pH dependence of steady-state O(2) consumption can be used to compare the rate and functional pK(a) of proton uptake by D pathways containing different initial proton acceptors. The removal of subunit III also promotes spontaneous suicide inactivation by CcO, greatly shortening its catalytic lifespan. Because the probability of suicide inactivation is controlled by the rate at which the D pathway delivers protons to the active site, measurements of catalytic lifespan provide a second method to compare the relative efficacy of proton uptake by engineered CcO III (-) forms. These simple experimental systems have been used to explore general questions of proton uptake by proteins, such as the functional value of an initial proton acceptor, whether an initial acceptor must be surface-exposed, which side chains will function as initial proton acceptors and whether multiple acceptors can speed proton uptake.
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Affiliation(s)
- Lakshman Varanasi
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS, USA.
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