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Ishigami I, Carbajo S, Zatsepin N, Hikita M, Conrad CE, Nelson G, Coe J, Basu S, Grant T, Seaberg MH, Sierra RG, Hunter MS, Fromme P, Fromme R, Rousseau DL, Yeh SR. Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography. J Am Chem Soc 2023; 145:22305-22309. [PMID: 37695261 PMCID: PMC10814876 DOI: 10.1021/jacs.3c07803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Cytochrome c oxidase (CcO) is a large membrane-bound hemeprotein that catalyzes the reduction of dioxygen to water. Unlike classical dioxygen binding hemeproteins with a heme b group in their active sites, CcO has a unique binuclear center (BNC) composed of a copper atom (CuB) and a heme a3 iron, where O2 binds and is reduced to water. CO is a versatile O2 surrogate in ligand binding and escape reactions. Previous time-resolved spectroscopic studies of the CO complexes of bovine CcO (bCcO) revealed that photolyzing CO from the heme a3 iron leads to a metastable intermediate (CuB-CO), where CO is bound to CuB, before it escapes out of the BNC. Here, with a pump-probe based time-resolved serial femtosecond X-ray crystallography, we detected a geminate photoproduct of the bCcO-CO complex, where CO is dissociated from the heme a3 iron and moved to a temporary binding site midway between the CuB and the heme a3 iron, while the locations of the two metal centers and the conformation of Helix-X, housing the proximal histidine ligand of the heme a3 iron, remain in the CO complex state. This new structure, combined with other reported structures of bCcO, allows for a clearer definition of the ligand dissociation trajectory as well as the associated protein dynamics.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- Electrical and Computer Engineering Department, University of California Los Angeles, Los Angeles, California 90045, United States
- Physics and Astronomy Department, University of California Los Angeles, Los Angeles, California 90045, United States
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- Chemistry and Physics, La Trobe University, Bundoora, VIC 3086, Australia
| | - Masahide Hikita
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Chelsie E Conrad
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Jesse Coe
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shibom Basu
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Thomas Grant
- Department of Structural Biology, University of Buffalo, Buffalo, New York 14203, United States
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Petra Fromme
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Raimund Fromme
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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Jancura D, Tomkova A, Sztachova T, Berka V, Fabian M. Examination of 'high-energy' metastable state of the oxidized (O H) bovine cytochrome c oxidase: Proton uptake and reaction with H 2O 2. Arch Biochem Biophys 2023; 747:109758. [PMID: 37748626 DOI: 10.1016/j.abb.2023.109758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
Reoxidized cytochrome c oxidase appears to be in a 'high-energy' metastable state (OH) in which part of the energy released in the redox reactions is stored. The OH is supposed to relax to the resting 'as purified' oxidized state (O) in a time exceeding 200 ms. The catalytic heme a3-CuB center of these two forms should differ in a protonation and ligation state and the transition of OH-to-O is suggested to be associated with a proton transfer into this center. Employing a stopped-flow and UV-Vis absorption spectroscopy we investigated a proton uptake during the predicted relaxation of OH. It is shown, using a pH indicator phenol red, that from the time when the oxidation of the fully reduced CcO is completed (∼25 ms) up to ∼10 min, there is no uptake of a proton from the external medium (pH 7.8). Moreover, interactions of the assumed OH, generated 100 ms after oxidation of the fully reduced CcO, and the O with H2O2 (1 mM), result in the formation of two ferryl intermediates of the catalytic center, P and F, with very similar kinetics and the amounts of the formed ferryl states in both cases. These results implicate that the relaxation time of the catalytic center during the OH-to-O transition is either shorter than 100 ms or there is no difference in the structure of heme a3-CuB center of these two forms.
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Affiliation(s)
- D Jancura
- Department of Biophysics, Faculty of Science, University of P. J. Safarik, Jesenna 5, 041 54, Kosice, Slovak Republic
| | - A Tomkova
- Department of Biophysics, Faculty of Science, University of P. J. Safarik, Jesenna 5, 041 54, Kosice, Slovak Republic
| | - T Sztachova
- Department of Biophysics, Faculty of Science, University of P. J. Safarik, Jesenna 5, 041 54, Kosice, Slovak Republic
| | - V Berka
- Department of Internal Medicine, University of Texas Health Science Center, 77030, Houston, Texas, USA
| | - M Fabian
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, University of P. J. Safarik, Jesenna 5, 041 54, Kosice, Slovak Republic.
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Ishigami I, Sierra RG, Su Z, Peck A, Wang C, Poitevin F, Lisova S, Hayes B, Moss FR, Boutet S, Sublett RE, Yoon CH, Yeh SR, Rousseau DL. Structural insights into functional properties of the oxidized form of cytochrome c oxidase. Nat Commun 2023; 14:5752. [PMID: 37717031 PMCID: PMC10505203 DOI: 10.1038/s41467-023-41533-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable OH state, and a reductive phase, in which OH is reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Cong Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Frank R Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Altos Labs, Redwood City, CA, 94065, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Robert E Sublett
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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Ishigami I, Carbajo S, Zatsepin N, Hikita M, Conrad CE, Nelson G, Coe J, Basu S, Grant T, Seaberg MH, Sierra RG, Hunter MS, Fromme P, Fromme R, Rousseau DL, Yeh SR. Detection of a geminate photoproduct of bovine cytochrome c oxidase by time-resolved serial femtosecond crystallography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539888. [PMID: 37214971 PMCID: PMC10197551 DOI: 10.1101/2023.05.08.539888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cytochrome c oxidase (C c O) is a large membrane-bound hemeprotein that catalyzes the reduction of dioxygen to water. Unlike classical dioxygen binding hemeproteins with a heme b group in their active sites, C c O has a unique binuclear center (BNC) comprised of a copper atom (Cu B ) and a heme a 3 iron, where O 2 binds and is reduced to water. CO is a versatile O 2 surrogate in ligand binding and escape reactions. Previous time-resolved spectroscopic studies of the CO complexes of bovine C c O (bC c O) revealed that photolyzing CO from the heme a 3 iron leads to a metastable intermediate (Cu B -CO), where CO is bound to Cu B , before it escapes out of the BNC. Here, with a time-resolved serial femtosecond X-ray crystallography-based pump-probe method, we detected a geminate photoproduct of the bC c O-CO complex, where CO is dissociated from the heme a 3 iron and moved to a temporary binding site midway between the Cu B and the heme a 3 iron, while the locations of the two metal centers and the conformation of the Helix-X, housing the proximal histidine ligand of the heme a 3 iron, remain in the CO complex state. This new structure, combined with other reported structures of bC c O, allows the full definition of the ligand dissociation trajectory, as well as the associated protein dynamics.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park. CA, 94025, USA
- Electrical & Computer Engineering Department, University of California Los Angeles, Los Angeles, CA 90045
- Physics & Astronomy Department, University of California Los Angeles, Los Angeles, CA 90045
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- Chemistry and Physics, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - Masahide Hikita
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Chelsie E. Conrad
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse Coe
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Shibom Basu
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas Grant
- Department of Structural Biology, University Buffalo, 955 Main Street, Buffalo, New York 14203, USA
| | - Matthew H. Seaberg
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park. CA, 94025, USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park. CA, 94025, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park. CA, 94025, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Denis L. Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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Shimada A, Tsukihara T, Yoshikawa S. Recent progress in experimental studies on the catalytic mechanism of cytochrome c oxidase. Front Chem 2023; 11:1108190. [PMID: 37214485 PMCID: PMC10194837 DOI: 10.3389/fchem.2023.1108190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Cytochrome c oxidase (CcO) reduces molecular oxygen (O2) to water, coupled with a proton pump from the N-side to the P-side, by receiving four electrons sequentially from the P-side to the O2-reduction site-including Fea3 and CuB-via the two low potential metal sites; CuA and Fea. The catalytic cycle includes six intermediates as follows, R (Fea3 2+, CuB 1+, Tyr244OH), A (Fea3 2+-O2, CuB 1+, Tyr244OH), Pm (Fea3 4+ = O2-, CuB 2+-OH-, Tyr244O•), F (Fea3 4+ = O2-, CuB 2+-OH-, Tyr244OH), O (Fea3 3+-OH-, CuB 2+-OH-, Tyr244OH), and E (Fea3 3+-OH-, CuB 1+-H2O, Tyr244OH). CcO has three proton conducting pathways, D, K, and H. The D and K pathways connect the N-side surface with the O2-reduction site, while the H-pathway is located across the protein from the N-side to the P-side. The proton pump is driven by electrostatic interactions between the protons to be pumped and the net positive charges created during the O2 reduction. Two different proton pump proposals, each including either the D-pathway or H-pathway as the proton pumping site, were proposed approximately 30 years ago and continue to be under serious debate. In our view, the progress in understanding the reaction mechanism of CcO has been critically rate-limited by the resolution of its X-ray crystallographic structure. The improvement of the resolutions of the oxidized/reduced bovine CcO up to 1.5/1.6 Å resolution in 2016 provided a breakthrough in the understanding of the reaction mechanism of CcO. In this review, experimental studies on the reaction mechanism of CcO before the appearance of the 1.5/1.6 Å resolution X-ray structures are summarized as a background description. Following the summary, we will review the recent (since 2016) experimental findings which have significantly improved our understanding of the reaction mechanism of CcO including: 1) redox coupled structural changes of bovine CcO; 2) X-ray structures of all six intermediates; 3) spectroscopic findings on the intermediate species including the Tyr244 radical in the Pm form, a peroxide-bound form between the A and Pm forms, and Fr, a one-electron reduced F-form; 4) time resolved X-ray structural changes during the photolysis of CO-bound fully reduced CcO using XFEL; 5) a simulation analysis for the Pm→Pr→F transition.
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Affiliation(s)
- Atsuhiro Shimada
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Tomitake Tsukihara
- Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo, Japan
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Shinya Yoshikawa
- Department of Life Science, Graduate School of Science, University of Hyogo, Hyogo, Japan
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Ishigami I, Sierra RG, Su Z, Peck A, Wang C, Poitevin F, Lisova S, Hayes B, Moss FR, Boutet S, Sublett RE, Yoon CH, Yeh SR, Rousseau DL. Structural basis for functional properties of cytochrome c oxidase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.530986. [PMID: 36993562 PMCID: PMC10055264 DOI: 10.1101/2023.03.20.530986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes, thereby establishing the proton gradient required for ATP synthesis1. The full turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized by molecular oxygen to the metastable oxidized OH state, and a reductive phase, in which OH is reduced back to the R state. During each of the two phases, two protons are translocated across the membranes2. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation2,3. How the O state structurally differs from OH remains an enigma in modern bioenergetics. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX)4, we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state5,6, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, a residue covalently linked to one of the three CuB ligands and critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide new insights into the proton translocation mechanism of CcO.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305 USA
| | - Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Cong Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Robert E. Sublett
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Denis L. Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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Bhunia S, Ghatak A, Dey A. Second Sphere Effects on Oxygen Reduction and Peroxide Activation by Mononuclear Iron Porphyrins and Related Systems. Chem Rev 2022; 122:12370-12426. [PMID: 35404575 DOI: 10.1021/acs.chemrev.1c01021] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation and reduction of O2 and H2O2 by synthetic and biosynthetic iron porphyrin models have proved to be a versatile platform for evaluating second-sphere effects deemed important in naturally occurring heme active sites. Advances in synthetic techniques have made it possible to install different functional groups around the porphyrin ligand, recreating artificial analogues of the proximal and distal sites encountered in the heme proteins. Using judicious choices of these substituents, several of the elegant second-sphere effects that are proposed to be important in the reactivity of key heme proteins have been evaluated under controlled environments, adding fundamental insight into the roles played by these weak interactions in nature. This review presents a detailed description of these efforts and how these have not only demystified these second-sphere effects but also how the knowledge obtained resulted in functional mimics of these heme enzymes.
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Affiliation(s)
- Sarmistha Bhunia
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, India
| | - Arnab Ghatak
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, India
| | - Abhishek Dey
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, India
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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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Silveira CM, Zuccarello L, Barbosa C, Caserta G, Zebger I, Hildebrandt P, Todorovic S. Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies. Molecules 2021; 26:4852. [PMID: 34443440 PMCID: PMC8398457 DOI: 10.3390/molecules26164852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022] Open
Abstract
Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.
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Affiliation(s)
- Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Lidia Zuccarello
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
| | - Giorgio Caserta
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Ingo Zebger
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Peter Hildebrandt
- Institut fur Chemie, Sekr. PC14, Technische Universitat Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany; (G.C.); (I.Z.); (P.H.)
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (C.M.S.); (L.Z.); (C.B.)
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10
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Capitanio G, Papa F, Papa S. The allosteric protein interactions in the proton-motive function of mammalian redox enzymes of the respiratory chain. Biochimie 2021; 189:1-12. [PMID: 34097987 DOI: 10.1016/j.biochi.2021.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/17/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022]
Abstract
Insight into mammalian respiratory complexes defines the role of allosteric protein interactions in their proton-motive activity. In cytochrome c oxidase (CxIV) conformational change of subunit I, caused by O2 binding to heme a32+-CuB+ and reduction, and stereochemical transitions coupled to oxidation/reduction of heme a and CuA, combined with electrostatic effects, determine the proton pumping activity. In ubiquinone-cytochrome c oxidoreductase (CxIII) conformational movement of Fe-S protein between cytochromes b and c1 is the key element of the proton-motive activity. In NADH-ubiquinone oxidoreductase (CxI) ubiquinone binding and reduction result in conformational changes of subunits in the quinone reaction structure which initiate proton pumping.
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Affiliation(s)
- Giuseppe Capitanio
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124, Bari, Italy.
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124, Bari, Italy.
| | - Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124, Bari, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy.
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11
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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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12
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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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13
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The structure of the oxidized state of cytochrome c oxidase - experiments and theory compared. J Inorg Biochem 2020; 206:111020. [PMID: 32062501 DOI: 10.1016/j.jinorgbio.2020.111020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 11/22/2022]
Abstract
Cytochrome c oxidase (CcO), the terminal enzyme in the respiratory chain, reduces molecular oxygen to water. Experimental data on the midpoint potentials of the heme iron/copper active site cofactors do not match the overall reaction energetics, and are also in conflict with the observed efficiency of energy conservation in CcO. Therefore it has been postulated that the ferric/cupric intermediate (the oxidized state) exists in two forms. One form, labelled OH, is presumably involved during catalytic turnover, and should have a high CuB midpoint potential due to a metastable high energy structure. When no more electrons are supplied, the OH state supposedly relaxes to the resting form, labelled O, with a lower energy and a lower midpoint potential. It has been suggested that there is a pure geometrical difference between the OH and O states, obtained by moving a water molecule inside the active site. It is shown here that the difference between the two forms of the oxidized state must be of a more chemical nature. The reason is that all types of geometrically relaxed structures of the oxidized intermediate have similar energies, all with a high proton coupled reduction potential in accordance with the postulated OH state. One hypothesized chemical modification of the OH state is the transfer of an extra proton, possibly internal, into the active site. Such a protonated state has several properties that agree with experimental data on the relaxed oxidized state, including a decreased midpoint potential.
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14
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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15
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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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16
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Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase. Proc Natl Acad Sci U S A 2019; 116:3572-3577. [PMID: 30808749 DOI: 10.1073/pnas.1814526116] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase (CcO) reduces dioxygen to water and harnesses the chemical energy to drive proton translocation across the inner mitochondrial membrane by an unresolved mechanism. By using time-resolved serial femtosecond crystallography, we identified a key oxygen intermediate of bovine CcO. It is assigned to the PR-intermediate, which is characterized by specific redox states of the metal centers and a distinct protein conformation. The heme a 3 iron atom is in a ferryl (Fe4+ = O2-) configuration, and heme a and CuB are oxidized while CuA is reduced. A Helix-X segment is poised in an open conformational state; the heme a farnesyl sidechain is H-bonded to S382, and loop-I-II adopts a distinct structure. These data offer insights into the mechanism by which the oxygen chemistry is coupled to unidirectional proton translocation.
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17
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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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18
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Wikström M, Sharma V. Proton pumping by cytochrome c oxidase – A 40 year anniversary. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:692-698. [DOI: 10.1016/j.bbabio.2018.03.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 12/21/2022]
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19
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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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20
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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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21
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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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22
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Mittra K, Sengupta K, Singha A, Bandyopadhyay S, Chatterjee S, Rana A, Samanta S, Dey A. Second sphere control of spin state: Differential tuning of axial ligand bonds in ferric porphyrin complexes by hydrogen bonding. J Inorg Biochem 2016; 155:82-91. [DOI: 10.1016/j.jinorgbio.2015.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/02/2015] [Accepted: 11/10/2015] [Indexed: 11/16/2022]
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23
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Mukherjee S, Mukherjee A, Bhagi-Damodaran A, Mukherjee M, Lu Y, Dey A. A biosynthetic model of cytochrome c oxidase as an electrocatalyst for oxygen reduction. Nat Commun 2015; 6:8467. [PMID: 26455726 PMCID: PMC4633646 DOI: 10.1038/ncomms9467] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 08/24/2015] [Indexed: 12/30/2022] Open
Abstract
Creating an artificial functional mimic of the mitochondrial enzyme cytochrome c oxidase (CcO) has been a long-term goal of the scientific community as such a mimic will not only add to our fundamental understanding of how CcO works but may also pave the way for efficient electrocatalysts for oxygen reduction in hydrogen/oxygen fuel cells. Here we develop an electrocatalyst for reducing oxygen to water under ambient conditions. We use site-directed mutants of myoglobin, where both the distal Cu and the redox-active tyrosine residue present in CcO are modelled. In situ Raman spectroscopy shows that this catalyst features very fast electron transfer rates, facile oxygen binding and O-O bond lysis. An electron transfer shunt from the electrode circumvents the slow dissociation of a ferric hydroxide species, which slows down native CcO (bovine 500 s(-1)), allowing electrocatalytic oxygen reduction rates of 5,000 s(-1) for these biosynthetic models.
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Affiliation(s)
- Sohini Mukherjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja SC Mullick Road, Jadavpur Kolkata 700032, India
| | - Arnab Mukherjee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Manjistha Mukherjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja SC Mullick Road, Jadavpur Kolkata 700032, India
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja SC Mullick Road, Jadavpur Kolkata 700032, India
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24
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Chatterjee S, Sengupta K, Hematian S, Karlin KD, Dey A. Electrocatalytic O2-Reduction by Synthetic Cytochrome c Oxidase Mimics: Identification of a "Bridging Peroxo" Intermediate Involved in Facile 4e(-)/4H(+) O2-Reduction. J Am Chem Soc 2015; 137:12897-905. [PMID: 26419806 DOI: 10.1021/jacs.5b06513] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A synthetic heme-Cu CcO model complex shows selective and highly efficient electrocatalytic 4e(-)/4H(+) O2-reduction to H2O with a large catalytic rate (>10(5) M(-1) s(-1)). While the heme-Cu model (FeCu) shows almost exclusive 4e(-)/4H(+) reduction of O2 to H2O (detected using ring disk electrochemistry and rotating ring disk electrochemistry), when imidazole is bound to the heme (Fe(Im)Cu), this same selective O2-reduction to water occurs only under slow electron fluxes. Surface enhanced resonance Raman spectroscopy coupled to dynamic electrochemistry data suggests the formation of a bridging peroxide intermediate during O2-reduction by both complexes under steady state reaction conditions, indicating that O-O bond heterolysis is likely to be the rate-determining step (RDS) at the mass transfer limited region. The O-O vibrational frequencies at 819 cm(-1) in (16)O2 (759 cm(-1) in (18)O2) for the FeCu complex and at 847 cm(-1) (786 cm(-1)) for the Fe(Im)Cu complex, indicate the formation of side-on and end-on bridging Fe-peroxo-Cu intermediates, respectively, during O2-reduction in an aqueous environment. These data suggest that side-on bridging peroxide intermediates are involved in fast and selective O2-reduction in these synthetic complexes. The greater amount of H2O2 production by the imidazole bound complex under fast electron transfer is due to 1e(-)/1H(+) O2-reduction by the distal Cu where O2 binding to the water bound low spin Fe(II) complex is inhibited.
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Affiliation(s)
- Sudipta Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Kushal Sengupta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Shabnam Hematian
- 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
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
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25
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
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26
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Wilson DF, Vinogradov SA. Mitochondrial cytochrome c oxidase: mechanism of action and role in regulating oxidative phosphorylation. J Appl Physiol (1985) 2014; 117:1431-9. [PMID: 25324518 DOI: 10.1152/japplphysiol.00737.2014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial oxidative phosphorylation has a central role in eukaryotic metabolism, providing the energy (ATP) required for survival. Regulation of this important pathway is, however, still not understood, largely due to limitations in the ability to measure the essential metabolites, including oxygen (pO2, oxygen pressure), ADP, and AMP. In addition, neither the mechanism of oxygen reduction by mitochondrial cytochrome c oxidase nor how its rate is controlled is understood, although this enzyme determines the rate of oxygen consumption and thereby the rate of ATP synthesis. Cytochrome c oxidase is responsible for reduction of molecular oxygen to water using reducing equivalents donated by cytochrome c and for site 3 energy coupling in oxidative phosphorylation. A mechanism-based model of the cytochrome c oxidase reaction is presented in which transfer of reducing equivalents from the lower- to the higher-potential region of the coupling site occurs against an opposing energy barrier, Q. The steady-state rate equation is fitted to data for the dependence of mitochondrial respiratory rate on cytochrome c reduction, oxygen pressure (pO2), and [ATP]/[ADP][Pi] at pH 6.5 to 8.35 (where Pi is inorganic phosphate). The fit of the rate expression to the experimental data is very good for all experimental conditions. Levels of the intermediates in oxygen reduction in the oxidase reaction site have been calculated. An intermediate in the reaction, tentatively identified as peroxide, bridged between the iron and copper atoms of the reaction site has a central role in coupling mitochondrial respiration to the [ATP]/[ADP][Pi].
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Affiliation(s)
- David F Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sergei A Vinogradov
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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27
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Wilson DF, Harrison DK, Vinogradov A. Mitochondrial cytochrome c oxidase and control of energy metabolism: measurements in suspensions of isolated mitochondria. J Appl Physiol (1985) 2014; 117:1424-30. [PMID: 25324517 DOI: 10.1152/japplphysiol.00736.2014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Cytochrome c oxidase is the enzyme responsible for oxygen consumption by mitochondrial oxidative phosphorylation and coupling site 3 of oxidative phosphorylation. In this role it determines the cellular rate of ATP synthesis by oxidative phosphorylation and is the key to understanding how energy metabolism is regulated. Four electrons are required for the reduction of oxygen to water, and these are provided by the one-electron donor, cytochrome c. The rate of oxygen consumption (ATP synthesis) is dependent on the fraction of cytochrome c reduced (fred), oxygen pressure (pO2), energy state ([ATP]/[ADP][Pi]), and pH. In coupled mitochondria (high energy state) and pO2 >60 torr, the rate increases in an exponential-like fashion with increasing fred. When the dependence on fred is fitted to the equation rate = A: (fred)(b), A: decreased from 100 to near 20, and B: increased from 1.3 to 4 as the pH of the medium increased from 6.5 to 8.3. During oxygen depletion from the medium fred progressively increases and the rate of respiration decreases. The respiratory rate falls to ½ (P50) by about 1.5 torr, at which point fred is substantially increased. The metabolically relevant dependence on pO2 is obtained by correcting for the increase in fred, in which case the P50 is 12 torr. Adding an uncoupler of oxidative phosphorylation eliminates the dependence of the cytochrome c oxidase activity on pH and energy state. The respiratory rate becomes proportional to fred and the P50 decreases to less than 1 torr.
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Affiliation(s)
- David F Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania;
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28
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Nomura T, Yanagisawa S, Shinzawa-Itoh K, Yoshikawa S, Ogura T. Effects of proton motive force on the structure and dynamics of bovine cytochrome C oxidase in phospholipid vesicles. Biochemistry 2014; 53:6382-91. [PMID: 25231381 DOI: 10.1021/bi501022j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A conventional method for reconstituting cytochrome c oxidase (CcO) into phospholipid vesicles (COV) has been modified to permit resonance Raman (RR) analysis in the presence and absence of proton motive force (ΔμH(+)). The COV has an average diameter of 20 nm and contains one CcO molecule within a unified orientation with CuA located outside the COV. The process of generation of ΔμH(+) across the membrane was monitored spectrophotometrically with rhodamine123 dye. The COV exhibits a respiratory control ratio (RCR) value of >30 and is tolerant to RR measurements with 10 mW laser illumination for 60 min at 441.6 nm. Structural perturbations at the heme sites caused by incorporation into vesicles were clarified by spectral comparisons between solubilized CcO and COV. Absorption spectroscopy revealed that the rate of electron transfer from cytochrome c to O2 is reduced significantly more in the presence of ΔμH(+) than in its absence. RR spectroscopic measurements indicate that CcO in COV in the "respiratory-controlled" state adopts a mixed-valence state (heme a(2+) and heme a3(3+)). This study establishes a supramolecular model system for experimentally examining the energy conversion protein machinery in the presence of ΔμH(+).
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Affiliation(s)
- Takashi Nomura
- Laboratory of Spectroscopy, Graduate School of Life Science, University of Hyogo , RSC-UH Leading Program Center, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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29
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Ishigami I, Hikita M, Egawa T, Yeh SR, Rousseau DL. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:98-108. [PMID: 25268561 DOI: 10.1016/j.bbabio.2014.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/11/2014] [Accepted: 09/20/2014] [Indexed: 11/19/2022]
Abstract
Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLoS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Masahide Hikita
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Denis L Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1138] [Impact Index Per Article: 113.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
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31
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Computational study of the activated O(H) state in the catalytic mechanism of cytochrome c oxidase. Proc Natl Acad Sci U S A 2013; 110:16844-9. [PMID: 24082138 DOI: 10.1073/pnas.1220379110] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Complex IV in the respiratory chain of mitochondria and bacteria catalyzes reduction of molecular oxygen to water, and conserves much of the liberated free energy as an electrochemical proton gradient, which is used for the synthesis of ATP. Photochemical electron injection experiments have shown that reduction of the ferric/cupric state of the enzyme's binuclear heme a3/CuB center is coupled to proton pumping across the membrane, but only if oxidation of the reduced enzyme by O2 immediately precedes electron injection. In contrast, reduction of the binuclear center in the "as-isolated" ferric/cupric enzyme is sluggish and without linkage to proton translocation. During turnover, the binuclear center apparently shuttles via a metastable but activated ferric/cupric state (O(H)), which may decay into a more stable catalytically incompetent form (O) in the absence of electron donors. The structural basis for the difference between these two states has remained elusive, and is addressed here using computational methodology. The results support the notion that CuB[II] is either three-coordinated in the O(H) state or shares an OH(-) ligand with heme a3 in a strained μ-hydroxo structure. Relaxation to state O is initiated by hydration of the binuclear site. The redox potential of CuB is expected, and found by density functional theory calculations, to be substantially higher in the O(H) state than in state O. Our calculations also suggest that the neutral radical form of the cross-linked tyrosine in the binuclear site may be more significant in the catalytic cycle than suspected so far.
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32
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Current advances in research of cytochrome c oxidase. Amino Acids 2013; 45:1073-87. [PMID: 23999646 DOI: 10.1007/s00726-013-1585-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/21/2013] [Indexed: 12/13/2022]
Abstract
The function of cytochrome c oxidase as a biomolecular nanomachine that transforms energy of redox reaction into protonmotive force across a biological membrane has been subject of intense research, debate, and controversy. The structure of the enzyme has been solved for several organisms; however details of its molecular mechanism of proton pumping still remain elusive. Particularly, the identity of the proton pumping site, the key element of the mechanism, is still open to dispute. The pumping mechanism has been for a long time one of the key unsolved issues of bioenergetics and biochemistry, but with the accelerating progress in this field many important details and principles have emerged. Current advances in cytochrome oxidase research are reviewed here, along with a brief discussion of the most complete proton pumping mechanism proposed to date, and a molecular basis for control of its efficiency.
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Pinakoulaki E, Daskalakis V, Ohta T, Richter OMH, Budiman K, Kitagawa T, Ludwig B, Varotsis C. The protein effect in the structure of two ferryl-oxo intermediates at the same oxidation level in the heme copper binuclear center of cytochrome c oxidase. J Biol Chem 2013; 288:20261-6. [PMID: 23723073 DOI: 10.1074/jbc.m113.468488] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Identification of the intermediates and determination of their structures in the reduction of dioxygen to water by cytochrome c oxidase (CcO) are particularly important to understanding both O2 activation and proton pumping by the enzyme. In this work, we report the products of the rapid reaction of O2 with the mixed valence form (CuA(2+), heme a(3+), heme a3(2+)-CuB(1+)) of the enzyme. The resonance Raman results show the formation of two ferryl-oxo species with characteristic Fe(IV)=O stretching modes at 790 and 804 cm(-1) at the peroxy oxidation level (PM). Density functional theory calculations show that the protein environment of the proximal H-bonded His-411 determines the strength of the distal Fe(IV)=O bond. In contrast to previous proposals, the PM intermediate is also formed in the reaction of Y167F with O2. These results suggest that in the fully reduced enzyme, the proton pumping ν(Fe(IV)=O) = 804 cm(-1) to ν(Fe(IV)=O) = 790 cm(-1) transition (P→F, where P is peroxy and F is ferryl) is triggered not only by electron transfer from heme a to heme a3 but also by the formation of the H-bonded form of the His-411-Fe(IV)=O conformer in the proximal site of heme a3. The implications of these results with respect to the role of an O=Fe(IV)-His-411-H-bonded form to the ring A propionate of heme a3-Asp-399-H2O site and, thus, to the exit/output proton channel (H2O) pool during the proton pumping P→F transition are discussed. We propose that the environment proximal to the heme a3 controls the spectroscopic properties of the ferryl intermediates in cytochrome oxidases.
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Affiliation(s)
- Eftychia Pinakoulaki
- Department of Chemistry, University of Cyprus, P. O. Box 20537, 1678 Nicosia, Cyprus
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Ogura T. Resonance Raman applications in investigations of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:575-8. [PMID: 22172733 DOI: 10.1016/j.bbabio.2011.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/24/2011] [Accepted: 11/24/2011] [Indexed: 10/14/2022]
Abstract
Recent applications of resonance Raman (RR) spectroscopy in investigations of cytochrome c oxidase (CcO) are reviewed. Red-excited RR spectra for the fully oxidized "as-isolated" CcO tuned to the ligand-to-metal charge transfer absorption band at 655nm exhibit a Raman band at 755cm(-1) assignable to the ν(OO) stretching mode of a peroxide. Binding of CN(-) diminishes the RR band concomitant with the loss of the charge transfer absorption band. This suggests that a peroxide forms a bridge between heme a(3) and Cu(B). Time-resolved RR spectroscopy of whole mitochondria identified a band at 571cm(-1) arising from the oxygenated intermediate at Δt=0.4, 0.6 and 1.4ms. Bands at 804 and 780cm(-1) of the P and F intermediates were observed at Δt=0.6 and 1.4ms, respectively. The coordination geometries of the three intermediates are essentially the same as the respective species observed for solubilized CcO. However, the lifetime of the oxygenated intermediate in mitochondria was significantly longer than the lifetime of this intermediate determined for solubilized CcO. This phenomenon is due either to the pH effect of mitochondrial matrix, the effect of ΔpH and/or ΔΨ across the membrane, or the effect of interactions with other membrane components and/or phospholipids.
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35
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STUCHEBRUKHOV ALEXEIA. ELECTRON TRANSFER REACTIONS COUPLED TO PROTON TRANSLOCATION: CYTOCHROME OXIDASE, PROTON PUMPS, AND BIOLOGICAL ENERGY TRANSDUCTION. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633603000318] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cytochrome oxidase (COX) is the terminal component of electron transport chain of the respiratory system in mitochondria, and one of the key enzymes responsible for energy generation in cells. COX functions as a proton pump that utilizes free energy of oxygen reduction for translocation of protons across the mitochondrion membrane. The proton gradient created in the process is later utilized to drive synthesis of ATP. Although the structure of COX has been recently resolved, the molecular mechanism of proton pumping remains unknown. In this paper, general principles and possible molecular mechanisms of energy transformations in this enzyme will be discussed. The main question is how exactly chemical energy of oxygen reduction and water formation is transformed into a proton gradient; or, how exactly electron transfer reactions are utilized to translocate protons across the mitochondrion membrane against the electrochemical gradient. A key to the solution of this problem is in understanding correlated transport of electrons and protons. Here, theoretical models are discussed for coupled electron and proton transfer reactions in which an electron is tunneling over long distance between two redox cofactors, and a coupled proton is moving along a proton conducting channel in a classical, diffusion-like random walk fashion. Such reactions are typical for COX and other enzymes involved in biological energy transformations.
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36
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Popović DM, Stuchebrukhov AA. Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:506-17. [PMID: 22086149 DOI: 10.1016/j.bbabio.2011.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/27/2011] [Accepted: 10/29/2011] [Indexed: 11/30/2022]
Abstract
A combined DFT/electrostatic approach is employed to study the coupling of proton and electron transfer reactions in cytochrome c oxidase (CcO) and its proton pumping mechanism. The coupling of the chemical proton to the internal electron transfer within the binuclear center is examined for the O→E transition. The novel features of the His291 pumping model are proposed, which involve timely well-synchronized sequence of the proton-coupled electron transfer reactions. The obtained pK(a)s and E(m)s of the key ionizable and redox-active groups at the different stages of the O→E transition are consistent with available experimental data. The PT step from E242 to H291 is examined in detail for various redox states of the hemes and various conformations of E242 side-chain. Redox potential calculations of the successive steps in the reaction cycle during the O→E transition are able to explain a cascade of equilibria between the different intermediate states and electron redistribution between the metal centers during the course of the catalytic activity. All four electrometric phases are discussed in the light of the obtained results, providing a robust support for the His291 model of proton pumping in CcO.
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Affiliation(s)
- Dragan M Popović
- Department of Chemistry, University of California, Davis, CA, USA.
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37
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Active site intermediates in the reduction of O(2) by cytochrome oxidase, and their derivatives. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:468-75. [PMID: 22079200 DOI: 10.1016/j.bbabio.2011.10.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 10/27/2011] [Accepted: 10/29/2011] [Indexed: 11/22/2022]
Abstract
The mechanism of dioxygen activation and reduction in cell respiration, as catalysed by cytochrome c oxidase, has a long history. The work by Otto Warburg, David Keilin and Britton Chance defined the dioxygen-binding heme iron centre, viz. das Atmungsferment, or cytochrome a(3). Chance brought the field further in the mid-1970's by ingenious low-temperature studies that for the first time identified the primary enzyme-substrate (ES) Michaelis complex of cell respiration, the dioxygen adduct of heme a(3), which he termed Compound A. Further work using optical, resonance Raman, EPR, and other sophisticated spectroscopic techniques, some of which with microsecond time resolution, has brought us to the situation today, where major principles of how O(2) reduction occurs in respiration are well understood. Nonetheless, some questions have remained open, for example concerning the precise structures, catalytic roles, and spectroscopic properties of the breakdown products of Compound A that have been called P, F (for peroxy and ferryl), and O (oxidised). This nomenclature has been known to be inadequate for some time already, and an alternative will be suggested here. In addition, the multiple forms of P, F and O states have been confusing, a situation that we endeavour to help clarifying. The P and F states formed artificially by reacting cytochrome oxidase with hydrogen peroxide are especially scrutinised, and some novel interpretations will be given that may account for previously unexplained observations.
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Durham B, Millett F. Design of photoactive ruthenium complexes to study electron transfer and proton pumping in cytochrome oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:567-74. [PMID: 21939635 DOI: 10.1016/j.bbabio.2011.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
Abstract
This review describes the development and application of photoactive ruthenium complexes to study electron transfer and proton pumping reactions in cytochrome c oxidase (CcO). CcO uses four electrons from Cc to reduce O(2) to two waters, and pumps four protons across the membrane. The electron transfer reactions in cytochrome oxidase are very rapid, and cannot be resolved by stopped-flow mixing techniques. Methods have been developed to covalently attach a photoactive tris(bipyridine)ruthenium group [Ru(II)] to Cc to form Ru-39-Cc. Photoexcitation of Ru(II) to the excited state Ru(II*), a strong reductant, leads to rapid electron transfer to the ferric heme group in Cc, followed by electron transfer to Cu(A) in CcO with a rate constant of 60,000s(-1). Ruthenium kinetics and mutagenesis studies have been used to define the domain for the interaction between Cc and CcO. New ruthenium dimers have also been developed to rapidly inject electrons into Cu(A) of CcO with yields as high as 60%, allowing measurement of the kinetics of electron transfer and proton release at each step in the oxygen reduction mechanism.
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Affiliation(s)
- Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA.
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Pavlou A, Soulimane T, Pinakoulaki E. Evidence for the Presence of Two Conformations of the Heme a3-CuB Pocket of Cytochrome caa3 from Thermus thermophilus. J Phys Chem B 2011; 115:11455-61. [DOI: 10.1021/jp2033356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Pavlou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Sciences Department and Materials & Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Eftychia Pinakoulaki
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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40
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Cytochrome c
oxidase: Intermediates of the catalytic cycle and their energy-coupled interconversion. FEBS Lett 2011; 586:630-9. [DOI: 10.1016/j.febslet.2011.08.037] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 11/20/2022]
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Yu MA, Egawa T, Shinzawa-Itoh K, Yoshikawa S, Yeh SR, Rousseau DL, Gerfen GJ. Radical formation in cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1295-304. [PMID: 21718686 DOI: 10.1016/j.bbabio.2011.06.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 06/14/2011] [Accepted: 06/15/2011] [Indexed: 11/16/2022]
Abstract
The formation of radicals in bovine cytochrome c oxidase (bCcO), during the O(2) redox chemistry and proton translocation, is an unresolved controversial issue. To determine if radicals are formed in the catalytic reaction of bCcO under single turnover conditions, the reaction of O(2) with the enzyme, reduced by either ascorbate or dithionite, was initiated in a custom-built rapid freeze quenching (RFQ) device and the products were trapped at 77K at reaction times ranging from 50μs to 6ms. Additional samples were hand mixed to attain multiple turnover conditions and quenched with a reaction time of minutes. X-band (9GHz) continuous wave electron paramagnetic resonance (CW-EPR) spectra of the reaction products revealed the formation of a narrow radical with both reductants. D-band (130GHz) pulsed EPR spectra allowed for the determination of the g-tensor principal values and revealed that when ascorbate was used as the reductant the dominant radical species was localized on the ascorbyl moiety, and when dithionite was used as the reductant the radical was the SO(2)(-) ion. When the contributions from the reductants are subtracted from the spectra, no evidence for a protein-based radical could be found in the reaction of O(2) with reduced bCcO. As a surrogate for radicals formed on reaction intermediates, the reaction of hydrogen peroxide (H(2)O(2)) with oxidized bCcO was studied at pH 6 and pH 8 by trapping the products at 50μs with the RFQ device to determine the initial reaction events. For comparison, radicals formed after several minutes of incubation were also examined, and X-band and D-band analysis led to the identification of radicals on Tyr-244 and Tyr-129. In the RFQ measurements, a peroxyl (ROO) species was formed, presumably by the reaction between O(2) and an amino acid-based radical. It is postulated that Tyr-129 may play a central role as a proton loading site during proton translocation by ejecting a proton upon formation of the radical species and then becoming reprotonated during its reduction via a chain of three water molecules originating from the region of the propionate groups of heme a(3). This article is part of a Special Issue entitled: "Allosteric cooperativity in respiratory proteins".
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Affiliation(s)
- Michelle A Yu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Abstract
The critical role of the ferryl intermediate in catalyzing the oxygen chemistry of monooxygenases, oxidases, or peroxidases has been known for decades. In contrast, its involvement in heme-based dioxygenases, such as human indoleamine 2,3-dioxygenase (hIDO), was not recognized until recently. In this study, H(2)O(2) was used as a surrogate to generate the ferryl intermediate of hIDO. Spectroscopic data demonstrate that the ferryl species is capable of oxidizing azinobis(3-ethylbenzothiazoline-6-sulfonic acid) but not L-Trp. Kinetic studies reveal that the conversion of the ferric enzyme to the ferryl intermediate facilitates the L-Trp binding rate by >400-fold; conversely, L-Trp binding to the enzyme retards the peroxide reaction rate by ∼9-fold, because of the significant elevation of the entropic barrier. The unfavorable entropic factor for the peroxide reaction highlights the scenario that the structure of hIDO is not optimized for utilizing H(2)O(2) as a co-substrate for oxidizing L-Trp. Titration studies show that the ferryl intermediate possesses two substrate-binding sites with a K(d) of 0.3 and 440 μM and that the electronic properties of the ferryl moiety are sensitive to the occupancy of the two substrate-binding sites. The implications of the data are discussed in the context of the structural and functional relationships of the enzyme.
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Affiliation(s)
- Changyuan Lu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Lucas MF, Rousseau DL, Guallar V. Electron transfer pathways in cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1305-13. [PMID: 21419097 DOI: 10.1016/j.bbabio.2011.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/08/2011] [Accepted: 03/10/2011] [Indexed: 10/18/2022]
Abstract
Mixed quantum mechanical/molecular mechanics calculations were used to explore the electron pathway of the terminal electron transfer enzyme, cytochrome c oxidase. This enzyme catalyzes the reduction of molecular oxygen to water in a multiple step process. Density functional calculations on the three redox centers allowed for the characterization of the electron transfer mechanism, following the sequence Cu(A)→heme a→heme a(3). This process is largely affected by the presence of positive charges, confirming the possibility of a proton coupled electron transfer. An extensive mapping of all residues involved in the electron transfer, between the Cu(A) center (donor) and the O(2) reduction site heme a(3)-Cu(B) (receptor), was obtained by selectively activating/deactivating different quantum regions. The method employed, called QM/MM e-pathway, allowed the identification of key residues along the possible electron transfer paths, consistent with experimental data. In particular, the role of arginines 481 and 482 appears crucial in the Cu(A)→heme a and in the heme a→heme a(3) electron transfer processes. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.
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Affiliation(s)
- M Fátima Lucas
- Barcelona Supercomputing Center, Jordi Girona, Barcelona, Spain
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Kaila VRI, Verkhovsky MI, Wikström M. Proton-coupled electron transfer in cytochrome oxidase. Chem Rev 2010; 110:7062-81. [PMID: 21053971 DOI: 10.1021/cr1002003] [Citation(s) in RCA: 402] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ville R I Kaila
- Helsinki Bioenergetics Group, Structural Biology and Biophysics Program, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014 Helsinki, Finland
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Yoshioka Y, Mitani M. B3LYP study on reduction mechanisms from O2 to H2O at the catalytic sites of fully reduced and mixed-valence bovine cytochrome c oxidases. Bioinorg Chem Appl 2010; 2010:182804. [PMID: 20396396 PMCID: PMC2852611 DOI: 10.1155/2010/182804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 11/27/2009] [Accepted: 01/05/2010] [Indexed: 11/26/2022] Open
Abstract
Reduction mechanisms of oxygen molecule to water molecules in the fully reduced (FR) and mixed-valence (MV) bovine cytochrome c oxidases (CcO) have been systematically examined based on the B3LYP calculations. The catalytic cycle using four electrons and four protons has been also shown consistently. The MV CcO catalyses reduction to produce one water molecule, while the FR CcO catalyses to produce two water molecules. One water molecule is added into vacant space between His240 and His290 in the catalytic site. This water molecule constructs the network of hydrogen bonds of Tyr244, farnesyl ethyl, and Thr316 that is a terminal residue of the K-pathway. It plays crucial roles for the proton transfer to the dioxygen to produce the water molecules in both MV and FR CcOs. Tyr244 functions as a relay of the proton transfer from the K-pathway to the added water molecule, not as donors of a proton and an electron to the dioxygen. The reduction mechanisms of MV and FR CcOs are strictly distinguished. In the FR CcO, the Cu atom at the Cu(B) site maintains the reduced state Cu(I) during the process of formation of first water molecule and plays an electron storage. At the final stage of formation of first water molecule, the Cu(I) atom releases an electron to Fe-O. During the process of formation of second water molecule, the Cu atom maintains the oxidized state Cu(II). In contrast with experimental proposals, the K-pathway functions for formation of first water molecule, while the D-pathway functions for second water molecule. The intermediates, P(M), P(R), F, and O, obtained in this work are compared with those proposed experimentally.
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Affiliation(s)
- Yasunori Yoshioka
- Chemistry Department for Materials, Graduate School of Engineering, Mie University, Kurima-machiya 1577, Tsu, Mie 514-8507, Japan.
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Sakaguchi M, Shinzawa-Itoh K, Yoshikawa S, Ogura T. A resonance Raman band assignable to the O–O stretching mode in the resting oxidized state of bovine heart cytochrome c oxidase. J Bioenerg Biomembr 2010; 42:241-3. [DOI: 10.1007/s10863-010-9282-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 03/07/2010] [Indexed: 10/19/2022]
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Daskalakis V, Farantos SC, Guallar V, Varotsis C. Vibrational resonances and CuB displacement controlled by proton motion in cytochrome c oxidase. J Phys Chem B 2010; 114:1136-43. [PMID: 19961168 DOI: 10.1021/jp910006k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (CcO), found in the inner mitochondrial membranes or in many bacteria, catalyzes the four-electron reduction of molecular oxygen to water. Four protons are pumped across the inner mitochondrial membrane through CcO. In this study, quantum mechanics/molecular mechanics and molecular dynamics calculations are used to probe the spectroscopic characteristics of the ferryl intermediates in the aa(3) CcO/O(2) reaction. These highly elaborate calculations, supported by several calculations on smaller model systems, demonstrate the sensitivity of vibrational frequencies on the Coulombic field of heme a(3) and their dependence on the distance of the adjacent Cu(B) to the heme a(3)-Fe atom. This distance seems to be associated with the protonation state of the heme a(3) propionate A, and we propose that it plays a crucial role on the mechanism of action of CcO. In detail, we link proton pumping activity in CcO enzyme (a) to a multiple (1:1:2) resonance among the frequencies of Fe(IV)=O bond stretching, the breathing mode of Histidine 411, and a bending mode of the His411-Fe(IV)=O species (aa(3) from Paracoccus denitrificans numbering) and (b) to Cu(B) displacement by electrostatic interactions toward the heme a(3) iron. We find that the vibrations of the His411-Fe(IV)=O unit become highly coupled depending on the protonation state of the heme a(3) ring A propionate/Asp399 pair, and we propose a mechanism for the resonance Raman enhancement of the bending mode delta(His411-Fe(IV)=O). Calculations on model systems demonstrate that the position of Cu(B) in relation to heme a(3) iron-oxo plays a crucial role in regulating that resonance. We also discuss the origin of the coupling between bending, delta(His411-Fe(IV)=O) and nu(Fe=O) stretching modes, and the role played by such vibrational coupling interactions or Cu(B) position in controlling functional properties of the enzyme, including electron/proton coupling as well as experimental spectra.
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Affiliation(s)
- Vangelis Daskalakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, P.O. Box 1527, 711 10 Heraklion, Greece.
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Abstract
In contrast to the wide spectrum of cytochrome P450 monooxygenases, there are only 2 heme-based dioxygenases in humans: tryptophan dioxygenase (hTDO) and indoleamine 2,3-dioxygenase (hIDO). hTDO and hIDO catalyze the same oxidative ring cleavage reaction of L-tryptophan to N-formyl kynurenine, the initial and rate-limiting step of the kynurenine pathway. Despite immense interest, the mechanism by which the 2 enzymes execute the dioxygenase reaction remains elusive. Here, we report experimental evidence for a key ferryl intermediate of hIDO that supports a mechanism in which the 2 atoms of dioxygen are inserted into the substrate via a consecutive 2-step reaction. This finding introduces a paradigm shift in our understanding of the heme-based dioxygenase chemistry, which was previously believed to proceed via simultaneous incorporation of both atoms of dioxygen into the substrate. The ferryl intermediate is not observable during the hTDO reaction, highlighting the structural differences between the 2 dioxygenases, as well as the importance of stereoelectronic factors in modulating the reactions.
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Zhang X, Chen Y. Phototriggered Metal-Ion Release from Phenolic Schiff Bases: A System for Metal-Ion Photodelivery. Chemphyschem 2009; 10:1993-5. [DOI: 10.1002/cphc.200900070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Koepke J, Olkhova E, Angerer H, Müller H, Peng G, Michel H. High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:635-45. [PMID: 19374884 DOI: 10.1016/j.bbabio.2009.04.003] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 04/03/2009] [Accepted: 04/08/2009] [Indexed: 11/19/2022]
Abstract
The structure of the two-subunit cytochrome c oxidase from Paracoccus denitrificans has been refined using X-ray cryodata to 2.25 A resolution in order to gain further insights into its mechanism of action. The refined structural model shows a number of new features including many additional solvent and detergent molecules. The electron density bridging the heme a(3) iron and Cu(B) of the active site is fitted best by a peroxo-group or a chloride ion. Two waters or OH(-) groups do not fit, one water (or OH(-)) does not provide sufficient electron density. The analysis of crystals of cytochrome c oxidase isolated in the presence of bromide instead of chloride appears to exclude chloride as the bridging ligand. In the D-pathway a hydrogen bonded chain of six water molecules connects Asn131 and Glu278, but the access for protons to this water chain is blocked by Asn113, Asn131 and Asn199. The K-pathway contains two firmly bound water molecules, an additional water chain seems to form its entrance. Above the hemes a cluster of 13 water molecules is observed which potentially form multiple exit pathways for pumped protons. The hydrogen bond pattern excludes that the Cu(B) ligand His326 is present in the imidazolate form.
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Affiliation(s)
- Juergen Koepke
- Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, Max-von-Laue-Str.3, D-60438 Frankfurt/Main, Germany
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