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Lasham J, Djurabekova A, Zickermann V, Vonck J, Sharma V. Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures. J Phys Chem B 2024; 128:2304-2316. [PMID: 38430110 DOI: 10.1021/acs.jpcb.3c07421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Classical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, the accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here, we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two large membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with titratable amino acids modeled in their standard protonation (charged) states, the structure diverges far from its starting conformation. In comparison, MD simulations performed with predetermined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results support the notion that it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to the launch of any conventional MD simulations. Furthermore, the combined approach of fast protonation state prediction and MD simulations can provide valuable information about the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states in proteinaceous environments currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions but also the atomic modeling of density data.
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Affiliation(s)
- Jonathan Lasham
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Amina Djurabekova
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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2
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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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3
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Gorriz RF, Volkenandt S, Imhof P. Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase. Int J Mol Sci 2023; 24:10464. [PMID: 37445646 DOI: 10.3390/ijms241310464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Cytochrome c Oxidase (CcO), a membrane protein of the respiratory chain, pumps protons against an electrochemical gradient by using the energy of oxygen reduction to water. The ("chemical") protons required for this reaction and those pumped are taken up via two distinct channels, named D-channel and K-channel, in a step-wise and highly regulated fashion. In the reductive phase of the catalytic cycle, both channels transport protons so that the pumped proton passes the D-channel before the "chemical" proton has crossed the K-channel. By performing molecular dynamics simulations of CcO in the O→E redox state (after the arrival of the first reducing electron) with various combinations of protonation states of the D- and K-channels, we analysed the effect of protonation on the two channels. In agreement with previous work, the amount of water observed in the D-channel was significantly higher when the terminal residue E286 was not (yet) protonated than when the proton arrived at this end of the D-channel and E286 was neutral. Since a sufficient number of water molecules in the channel is necessary for proton transport, this can be understood as E286 facilitating its own protonation. K-channel hydration shows an even higher dependence on the location of the excess proton in the K-channel. Also in agreement with previous work, the K-channel exhibits a very low hydration level that likely hinders proton transfer when the excess proton is located in the lower part of the K-channel, that is, on the N-side of S365. Once the proton has passed S365 (towards the reaction site, the bi-nuclear centre (BNC)), the amount of water in the K-channel provides hydrogen-bond connectivity that renders proton transfer up to Y288 at the BNC feasible. No significant direct effect of the protonation state of one channel on the hydration level, hydrogen-bond connectivity, or interactions between protein residues in the other channel could be observed, rendering proton conductivity in the two channels independent of each other. Regulation of the order of proton uptake and proton passage in the two channels such that the "chemical" proton leaves its channel last must, therefore, be achieved by other means of communication, such as the location of the reducing electron.
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Affiliation(s)
- Rene F Gorriz
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Senta Volkenandt
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Petra Imhof
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
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4
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Gorriz RF, Imhof P. Interplay of Hydration and Protonation Dynamics in the K-Channel of Cytochrome c Oxidase. Biomolecules 2022; 12:biom12111615. [PMID: 36358964 PMCID: PMC9687966 DOI: 10.3390/biom12111615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Cytochrome c oxidase is a membrane protein of the respiratory chain that consumes protons and molecular oxygen to produce water and uses the resulting energy to pump protons across the membrane. Our molecular dynamics simulations with an excess proton located at different positions in one of the proton-conducting channels, the K-channel, show a clear dependence of the number of water molecules inside the channel on the proton position. A higher hydration level facilitates the formation of hydrogen-bonded chains along which proton transfer can occur. However, a sufficiently high hydration level for such proton transport is observed only when the excess proton is located above S365, i.e., the lower third of the channel. From the channel entrance up to this point, proton transport is via water molecules as proton carriers. These hydronium ions move with their surrounding water molecules, up to K362, filling and widening the channel. The conformation of K362 depends on its own protonation state and on the hydration level, suggesting its role to be proton transport from a hydronium ion at the height of K362 to the upper part of the channel via a conformational change. The protonation-dependent conformational dynamics of E101 at the bottom of the channel renders proton transfer via E101 unlikely. Instead, its role is rather that of an amplifier of H96’s proton affinity, suggesting H96 as the initial proton acceptor.
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Affiliation(s)
- Rene F. Gorriz
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Petra Imhof
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
- Correspondence:
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5
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Di Trani JM, Moe A, Riepl D, Saura P, Kaila VRI, Brzezinski P, Rubinstein JL. Structural basis of mammalian complex IV inhibition by steroids. Proc Natl Acad Sci U S A 2022; 119:e2205228119. [PMID: 35858451 PMCID: PMC9335260 DOI: 10.1073/pnas.2205228119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/18/2022] [Indexed: 01/21/2023] Open
Abstract
The mitochondrial electron transport chain maintains the proton motive force that powers adenosine triphosphate (ATP) synthesis. The energy for this process comes from oxidation of reduced nicotinamide adenine dinucleotide (NADH) and succinate, with the electrons from this oxidation passed via intermediate carriers to oxygen. Complex IV (CIV), the terminal oxidase, transfers electrons from the intermediate electron carrier cytochrome c to oxygen, contributing to the proton motive force in the process. Within CIV, protons move through the K and D pathways during turnover. The former is responsible for transferring two protons to the enzyme's catalytic site upon its reduction, where they eventually combine with oxygen and electrons to form water. CIV is the main site for respiratory regulation, and although previous studies showed that steroid binding can regulate CIV activity, little is known about how this regulation occurs. Here, we characterize the interaction between CIV and steroids using a combination of kinetic experiments, structure determination, and molecular simulations. We show that molecules with a sterol moiety, such as glyco-diosgenin and cholesteryl hemisuccinate, reversibly inhibit CIV. Flash photolysis experiments probing the rapid equilibration of electrons within CIV demonstrate that binding of these molecules inhibits proton uptake through the K pathway. Single particle cryogenic electron microscopy (cryo-EM) of CIV with glyco-diosgenin reveals a previously undescribed steroid binding site adjacent to the K pathway, and molecular simulations suggest that the steroid binding modulates the conformational dynamics of key residues and proton transfer kinetics within this pathway. The binding pose of the sterol group sheds light on possible structural gating mechanisms in the CIV catalytic cycle.
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Affiliation(s)
- Justin M. Di Trani
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada M5G 0A4
| | - Agnes Moe
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Daniel Riepl
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada M5G 0A4
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 1L7
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
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6
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Dragelj J, Mroginski MA, Knapp EW. Beating Heart of Cytochrome c Oxidase: The Shared Proton of Heme a3 Propionates. J Phys Chem B 2021; 125:9668-9677. [PMID: 34427096 DOI: 10.1021/acs.jpcb.1c03619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cytochrome c oxidase (CcO) pumps protons from the N-side to the P-side and consumes electrons from the P-side of the mitochondrial membrane driven by energy gained from reduction of dioxygen to water. ATP synthesis uses the resulting proton gradient and electrostatic potential difference. Since the distance a proton travels through CcO is too large for a one-step transfer process, proton-loading sites (PLS) that can carry protons transiently are necessary. One specific pump-active PLS couples to the redox reaction, thus energizing the proton to move across the membrane against electric potential and proton gradient. The PLS should also prevent proton backflow. Therefore, the propionates of the two redox-active hemes in CcO were suggested as PLS candidates although, according to CcO crystal structures, none of the four propionates can be protonated on account of strong H-bonds. Here, we show that modeling the local structure around heme a3 propionates enhances significantly their capability of carrying a proton jointly. This was not possible for the propionates of heme a. The modeled structures are stable in molecular dynamics simulations (MDS) and are energetically similar to the crystal structure. Precise electrostatic energy computations of MDS data are used to estimate the pKA values of all titratable residues in CcO. For the modeled structures, the heme a3 propionates have pKA values high enough to host a proton transiently but not too high to fix the proton permanently. The change in pKA throughout the redox reaction is sufficient to push the proton to the P-side of the membrane and to provide the protons with the necessary amount of energy for ATP synthesis.
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Affiliation(s)
- Jovan Dragelj
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Fabeckstrasse 36a, 14195 Berlin, Germany.,Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Ernst Walter Knapp
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Fabeckstrasse 36a, 14195 Berlin, Germany
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7
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Protonation Dynamics in the K-Channel of Cytochrome c Oxidase Estimated from Molecular Dynamics Simulations. Processes (Basel) 2021. [DOI: 10.3390/pr9020265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Proton transfer reactions are one of the most fundamental processes in biochemistry. We present a simplistic approach for estimating proton transfer probabilities in a membrane protein, cytochrome c oxidase. We combine short molecular dynamics simulations at discrete protonation states with a Monte Carlo approach to exchange between those states. Requesting for a proton transfer the existence of a hydrogen-bonded connection between the two source and target residues of the exchange, restricts the acceptance of transfers to only those in which a proton-relay is possible. Together with an analysis of the hydrogen-bonded connectivity in one of the proton-conducting channels of cytochrome c oxidase, this approach gives insight into the protonation dynamics of the hydrogen-bonded networks. The connectivity and directionality of the networks are coupled to the conformation of an important protein residue in the channel, K362, rendering proton transfer in the entire channel feasible in only one of the two major conformations. Proton transport in the channel can thus be regulated by K362 not only through its possible role as a proton carrier itself, but also by allowing or preventing proton transport via water residues.
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8
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Wolf A, Dragelj J, Wonneberg J, Stellmacher J, Balke J, Woelke AL, Hodoscek M, Knapp EW, Alexiev U. The redox-coupled proton-channel opening in cytochrome c oxidase. Chem Sci 2020. [DOI: 10.1039/c9sc06463j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The interplay of cytochrome c oxidase's cofactor electrostatics, long-range conformational changes, H-bond rearrangement, and water dynamics enables transient proton-channel activation.
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Affiliation(s)
- Alexander Wolf
- Physics Department
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Jovan Dragelj
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | | | | | - Jens Balke
- Physics Department
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Anna Lena Woelke
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Department of Chemistry
| | - Milan Hodoscek
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
- National Institute of Chemistry
| | - Ernst Walter Knapp
- Institute of Chemistry and Biochemistry
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - Ulrike Alexiev
- Physics Department
- Freie Universität Berlin
- 14195 Berlin
- Germany
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9
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Vilhjálmsdóttir J, Albertsson I, Blomberg MRA, Ädelroth P, Brzezinski P. Proton transfer in uncoupled variants of cytochrome c oxidase. FEBS Lett 2019; 594:813-822. [PMID: 31725900 DOI: 10.1002/1873-3468.13679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/09/2019] [Indexed: 11/08/2022]
Abstract
Cytochrome c oxidase is a membrane-bound redox-driven proton pump that harbors two proton-transfer pathways, D and K, which are used at different stages of the reaction cycle. Here, we address the question if a D pathway with a modified energy landscape for proton transfer could take over the role of the K pathway when the latter is blocked by a mutation. Our data indicate that structural alterations near the entrance of the D pathway modulate energy barriers that influence proton transfer to the proton-loading site. The data also suggest that during reduction of the catalytic site, its protonation has to occur via the K pathway and that this proton transfer to the catalytic site cannot take place through the D pathway.
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Affiliation(s)
- Jóhanna Vilhjálmsdóttir
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Ingrid Albertsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Margareta R A Blomberg
- Department of Organic Chemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
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10
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Wolf A, Wonneberg J, Balke J, Alexiev U. Electronation-dependent structural change at the proton exit side of cytochrome c oxidase as revealed by site-directed fluorescence labeling. FEBS J 2019; 287:1232-1246. [PMID: 31597007 DOI: 10.1111/febs.15084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/17/2019] [Accepted: 10/04/2019] [Indexed: 02/05/2023]
Abstract
Cytochrome c oxidase (CcO), the terminal enzyme of the respiratory chain of mitochondria and many aerobic prokaryotes that function as a redox-coupled proton pump, catalyzes the reduction of molecular oxygen to water. As part of the respiratory chain, CcO contributes to the proton motive force driving ATP synthesis. While many aspects of the enzyme's catalytic mechanisms have been established, a clear picture of the proton exit pathway(s) remains elusive. Here, we aim to gain insight into the molecular mechanisms of CcO through the development of a new homologous mutagenesis/expression system in Paracoccus denitrificans, which allows mutagenesis of CcO subunits 1, 2, and 3. Our system provides true single thiol-reactive CcO variants in a three-subunit base variant with unique labeling sites for the covalent attachment of reporter groups sensitive to nanoenvironmental factors like protonation, polarity, and hydration. To this end, we exchanged six residues on both membrane sides of CcO for cysteines. We show redox-dependent wetting changes at the proton uptake channel and increased polarity at the proton exit side of CcO upon electronation. We suggest an electronation-dependent conformational change to play a role in proton exit from CcO.
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Affiliation(s)
- Alexander Wolf
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Juliane Wonneberg
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Jens Balke
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Ulrike Alexiev
- Institute of Experimental Physics, Freie Universität Berlin, Germany
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11
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Supekar S, Kaila VRI. Dewetting transitions coupled to K-channel activation in cytochrome c oxidase. Chem Sci 2018; 9:6703-6710. [PMID: 30310604 PMCID: PMC6115622 DOI: 10.1039/c8sc01587b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/08/2018] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane.
Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane. CcO employs the so-called D- and K-channels for proton uptake, but the molecular mechanism for activation of the K-channel has remained elusive for decades. We show here by combining large-scale atomistic molecular simulations with graph-theoretical water network analysis, and hybrid quantum/classical (QM/MM) free energy calculations, that the K-channel is activated by formation of a reactive oxidized intermediate in the binuclear heme a3/CuB active site. This state induces electrostatic, hydration, and conformational changes that lower the barrier for proton transfer along the K-channel by dewetting pathways that connect the D-channel with the active site. Our combined results reconcile previous experimental findings and indicate that water dynamics plays a decisive role in the proton pumping machinery in CcO.
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Affiliation(s)
- Shreyas Supekar
- Department Chemie , Technische Universität München , Lichtenbergstraße 4 , D-85748 Garching , Germany .
| | - Ville R I Kaila
- Department Chemie , Technische Universität München , Lichtenbergstraße 4 , D-85748 Garching , Germany .
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12
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Ghane T, Gorriz RF, Wrzalek S, Volkenandt S, Dalatieh F, Reidelbach M, Imhof P. Hydrogen-Bonded Network and Water Dynamics in the D-channel of Cytochrome c Oxidase. J Membr Biol 2018; 251:299-314. [PMID: 29435610 DOI: 10.1007/s00232-018-0019-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/06/2018] [Indexed: 01/09/2023]
Abstract
Proton transfer in cytochrome c oxidase (CcO) from the cellular inside to the binuclear redox centre as well as proton pumping through the membrane takes place through proton entrance via two distinct pathways, the D- and K-channel. Both channels show a dependence of their hydration level on the protonation states of their key residues, K362 for the K-channel, and E286 or D132 for the D-channel. In the oxidative half of CcO's catalytic cycle the D-channel is the proton-conducting path. For this channel, an interplay of protonation state of the D-channel residues with the water and hydrogen-bond dynamics has been observed in molecular dynamics simulations of the CcO protein, embedded in a lipid bi-layer, modelled in different protonation states. Protonation of residue E286 at the end of the D-channel results in a hydrogen-bonded network pointing from E286 to N139, that is against proton transport, and favouring N139 conformations which correspond to a closed asparagine gate (formed by residues N121 and N139). Consequently, the hydration level is lower than with unprotonated E286. In those models, the Asn gate is predominantly open, allowing water molecules to pass and thus increase the hydration level. The hydrogen-bonded network in these states exhibits longer life times of the Asn residues with water than other models and shows the D-channel to be traversable from the entrance, D132, to exit, E286. The D-channel can thus be regarded as auto-regulated with respect to proton transport, allowing proton passage only when required, that is the proton is located at the lower part of the D-channel (D132 to Asn gate) and not at the exit (E286).
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Affiliation(s)
- Tahereh Ghane
- Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Rene F Gorriz
- Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Sandro Wrzalek
- Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Senta Volkenandt
- Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Ferand Dalatieh
- Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.,R Institute GmbH, Dortustraße 48, 14467, Potsdam, Germany
| | - Marco Reidelbach
- Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Petra Imhof
- Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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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: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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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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Sharma V, Jambrina PG, Kaukonen M, Rosta E, Rich PR. Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations. Proc Natl Acad Sci U S A 2017; 114:E10339-E10348. [PMID: 29133387 PMCID: PMC5715751 DOI: 10.1073/pnas.1708628114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Proton pumping A-type cytochrome c oxidase (CcO) terminates the respiratory chains of mitochondria and many bacteria. Three possible proton transfer pathways (D, K, and H channels) have been identified based on structural, functional, and mutational data. Whereas the D channel provides the route for all pumped protons in bacterial A-type CcOs, studies of bovine mitochondrial CcO have led to suggestions that its H channel instead provides this route. Here, we have studied H-channel function by performing atomistic molecular dynamics simulations on the entire, as well as core, structure of bovine CcO in a lipid-solvent environment. The majority of residues in the H channel do not undergo large conformational fluctuations. Its upper and middle regions have adequate hydration and H-bonding residues to form potential proton-conducting channels, and Asp51 exhibits conformational fluctuations that have been observed crystallographically. In contrast, throughout the simulations, we do not observe transient water networks that could support proton transfer from the N phase toward heme a via neutral His413, regardless of a labile H bond between Ser382 and the hydroxyethylfarnesyl group of heme a In fact, the region around His413 only became sufficiently hydrated when His413 was fixed in its protonated imidazolium state, but its calculated pKa is too low for this to provide the means to create a proton transfer pathway. Our simulations show that the electric dipole moment of residues around heme a changes with the redox state, hence suggesting that the H channel could play a more general role as a dielectric well.
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Affiliation(s)
- Vivek Sharma
- Department of Physics, University of Helsinki, FI-00014, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pablo G Jambrina
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Markus Kaukonen
- Department of Physics, University of Helsinki, FI-00014, Helsinki, Finland
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Peter R Rich
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
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15
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Protonation-State-Dependent Communication in Cytochrome c Oxidase. Biophys J 2017; 113:817-828. [PMID: 28834718 DOI: 10.1016/j.bpj.2017.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/05/2017] [Indexed: 11/21/2022] Open
Abstract
Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both a redox enzyme and a proton pump, proton transfer into the protein toward the BNC or toward a proton loading site (and ultimately through the membrane) must be highly regulated. The PR → F transition is the first step in a catalytic cycle that requires proton transfer from the bulk at the N-side to the BNC. Molecular dynamics simulations of the PR → F intermediate of this transition, with 16 different combinations of protonation states of key residues in the D- and K-channel, show the impact of the K-channel on the D-channel to be protonation-state dependent. Strength as well as means of communication, correlations in positions, or communication along the hydrogen-bonded network depends on the protonation state of the K-channel residue K362. The conformational and hydrogen-bond dynamics of the D-channel residue N139 is regulated by an interplay of protonation in the D-channel and K362. N139 thus assumes a gating function by which proton passage through the D-channel toward E286 is likely facilitated for states with protonated K362 and unprotonated E286. In contrast, proton passage through the D-channel is hindered by N139's preference for a closed conformation in situations with protonated E286.
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16
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Magalhães PR, Oliveira ASF, Campos SRR, Soares CM, Baptista AM. Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study. J Chem Inf Model 2017; 57:256-266. [PMID: 28095694 DOI: 10.1021/acs.jcim.6b00575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c oxidase (CcO) couples the reduction of dioxygen to water with transmembrane proton pumping, which leads to the generation of an electrochemical gradient. In this study we analyze how one of the components of the electrochemical gradient, the difference in pH across the membrane, or ΔpH, influences the protonation states of residues in CcO. We modified our continuum electrostatics/Monte Carlo (CE/MC) method in order to include the ΔpH and applied it to the study of CcO, in what is, to our best knowledge, the first CE/MC study of CcO in the presence of a pH gradient. The inclusion of a transmembrane pH gradient allows for the identification of residues whose titration behavior depends on the pH on both sides of the membrane. Among the several residues with unusual titration profiles, three are well-known key residues in the proton transfer process of CcO: E286I, Y288I, and K362I. All three residues have been previously identified as being critical for the catalytic or proton pumping functions of CcO. Our results suggest that when the pH gradient increases, these residues may be part of a regulatory mechanism to stem the proton flow.
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Affiliation(s)
- Pedro R Magalhães
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , 2781-901 Oeiras, Portugal
| | - A Sofia F Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , 2781-901 Oeiras, Portugal
| | - Sara R R Campos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , 2781-901 Oeiras, Portugal
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , 2781-901 Oeiras, Portugal
| | - António M Baptista
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , 2781-901 Oeiras, Portugal
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17
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Helabad MB, Ghane T, Reidelbach M, Woelke AL, Knapp EW, Imhof P. RETRACTED: Protonation State-Dependent Communication in Cytochrome c Oxidase. Biophys J 2016; 111:492-503. [DOI: 10.1016/j.bpj.2016.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 06/22/2016] [Accepted: 06/30/2016] [Indexed: 11/29/2022] Open
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18
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Oliveira ASF, Campos SRR, Baptista AM, Soares CM. Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:759-71. [PMID: 27033303 DOI: 10.1016/j.bbabio.2016.03.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/18/2016] [Accepted: 03/23/2016] [Indexed: 12/11/2022]
Abstract
Cytochrome c oxidases (CcOs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes reduce dioxygen (O(2)) to water and, simultaneously, generate a transmembrane electrochemical proton gradient. Despite their importance in the aerobic metabolism and the large amount of structural and biochemical data available for the A1-type CcO family, there is still no consensually accepted description of the molecular mechanisms operating in this protein. A substantial number of questions about the CcO's working mechanism remain to be answered, including how the protonation behavior of some key residues is modulated during a reduction cycle and how is the conformation of the protein affected by protonation. The main objective of this work was to study the protonation-conformation coupling in CcOs and identify the molecular factors that control the protonation state of some key residues. In order to directly capture the interplay between protonation and conformational effects, we have performed constant-pH MD simulations of an A1-type CcO inserted into a lipid bilayer in two redox states (oxidized and reduced) at physiological pH. From the simulations, we were able to identify several groups with unusual titration behavior that are highly dependent on the protein redox state, including the A-propionate from heme a and the D-propionate from heme a3, two key groups possibly involved in proton pumping. The protonation state of these two groups is heavily influenced by subtle conformational changes in the protein (notably of R481(I) and R482(I)) and by small changes in the hydrogen bond network.
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Affiliation(s)
- A Sofia F Oliveira
- ITQB, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sara R R Campos
- ITQB, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - António M Baptista
- ITQB, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cláudio M Soares
- ITQB, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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19
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Sakalli I, Knapp EW. pK(A) in proteins solving the Poisson-Boltzmann equation with finite elements. J Comput Chem 2015; 36:2147-57. [PMID: 26284944 DOI: 10.1002/jcc.24053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/24/2015] [Accepted: 07/30/2015] [Indexed: 11/12/2022]
Abstract
Knowledge on pK(A) values is an eminent factor to understand the function of proteins in living systems. We present a novel approach demonstrating that the finite element (FE) method of solving the linearized Poisson-Boltzmann equation (lPBE) can successfully be used to compute pK(A) values in proteins with high accuracy as a possible replacement to finite difference (FD) method. For this purpose, we implemented the software molecular Finite Element Solver (mFES) in the framework of the Karlsberg+ program to compute pK(A) values. This work focuses on a comparison between pK(A) computations obtained with the well-established FD method and with the new developed FE method mFES, solving the lPBE using protein crystal structures without conformational changes. Accurate and coarse model systems are set up with mFES using a similar number of unknowns compared with the FD method. Our FE method delivers results for computations of pK(A) values and interaction energies of titratable groups, which are comparable in accuracy. We introduce different thermodynamic cycles to evaluate pK(A) values and we show for the FE method how different parameters influence the accuracy of computed pK(A) values.
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Affiliation(s)
- Ilkay Sakalli
- Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Fabeckstr. 36a, 14195, Berlin, Germany
| | - Ernst-Walter Knapp
- Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Fabeckstr. 36a, 14195, Berlin, Germany
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Proton transfer in the K-channel analog of B-type Cytochrome c oxidase from Thermus thermophilus. Biophys J 2015; 107:2177-84. [PMID: 25418102 DOI: 10.1016/j.bpj.2014.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/03/2014] [Accepted: 09/11/2014] [Indexed: 01/08/2023] Open
Abstract
A key enzyme in aerobic metabolism is cytochrome c oxidase (CcO), which catalyzes the reduction of molecular oxygen to water in the mitochondrial and bacterial membranes. Substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochemical gradient. The well-studied A-type CcO uses two different entry channels for protons: the D-channel for all pumped and two consumed protons, and the K-channel for the other two consumed protons. In contrast, the B-type CcO uses only a single proton input channel for all consumed and pumped protons. It has the same location as the A-type K-channel (and thus is named the K-channel analog) without sharing any significant sequence homology. In this study, we performed molecular-dynamics simulations and electrostatic calculations to characterize the K-channel analog in terms of its energetic requirements and functionalities. The function of Glu-15B as a proton sink at the channel entrance is demonstrated by its rotational movement out of the channel when it is deprotonated and by its high pKA value when it points inside the channel. Tyr-244 in the middle of the channel is identified as the valve that ensures unidirectional proton transfer, as it moves inside the hydrogen-bond gap of the K-channel analog only while being deprotonated. The electrostatic energy landscape was calculated for all proton-transfer steps in the K-channel analog, which functions via proton-hole transfer. Overall, the K-channel analog has a very stable geometry without large energy barriers.
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