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Tumbic GW, Li J, Jiang T, Hossan MY, Feng C, Thielges MC. Interdomain Interactions Modulate the Active Site Dynamics of Human Inducible Nitric Oxide Synthase. J Phys Chem B 2022; 126:6811-6819. [PMID: 36056879 PMCID: PMC10110350 DOI: 10.1021/acs.jpcb.2c04091] [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: 11/28/2022]
Abstract
Nitric oxide synthase (NOS) is a homodimeric flavohemoprotein responsible for catalyzing the oxidation of l-arginine (l-Arg) to citrulline and nitric oxide. Electrons are supplied for the reaction via interdomain electron transfer between an N-terminal heme-containing oxygenase domain and a FMN-containing (sub)domain of a C-terminal reductase domain. Extensive attention has focused on elucidating how conformational dynamics regulate electron transfer between the domains. Here we investigate the impact of the interdomain FMN-heme interaction on the heme active site dynamics of inducible NOS (iNOS). Steady state linear and time-resolved two-dimensional infrared (2D IR) spectroscopy was applied to probe a CO ligand at the heme within the oxygenase domain for full-length and truncated or mutated constructs of human iNOS. Whereas the linear IR spectra of the CO ligand were identical among the constructs, 2D IR spectroscopy revealed variation in the frequency dynamics. The wild-type constructs that can properly form the FMN/oxygenase docked state due to the presence of both the FMN and oxygenase domains showed slower dynamics than the oxygenase domain alone. Introduction of the mutation (E546N) predicted to perturb electrostatic interactions between the domains resulted in measured dynamics intermediate between those for the full-length and individual oxygenase domain, consistent with perturbation to the docked/undocked equilibrium. These results indicate that docking of the FMN domain to the oxygenase domain not only brings the FMN cofactor within electron transfer distance of the heme domain but also modulates the dynamics sensed by the CO ligand within the active site in a way expected to promote efficient electron transfer.
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Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jinghui Li
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Ting Jiang
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Changjian Feng
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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2
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Dixit VA, Blumberger J, Vyas SK. Methemoglobin formation in mutant hemoglobin α chains: electron transfer parameters and rates. Biophys J 2021; 120:3807-3819. [PMID: 34265263 DOI: 10.1016/j.bpj.2021.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/06/2021] [Accepted: 07/07/2021] [Indexed: 11/26/2022] Open
Abstract
Hemoglobin-mediated transport of dioxygen (O2) critically depends on the stability of the reduced (Fe2+) form of the heme cofactors. Some protein mutations stabilize the oxidized (Fe3+) state (methemoglobin, Hb M), causing methemoglobinemia, and can be lethal above 30%. The majority of the analyses of factors influencing Hb oxidation are retrospective and give insights only for inner-sphere mutations of heme (His58, His87). Herein, we report the first all-atom molecular dynamics simulations on both redox states and calculations of the Marcus electron transfer (ET) parameters for the α chain Hb oxidation and reduction rates for Hb M. The Hb wild-type (WT) and most of the studied α chain variants maintain globin structure except the Hb M Iwate (H87Y). The mutants forming Hb M tend to have lower redox potentials and thus stabilize the oxidized (Fe3+) state (in particular, the Hb Miyagi variant with K61E mutation). Solvent reorganization (λsolv 73-96%) makes major contributions to reorganization free energy, whereas protein reorganization (λprot) accounts for 27-30% except for the Miyagi and J-Buda variants (λprot ∼4%). Analysis of heme-solvent H-bonding interactions among variants provide insights into the role of Lys61 residue in stabilizing the Fe2+ state. Semiclassical Marcus ET theory-based calculations predict experimental kET for the Cyt b5-Hb complex and provide insights into relative reduction rates for Hb M in Hb variants. Thus, our methodology provides a rationale for the effect of mutations on the structure, stability, and Hb oxidation reduction rates and has potential for identification of mutations that result in methemoglobinemia.
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Affiliation(s)
- Vaibhav A Dixit
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani (BITS-Pilani), Rajasthan, India.
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Shivam Kumar Vyas
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani (BITS-Pilani), Rajasthan, India
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3
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Di Rocco G, Bighi B, Borsari M, Bortolotti CA, Ranieri A, Sola M, Battistuzzi G. Electron Transfer and Electrocatalytic Properties of the Immobilized Met80Ala Cytochrome
c
Variant in Dimethylsulfoxide. ChemElectroChem 2021. [DOI: 10.1002/celc.202100499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Giulia Di Rocco
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Beatrice Bighi
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Marco Borsari
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Carlo Augusto Bortolotti
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Antonio Ranieri
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Marco Sola
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Gianantonio Battistuzzi
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
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4
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Kudisch B, Oblinsky DG, Black MJ, Zieleniewska A, Emmanuel MA, Rumbles G, Hyster TK, Scholes GD. Active-Site Environmental Factors Customize the Photophysics of Photoenzymatic Old Yellow Enzymes. J Phys Chem B 2020; 124:11236-11249. [PMID: 33231450 DOI: 10.1021/acs.jpcb.0c09523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of non-natural photoenzymatic systems has reinvigorated the study of photoinduced electron transfer (ET) within protein active sites, providing new and unique platforms for understanding how biological environments affect photochemical processes. In this work, we use ultrafast spectroscopy to compare the photoinduced electron transfer in known photoenzymes. 12-Oxophytodienoate reductase 1 (OPR1) is compared to Old Yellow Enzyme 1 (OYE1) and morphinone reductase (MR). The latter enzymes are structurally homologous to OPR1. We find that slight differences in the amino acid composition of the active sites of these proteins determine their distinct electron-transfer dynamics. Our work suggests that the inside of a protein active site is a complex/heterogeneous dielectric network where genetically programmed heterogeneity near the site of biological ET can significantly affect the presence and lifetime of various intermediate states. Our work motivates additional tunability of Old Yellow Enzyme active-site reorganization energy and electron-transfer energetics that could be leveraged for photoenzymatic redox approaches.
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Affiliation(s)
- Bryan Kudisch
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Daniel G Oblinsky
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Michael J Black
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Anna Zieleniewska
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Megan A Emmanuel
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Garry Rumbles
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Department of Chemistry and RASEI, University of Colorado Boulder, Colorado 80309, United States
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
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5
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Rebollar L, Intikhab S, Snyder JD, Tang MH. Kinetic Isotope Effects Quantify pH-Sensitive Water Dynamics at the Pt Electrode Interface. J Phys Chem Lett 2020; 11:2308-2313. [PMID: 32125855 DOI: 10.1021/acs.jpclett.0c00185] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The pH-dependent kinetics of the hydrogen oxidation and evolution reactions (HERs and HORs) remain a fundamental conundrum in modern electrochemistry. Recent efforts have focused on the impact of the interfacial water network on the reaction kinetics. In this work, we quantify the importance of interfacial water dynamics on the overall hydrogen reaction kinetics with kinetic isotope effect (KIE) voltammetry experiments on single-crystal Pt(111) and Pt(110). Our results find a surface-sensitive KIE for both the HER and the HOR that is measurable in base but not in acid. Remarkably, the HOR in KOD on Pt(111) yields a KIE of up to 3.4 at moderate overpotentials, greater than any expected secondary KIE values, yet the HOR in DClO4 yields no measurable KIE. These results provide direct evidence that solvent dynamics play a crucial role in the alkaline but not in the acidic hydrogen reactions, thus reinforcing the importance of "beyond adsorption" phenomena in modern electrocatalysis.
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Affiliation(s)
- Luis Rebollar
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Saad Intikhab
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Joshua D Snyder
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Maureen H Tang
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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6
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The Fe (III)/Fe(II) redox couple as a probe of immobilized tobacco peroxidase: Effect of the immobilization protocol. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2018.12.153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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7
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BagdŽiūnas G, Ramanavičius A. Towards direct enzyme wiring: a theoretical investigation of charge carrier transfer mechanisms between glucose oxidase and organic semiconductors. Phys Chem Chem Phys 2019; 21:2968-2976. [PMID: 30671578 DOI: 10.1039/c8cp07233g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a general theoretical and numerical approach based on semiconductor theory, which could be applied to a study of direct enzyme wiring, has been discussed. Marcus-Hush theory was applied to evaluate the potential transfer of charge carriers (holes and electrons) between glucose oxidase (GOx) and organic semiconductors. Two mechanisms of multistep hopping of charge to/from the oxidised/reduced flavin-based moiety through residues of aromatic amino acids located in GOx and long range charge direct tunnelling from the cofactor to the organic semiconductor surface have been proposed and evaluated. It was determined that the hole-hopping mechanism is possible and proceeds at a low ionization potential of the organic semiconductor. The calculations reveal that hopping of electrons is blocked, but direct electron tunnelling between the cofactor and the organic semiconductor is still probable. The most optimal conditions and tunable characteristics of GOx-based biosensors such as the ionization potential, electron affinity of organic semiconductors and distance between the enzyme and surface were estimated for the first time.
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Affiliation(s)
- Gintautas BagdŽiūnas
- Department of Material Science and Electrical Engineering, Center for Physical Sciences and Technology, Saulėtekio av. 3, Vilnius, LT-10257, Lithuania.
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8
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Ptushenko VV, Krishtalik LI. Reorganization energies of the electron transfer reactions involving quinones in the reaction center of Rhodobacter sphaeroides. PHOTOSYNTHESIS RESEARCH 2018; 138:167-175. [PMID: 30022339 DOI: 10.1007/s11120-018-0560-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
In framework of the continuum electrostatics theory, the reorganization energies of the electron transfers QA--QB (fast phase), Bph--QA, P+-QA-, and P+-QB- in the photosynthetic bacterial reaction center have been calculated. The calculations were based on the static dielectric permittivity spatial distribution derived from the data on the electrogenesis, with the corresponding characteristic times relatively close to the reaction times of QA--QB (fast phase) and Bph--QA but much shorter than those times of the latter two recombination reactions. The calculated reorganization energies were reasonably close to the experimental estimates for QA--QB (fast phase) and Bph--QA but substantially lower than those of P+-QA- and P+-QB-. A higher effective dielectric permittivity contributes to this effect, but the dominant contribution is most probably made by a non-dielectric relaxation, especially for the P+-QB- recombination influenced by the proton transfer. This situation calls for reconsidering of the current electron transfer rate estimates.
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Affiliation(s)
- Vasily V Ptushenko
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia.
| | - Lev I Krishtalik
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia.
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9
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Litman YE, Rodríguez HB, Braslavsky SE, San Román E. Photophysics of Xanthene Dyes at High Concentrations in Solid Environments: Charge Transfer Assisted Triplet Formation. Photochem Photobiol 2018; 94:865-874. [DOI: 10.1111/php.12978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/01/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yair E. Litman
- Departamento de Química Inorgánica, Analítica y Química Física; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Buenos Aires Argentina
| | - Hernán B. Rodríguez
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA); CCT-La Plata-CONICET; Universidad Nacional de La Plata (UNLP); La Plata Argentina
| | - Silvia E. Braslavsky
- Departamento de Química Inorgánica, Analítica y Química Física; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Buenos Aires Argentina
- Instituto de Química Física de los Materiales; Medio Ambiente y Energía (INQUIMAE); CONICET - Universidad de Buenos Aires; Buenos Aires Argentina
- Max Planck Institute for Chemical Energy Conversion; Mülheim an der Ruhr Germany
| | - Enrique San Román
- Departamento de Química Inorgánica, Analítica y Química Física; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Buenos Aires Argentina
- Instituto de Química Física de los Materiales; Medio Ambiente y Energía (INQUIMAE); CONICET - Universidad de Buenos Aires; Buenos Aires Argentina
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10
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Cherepanov DA, Milanovsky GE, Gopta OA, Balasubramanian R, Bryant DA, Semenov AY, Golbeck JH. Electron–Phonon Coupling in Cyanobacterial Photosystem I. J Phys Chem B 2018; 122:7943-7955. [DOI: 10.1021/acs.jpcb.8b03906] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitry A. Cherepanov
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 117977 Moscow, Russia
| | - Georgy E. Milanovsky
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
| | - Oksana A. Gopta
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Ramakrishnan Balasubramanian
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
- Department of Chemistry and Biochemistry, Montana State University, 103 Chemistry and Biochemistry Building, PO Box 173400, Bozeman, Montana 59717, United States
| | - Alexey Yu. Semenov
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Leninskye Gory,
1, Building 40, 119992 Moscow, Russia
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 117977 Moscow, Russia
| | - John H. Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, 328 Frear Laboratory, University Park, Pennsylvania 16802, United States
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11
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Gnandt D, Na S, Koslowski T. Simulating biological charge transfer: Continuum dielectric theory or molecular dynamics? Biophys Chem 2018; 241:1-7. [PMID: 30036762 DOI: 10.1016/j.bpc.2018.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
Abstract
We study the thermodynamic parameters of Marcus's theory of charge transfer, the driving forces and the reorganization energies, using two widely applied approaches to bioenergetic problems that seem to be radically different: continuum dielectric theory via a numerical solution of Poisson's equation, and the thermodynamic integration approach based upon classical Newtonian molecular dynamics, as perfomed by Na et al., PCCP 19, 18,938 (2017). With application to a nitrite reductase NrfHA protein heterodimer, we obtain an excellent agreement between the respective driving forces with an r.m.s. deviation of 1.7 kcal/mol, and a lower limit to the reorganization energies. The computational methods turn out to be mutually supportive: molecular dynamics can be used to determine the parameters of a dielectric theory computation, which on the other hand can be used to properly rescale the reorganization energies and partition them into aqueous and protein contributions. In addition, we use the electrostatic approach to study the influence of Ca2+ ions on the free energy landscape of charge transfer.
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Affiliation(s)
- David Gnandt
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany
| | - Sehee Na
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany.
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12
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The cytochrome b6f complex: DFT modeling of the first step of plastoquinol oxidation by the iron-sulfur protein. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Pereira AR, Luz RAS, Lima FCDA, Crespilho FN. Protein Oligomerization Based on Brønsted Acid Reaction. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andressa R. Pereira
- São
Carlos Institute of Chemistry, University of São Paulo, 13560-970 São Paulo, Brazil
| | - Roberto A. S. Luz
- São
Carlos Institute of Chemistry, University of São Paulo, 13560-970 São Paulo, Brazil
| | - Filipe C. D. A. Lima
- Federal Institute of Education, Science and Technology of São Paulo, Campus Matão, 15991-502 São Paulo, Brazil
| | - Frank N. Crespilho
- São
Carlos Institute of Chemistry, University of São Paulo, 13560-970 São Paulo, Brazil
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14
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15
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Olshansky L, Greene BL, Finkbeiner C, Stubbe J, Nocera DG. Photochemical Generation of a Tryptophan Radical within the Subunit Interface of Ribonucleotide Reductase. Biochemistry 2016; 55:3234-40. [PMID: 27159163 PMCID: PMC4929995 DOI: 10.1021/acs.biochem.6b00292] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Escherichia coli class Ia ribonucleotide reductase (RNR) achieves forward and reverse proton-coupled electron transfer (PCET) over a pathway of redox active amino acids (β-Y122 ⇌ β-Y356 ⇌ α-Y731 ⇌ α-Y730 ⇌ α-C439) spanning ∼35 Å and two subunits every time it turns over. We have developed photoRNRs that allow radical transport to be phototriggered at tyrosine (Y) or fluorotyrosine (FnY) residues along the PCET pathway. We now report a new photoRNR in which photooxidation of a tryptophan (W) residue replacing Y356 within the α/β subunit interface proceeds by a stepwise ET/PT (electron transfer then proton transfer) mechanism and provides an orthogonal spectroscopic handle with respect to radical pathway residues Y731 and Y730 in α. This construct displays an ∼3-fold enhancement in photochemical yield of W(•) relative to F3Y(•) and a ∼7-fold enhancement relative to Y(•). Photogeneration of the W(•) radical occurs with a rate constant of (4.4 ± 0.2) × 10(5) s(-1), which obeys a Marcus correlation for radical generation at the RNR subunit interface. Despite the fact that the Y → W variant displays no enzymatic activity in the absence of light, photogeneration of W(•) within the subunit interface results in 20% activity for turnover relative to wild-type RNR under the same conditions.
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Affiliation(s)
- Lisa Olshansky
- Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, MA 02138–2902;
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307; .
| | - Brandon L. Greene
- Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, MA 02138–2902;
| | - Chelsea Finkbeiner
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307; .
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307; .
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, MA 02138–2902;
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16
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Zhang W, Gan S, Vezzoli A, Davidson RJ, Milan DC, Luzyanin KV, Higgins SJ, Nichols RJ, Beeby A, Low PJ, Li B, Niu L. Single-Molecule Conductance of Viologen-Cucurbit[8]uril Host-Guest Complexes. ACS NANO 2016; 10:5212-5220. [PMID: 27055002 DOI: 10.1021/acsnano.6b00786] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The local molecular environment is a critical factor which should be taken into account when measuring single-molecule electrical properties in condensed media or in the design of future molecular electronic or single molecule sensing devices. Supramolecular interactions can be used to control the local environment in molecular assemblies and have been used to create microenvironments, for instance, for chemical reactions. Here, we use supramolecular interactions to create microenvironments which influence the electrical conductance of single molecule wires. Cucurbit[8]uril (CB[8]) with a large hydrophobic cavity was used to host the viologen (bipyridinium) molecular wires forming a 1:1 supramolecular complex. Significant increases in the viologen wire single molecule conductances are observed when it is threaded into CB[8] due to large changes of the molecular microenvironment. The results were interpreted within the framework of a Marcus-type model for electron transfer as arising from a reduction in outer-sphere reorganization energy when the viologen is confined within the hydrophobic CB[8] cavity.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Electroanalytical Chemistry, CAS Center for Excellence in Nanoscience, c/o Engineering Laboratory for Modern Analytical Techniques, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Shiyu Gan
- State Key Laboratory of Electroanalytical Chemistry, CAS Center for Excellence in Nanoscience, c/o Engineering Laboratory for Modern Analytical Techniques, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
| | - Andrea Vezzoli
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Ross J Davidson
- Department of Chemistry, Durham University , South Road, Durham DH1 3LE, United Kingdom
| | - David C Milan
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Konstantin V Luzyanin
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Simon J Higgins
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Richard J Nichols
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Andrew Beeby
- Department of Chemistry, Durham University , South Road, Durham DH1 3LE, United Kingdom
| | - Paul J Low
- School of Chemistry and Biochemistry, University of Western Australia , 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Buyi Li
- Department of Chemistry, University of Liverpool , Crown Street, Liverpool L69 7ZD, United Kingdom
| | - Li Niu
- State Key Laboratory of Electroanalytical Chemistry, CAS Center for Excellence in Nanoscience, c/o Engineering Laboratory for Modern Analytical Techniques, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
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17
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Lemkul J, Huang J, Roux B, MacKerell AD. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chem Rev 2016; 116:4983-5013. [PMID: 26815602 PMCID: PMC4865892 DOI: 10.1021/acs.chemrev.5b00505] [Citation(s) in RCA: 371] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 11/28/2022]
Abstract
Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena.
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Affiliation(s)
- Justin
A. Lemkul
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Jing Huang
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
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Olshansky L, Stubbe J, Nocera DG. Charge-Transfer Dynamics at the α/β Subunit Interface of a Photochemical Ribonucleotide Reductase. J Am Chem Soc 2016; 138:1196-205. [PMID: 26710997 PMCID: PMC4924928 DOI: 10.1021/jacs.5b09259] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides to provide the monomeric building blocks for DNA replication and repair. Nucleotide reduction occurs by way of multistep proton-coupled electron transfer (PCET) over a pathway of redox active amino acids spanning ∼35 Å and two subunits (α2 and β2). Despite the fact that PCET in RNR is rapid, slow conformational changes mask examination of the kinetics of these steps. As such, we have pioneered methodology in which site-specific incorporation of a [Re(I)] photooxidant on the surface of the β2 subunit (photoβ2) allows photochemical oxidation of the adjacent PCET pathway residue β-Y356 and time-resolved spectroscopic observation of the ensuing reactivity. A series of photoβ2s capable of performing photoinitiated substrate turnover have been prepared in which four different fluorotyrosines (FnYs) are incorporated in place of β-Y356. The FnYs are deprotonated under biological conditions, undergo oxidation by electron transfer (ET), and provide a means by which to vary the ET driving force (ΔG°) with minimal additional perturbations across the series. We have used these features to map the correlation between ΔG° and kET both with and without the fully assembled photoRNR complex. The photooxidation of FnY356 within the α/β subunit interface occurs within the Marcus inverted region with a reorganization energy of λ ≈ 1 eV. We also observe enhanced electronic coupling between donor and acceptor (HDA) in the presence of an intact PCET pathway. Additionally, we have investigated the dynamics of proton transfer (PT) by a variety of methods including dependencies on solvent isotopic composition, buffer concentration, and pH. We present evidence for the role of α2 in facilitating PT during β-Y356 photooxidation; PT occurs by way of readily exchangeable positions and within a relatively "tight" subunit interface. These findings show that RNR controls ET by lowering λ, raising HDA, and directing PT both within and between individual polypeptide subunits.
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Affiliation(s)
- Lisa Olshansky
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry and Chemical Biology, 12 Oxford St., Harvard University, Cambridge, Massachusetts 02138, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, 12 Oxford St., Harvard University, Cambridge, Massachusetts 02138, United States
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Dow BA, Davidson VL. Converting the bis-FeIV state of the diheme enzyme MauG to Compound I decreases the reorganization energy for electron transfer. Biochem J 2016; 473:67-72. [PMID: 26494530 PMCID: PMC4860820 DOI: 10.1042/bj20150998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/22/2015] [Indexed: 11/17/2022]
Abstract
The electron transfer (ET) properties of two types of high-valent hemes were studied within the same protein matrix; the bis-Fe(IV) state of MauG and the Compound I state of Y294H MauG. The latter is formed as a consequence of mutation of the tyrosine which forms the distal axial ligand of the six-coordinate heme that allows it to stabilize Fe(IV) in the absence of an external ligand. The rates of the ET reaction of each high-valent species with the type I copper protein, amicyanin, were determined at different temperatures and analysed by ET theory. The reaction with bis-Fe(IV) wild-type (WT) MauG exhibited a reorganization energy (λ) that was 0.39 eV greater than that for the reaction of Compound I Y295H MauG. It is concluded that the delocalization of charge over the two hemes in the bis-Fe(IV) state is responsible for the larger λ, relative to the Compound I state in which the Fe(V) equivalent is isolated on one heme. Although the increase in λ decreases the rate of ET, the delocalization of charge decreases the ET distance to its natural substrate protein, thus increasing the ET rate. This describes how proteins can balance different ET properties of complex redox cofactors to optimize each system for its particular ET or catalytic reaction.
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Affiliation(s)
- Brian A Dow
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, U.S.A
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, U.S.A.
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20
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Molinas MF, Benavides L, Castro MA, Murgida DH. Stability, redox parameters and electrocatalytic activity of a cytochrome domain from a new subfamily. Bioelectrochemistry 2015; 105:25-33. [DOI: 10.1016/j.bioelechem.2015.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/21/2015] [Accepted: 05/03/2015] [Indexed: 11/24/2022]
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Huang J, Lopes PM, Roux B, MacKerell AD. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. J Phys Chem Lett 2014; 5:3144-3150. [PMID: 25247054 PMCID: PMC4167036 DOI: 10.1021/jz501315h] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/27/2014] [Indexed: 05/13/2023]
Abstract
In this Perspective, we summarize recent efforts to include the explicit treatment of induced electronic polarization in biomolecular force fields. Methods used to treat polarizability, including the induced dipole, fluctuating charge, and classical Drude oscillator models, are presented, including recent advances in force fields using those methods. This is followed by recent results obtained with the Drude model, including microsecond molecular dynamics (MD) simulations of multiple proteins in explicit solvent. Results show significant variability of backbone and side-chain dipole moments as a function of environment, including significant changes during individual simulations. Dipole moments of water in the vicinity of the proteins reveal small but systematic changes, with the direction of the changes dependent on the environment. Analyses of the full proteins show that the polarizable Drude model leads to larger values of the dielectric constant of the protein interior, especially in the case of hydrophobic regions. These results indicate that the inclusion of explicit electronic polarizability leads to significant differences in the physical forces affecting the structure and dynamics of proteins, which can be investigated in a computationally tractable fashion in the context of the Drude model.
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Affiliation(s)
- Jing Huang
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Room 629, Baltimore, Maryland 21201, United States
| | - Pedro
E. M. Lopes
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Room 629, Baltimore, Maryland 21201, United States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Room 629, Baltimore, Maryland 21201, United States
- E-mail: . Phone: (410) 706-7442. Fax: (410) 706-5017
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Crofts AR, Hong S, Wilson C, Burton R, Victoria D, Harrison C, Schulten K. The mechanism of ubihydroquinone oxidation at the Qo-site of the cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1362-77. [PMID: 23396004 PMCID: PMC3995752 DOI: 10.1016/j.bbabio.2013.01.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 12/12/2012] [Accepted: 01/18/2013] [Indexed: 01/04/2023]
Abstract
1. Recent results suggest that the major flux is carried by a monomeric function, not by an intermonomer electron flow. 2. The bifurcated reaction at the Qo-site involves sequential partial processes, - a rate limiting first electron transfer generating a semiquinone (SQ) intermediate, and a rapid second electron transfer in which the SQ is oxidized by the low potential chain. 3. The rate constant for the first step in a strongly endergonic, proton-first-then-electron mechanism, is given by a Marcus-Brønsted treatment in which a rapid electron transfer is convoluted with a weak occupancy of the proton configuration needed for electron transfer. 4. A rapid second electron transfer pulls the overall reaction over. Mutation of Glu-295 of cyt b shows it to be a key player. 5. In more crippled mutants, electron transfer is severely inhibited and the bell-shaped pH dependence of wildtype is replaced by a dependence on a single pK at ~8.5 favoring electron transfer. Loss of a pK ~6.5 is explained by a change in the rate limiting step from the first to the second electron transfer; the pK ~8.5 may reflect dissociation of QH. 6. A rate constant (<10(3)s(-1)) for oxidation of SQ in the distal domain by heme bL has been determined, which precludes mechanisms for normal flux in which SQ is constrained there. 7. Glu-295 catalyzes proton exit through H(+) transfer from QH, and rotational displacement to deliver the H(+) to exit channel(s). This opens a volume into which Q(-) can move closer to the heme to speed electron transfer. 8. A kinetic model accounts well for the observations, but leaves open the question of gating mechanisms. For the first step we suggest a molecular "escapement"; for the second a molecular ballet choreographed through coulombic interactions. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Antony R Crofts
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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Kobori T, Sodeyama K, Otsuka T, Tateyama Y, Tsuneyuki S. Trimer effects in fragment molecular orbital-linear combination of molecular orbitals calculation of one-electron orbitals for biomolecules. J Chem Phys 2013; 139:094113. [DOI: 10.1063/1.4818599] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Gunner MR, Amin M, Zhu X, Lu J. Molecular mechanisms for generating transmembrane proton gradients. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:892-913. [PMID: 23507617 PMCID: PMC3714358 DOI: 10.1016/j.bbabio.2013.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/28/2013] [Accepted: 03/01/2013] [Indexed: 01/02/2023]
Abstract
Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side.
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Affiliation(s)
- M R Gunner
- Department of Physics, City College of New York, New York, NY 10031, USA.
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