1
|
Camilo SRG, Curtolo F, Galassi VV, Arantes GM. Tunneling and Nonadiabatic Effects on a Proton-Coupled Electron Transfer Model for the Q o Site in Cytochrome bc1. J Chem Inf Model 2021; 61:1840-1849. [PMID: 33793213 DOI: 10.1021/acs.jcim.1c00008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cytochrome bc1 is a fundamental enzyme for cellular respiration and photosynthesis. This dimeric protein complex catalyzes a proton-coupled electron transfer (PCET) from the reduced coenzyme-Q substrate (Q) to a bimetallic iron-sulfur cluster in the Qo active site. Herein, we combine molecular dynamics simulations of the complete cytochrome bc1 protein with electronic-structure calculations of truncated models and a semiclassical tunneling theory to investigate the electron-proton adiabaticity of the initial reaction catalyzed in the Qo site. After sampling possible orientations between the Q substrate and a histidine side chain that functions as hydrogen acceptor, we find that a truncated model composed by ubiquinol-methyl and imidazole-iron(III)-sulfide captures the expected changes in oxidation and spin states of the electron donor and acceptor. Diabatic electronic surfaces obtained for this model with multiconfigurational wave function calculations demonstrate that this reaction is electronic nonadiabatic, and proton tunneling is faster than mixing of electronic configurations. These results indicate the formalism that should be used to calculate vibronic couplings and kinetic parameters for the initial reaction in the Qo site of cytochrome bc1. This framework for molecular simulation may also be applied to investigate other PCET reactions in the Q-cycle or in various metalloproteins that catalyze proton translocation coupled to redox processes.
Collapse
Affiliation(s)
- Sofia R G Camilo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Vanesa V Galassi
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| |
Collapse
|
2
|
Barragan AM, Soudackov AV, Luthey-Schulten Z, Hammes-Schiffer S, Schulten K, Solov'yov IA. Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc1 Complex. J Am Chem Soc 2021; 143:715-723. [PMID: 33397104 DOI: 10.1021/jacs.0c07799] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The cytochrome bc1 complex is a transmembrane enzymatic protein complex that plays a central role in cellular energy production and is present in both photosynthetic and respiratory chain organelles. Its reaction mechanism is initiated by the binding of a quinol molecule to an active site, followed by a series of charge transfer reactions between the quinol and protein subunits. Previous work hypothesized that the primary reaction was a concerted proton-coupled electron transfer (PCET) reaction because of the apparent absence of intermediate states associated with single proton or electron transfer reactions. In the present study, the kinetics of the primary bc1 complex PCET reaction is investigated with a vibronically nonadiabatic PCET theory in conjunction with all-atom molecular dynamics simulations and electronic structure calculations. The computed rate constants and relatively high kinetic isotope effects are consistent with experimental measurements on related biomimetic systems. The analysis implicates a concerted PCET mechanism with significant hydrogen tunneling and nonadiabatic effects in the bc1 complex. Moreover, the employed theoretical framework is shown to serve as a general strategy for describing PCET reactions in bioenergetic systems.
Collapse
Affiliation(s)
- Angela M Barragan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Alexander V Soudackov
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Zaida Luthey-Schulten
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Klaus Schulten
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Strasse 9-11, Oldenburg 26111, Germany
| |
Collapse
|
3
|
Zieba AA, Richardson C, Lucero C, Dieng SD, Gindt YM, Schelvis JPM. Evidence for concerted electron proton transfer in charge recombination between FADH- and 306Trp• in Escherichia coli photolyase. J Am Chem Soc 2011; 133:7824-36. [PMID: 21534528 DOI: 10.1021/ja2001488] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proton-coupled electron-transfer (PCET) is a mechanism of great importance in protein electron transfer and enzyme catalysis, and the involvement of aromatic amino acids in this process is of much interest. The DNA repair enzyme photolyase provides a natural system that allows for the study of PCET using a neutral radical tryptophan (Trp(•)). In Escherichia coli photolyase, photoreduction of the flavin adenine dinucleotide (FAD) cofactor in its neutral radical semiquinone form (FADH(•)) results in the formation of FADH(-) and (306)Trp(•). Charge recombination between these two intermediates requires the uptake of a proton by (306)Trp(•). The rate constant of charge recombination has been measured as a function of temperature in the pH range from 5.5 to 10.0, and the data are analyzed with both classical Marcus and semi-classical Hopfield electron transfer theory. The reorganization energy associated with the charge recombination process shows a pH dependence ranging from 2.3 eV at pH ≤ 7 and 1.2 eV at pH(D) 10.0. These findings indicate that at least two mechanisms are involved in the charge recombination reaction. Global analysis of the data supports the hypothesis that PCET during charge recombination can follow two different mechanisms with an apparent switch around pH 6.5. At lower pH, concerted electron proton transfer (CEPT) is the favorable mechanism with a reorganization energy of 2.1-2.3 eV. At higher pH, a sequential mechanism becomes dominant with rate-limiting electron-transfer followed by proton uptake which has a reorganization energy of 1.0-1.3 eV. The observed 'inverse' deuterium isotope effect at pH < 8 can be explained by a solvent isotope effect that affects the free energy change of the reaction and masks the normal, mass-related kinetic isotope effect that is expected for a CEPT mechanism. To the best of our knowledge, this is the first time that a switch in PCET mechanism has been observed in a protein.
Collapse
Affiliation(s)
- Agnieszka A Zieba
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, USA
| | | | | | | | | | | |
Collapse
|
4
|
Tcherkez G, Farquhar GD. On the effect of heavy water (D 2O) on carbon isotope fractionation in photosynthesis. FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:201-212. [PMID: 32688774 DOI: 10.1071/fp07282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Accepted: 02/18/2008] [Indexed: 06/11/2023]
Abstract
Internal conductance to carbon dioxide is a key aspect of leaf photosynthesis although is still not well understood. It is thought that it comprises two components, namely, a gas phase component (diffusion from intercellular spaces to cell walls) and a liquid phase component (dissolution, diffusion in water, hydration equilibrium). Here we use heavy water (D2O), which is known to slow down CO2 hydration by a factor of nearly three. Using 12C/13C stable isotope techniques and Xanthium strumarium L. leaves, we show that the on-line carbon isotope discrimination (Δ13C, or Δobs) associated with photosynthesis is not significantly decreased by heavy water, and that the internal conductance, estimated with relationships involving the deviation of Δ13C, decreased by 8-40% in 21% O2. It is concluded that in typical conditions, the CO2-hydration equilibrium does not exert an effect on CO2 assimilation larger than 9%. The carbon isotope discrimination associated with CO2 addition to ribulose-1,5,bisphosphate by Rubisco is slightly decreased by heavy water. This effect is proposed to originate from the use of solvent-derived proton/deuteron during the last step of the catalytic cycle of the enzyme (hydration/cleavage).
Collapse
Affiliation(s)
- Guillaume Tcherkez
- Plateforme Métabolisme-Métabolome, IFR87, Université Paris-Sud XI, 91405 Orsay, France
| | - Graham D Farquhar
- Environmental Biology Group, Research School of Biological Sciences, Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
5
|
Nelson ME, Finazzi G, Wang QJ, Middleton-Zarka KA, Whitmarsh J, Kallas T. Cytochrome b6 Arginine 214 of Synechococcus sp. PCC 7002, a Key Residue for Quinone-reductase Site Function and Turnover of the Cytochrome bf Complex. J Biol Chem 2005; 280:10395-402. [PMID: 15632120 DOI: 10.1074/jbc.m410948200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quinone-reductase (Q(i)) domains of cyanobacterial/chloroplast cytochrome bf and bacterial/mitochondrial bc complexes differ markedly, and the cytochrome bf Q(i) site mechanism remains largely enigmatic. To investigate the bf Q(i) domain, we constructed the mutation R214H, which substitutes histidine for a conserved arginine in the cytochrome b(6) polypeptide of the cyanobacterium Synechococcus sp. SPCC 7002. At high light intensity, the R214H mutant grew approximately 2.5-fold more slowly than the wild type. Slower growth arose from correspondingly slower overall turnover of the bf complex. Specifically, as shown in single flash turnover experiments of cytochrome b(6) reduction and oxidation, the R214H mutation partially blocked electron transfer to the Q(i) site, mimicking the effect of the Q(i) site inhibitor 2-N-4-hydroxyquinoline-N-oxide. The kinetics of cytochrome b(6) oxidation were largely unaffected by hydrogen-deuterium exchange in the mutant but were slowed considerably in the wild type. This suggests that although protonation events influenced the kinetics of cytochrome b(6) oxidation at the Q(i) site in the wild type, electron flow limited this reaction in the R214H mutant. Redox titration of membranes revealed midpoint potentials (E(m,7)) of the two b hemes similar to those in the wild type. Our data define cytochrome b(6) Arg(214) as a key residue for Q(i) site catalysis and turnover of the cytochrome bf complex. In the recent cytochrome bf structures, Arg(214) lies near the Q(i) pocket and the newly discovered c(i) or x heme. We propose a model for Q(i) site function and a role for Arg(214) in plastoquinone binding.
Collapse
Affiliation(s)
- Matthew E Nelson
- Department of Biology and Microbiology, University of Wisconsin-Oshkosh, Oshkosh, Wisconsin 54901, USA
| | | | | | | | | | | |
Collapse
|
6
|
Yan J, Cramer WA. Functional insensitivity of the cytochrome b6f complex to structure changes in the hinge region of the Rieske iron-sulfur protein. J Biol Chem 2003; 278:20925-33. [PMID: 12672829 DOI: 10.1074/jbc.m212616200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structure analysis of the cytochrome bc1 complex in the presence and absence of Qp quinol analog inhibitors implied that a large amplitude motion of the Rieske iron-sulfur protein (ISP) is required to mediate electron transfer from ubiquinol to cytochrome c1. Studies of the functional consequences of mutagenesis of an 8-residue ISP "hinge" region in the bc1 complex showed it to be sensitive to structure perturbation, implying that optimum flexibility and length are required for the large amplitude motion. Mutagenesis-function analysis carried out on the ISP hinge region of the cytochrome b6 f complex using the cyanobacterium Synechococcus sp. PCC 7002 showed the following. (i) Of three petC genes, only that in the petCA operon codes for functional ISP. (ii) The function of the complex was insensitive to changes in the hinge region that increased flexibility, decreased flexibility by substitutions of 4-6 Pro residues, shortened the hinge by a 1-residue deletion, or elongated it by insertion of 4 residues. The latter change increased sensitivity to Qp inhibitors, whereas deletion of 2 residues resulted in a loss of inhibitor sensitivity and a decrease in activity, indicating a minimum hinge length of 7 residues required for optimum binding of ISP at the Qp site. Thus, in contrast to the bc1 complex, the function of the b6 f complex was insensitive to sequence changes in the ISP hinge that altered its length or flexibility. This implies that either the barriers to motion or the amplitude of ISP motion required for function is smaller than in the bc1 complex.
Collapse
Affiliation(s)
- Jiusheng Yan
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-2054,USA
| | | |
Collapse
|
7
|
Soriano GM, Guo LW, De Vitry C, Kallas T, Cramer WA. Electron transfer from the Rieske iron-sulfur protein (ISP) to cytochrome f in vitro. Is a guided trajectory of the ISP necessary for competent docking? J Biol Chem 2002; 277:41865-71. [PMID: 12207018 DOI: 10.1074/jbc.m205772200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The time course of electron transfer in vitro between soluble domains of the Rieske iron-sulfur protein (ISP) and cytochrome f subunits of the cytochrome b(6)f complex of oxygenic photosynthesis was measured by stopped-flow mixing. The domains were derived from Chlamydomonas reinhardtii and expressed in Escherichia coli. The expressed 142-residue soluble ISP apoprotein was reconstituted with the [2Fe-2S] cluster. The second-order rate constant, k(2)((ISP-f)) = 1.5 x 10(6) m(-1) s(-1), for ISP to cytochrome f electron transfer was <10(-2) of the rate constant at low ionic strength, k(2)((f-PC))(> 200 x 10(6) m(-1) s(-1)), for the reduction of plastocyanin by cytochrome f, and approximately 1/30 of k(2)((f-PC)) at the ionic strength estimated for the thylakoid interior. In contrast to k(2)((f-PC)), k(2)((ISP-f)) was independent of pH and ionic strength, implying no significant role of electrostatic interactions. Effective pK values of 6.2 and 8.3, respectively, of oxidized and reduced ISP were derived from the pH dependence of the amplitude of cytochrome f reduction. The first-order rate constant, k(1)((ISP-f)), predicted from k(2)((ISP-f)) is approximately 10 and approximately 150 times smaller than the millisecond and microsecond phases of cytochrome f reduction observed in vivo. It is proposed that in the absence of electrostatic guidance, a productive docking geometry for fast electron transfer is imposed by the guided trajectory of the ISP extrinsic domain. The requirement of a specific electrically neutral docking configuration for ISP electron transfer is consistent with structure data for the related cytochrome bc(1) complex.
Collapse
Affiliation(s)
- Glenda M Soriano
- Department of Biological Sciences and Program in Biochemistry/Molecular Biology, Purdue University, West Lafayette, Indiana 47907-1392, USA
| | | | | | | | | |
Collapse
|