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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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2
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Siletsky SA, Belevich I, Belevich NP, Soulimane T, Wikström M. Time-resolved generation of membrane potential by ba 3 cytochrome c oxidase from Thermus thermophilus coupled to single electron injection into the O and O H states. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:915-926. [PMID: 28807731 DOI: 10.1016/j.bbabio.2017.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 10/19/2022]
Abstract
Two electrogenic phases with characteristic times of ~14μs and ~290μs are resolved in the kinetics of membrane potential generation coupled to single-electron reduction of the oxidized "relaxed" O state of ba3 oxidase from T. thermophilus (O→E transition). The rapid phase reflects electron redistribution between CuA and heme b. The slow phase includes electron redistribution from both CuA and heme b to heme a3, and electrogenic proton transfer coupled to reduction of heme a3. The distance of proton translocation corresponds to uptake of a proton from the inner water phase into the binuclear center where heme a3 is reduced, but there is no proton pumping and no reduction of CuB. Single-electron reduction of the oxidized "unrelaxed" state (OH→EH transition) is accompanied by electrogenic reduction of the heme b/heme a3 pair by CuA in a "fast" phase (~22μs) and transfer of protons in "middle" and "slow" electrogenic phases (~0.185ms and ~0.78ms) coupled to electron redistribution from the heme b/heme a3 pair to the CuB site. The "middle" and "slow" electrogenic phases seem to be associated with transfer of protons to the proton-loading site (PLS) of the proton pump, but when all injected electrons reach CuB the electronic charge appears to be compensated by back-leakage of the protons from the PLS into the binuclear site. Thus proton pumping occurs only to the extent of ~0.1 H+/e-, probably due to the formed membrane potential in the experiment.
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Affiliation(s)
- Sergey A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.
| | - Ilya Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
| | - Nikolai P Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
| | - Tewfik Soulimane
- Department of Chemical Sciences and Bernal Research Institute, University of Limerick, Ireland
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Finland
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3
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Lyons JA, Hilbers F, Caffrey M. Structure and Function of Bacterial Cytochrome c Oxidases. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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4
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Cao Y, He ZN, Shi ZP, Enock M. Improving the stability of glutamate fermentation by Corynebacterium glutamicum via supplementing sorbitol or glycerol. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-014-0032-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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5
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Affiliation(s)
- Jay R. Winkler
- Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125
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6
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Heering HA. Analysis of protein film voltammograms as Michaelis–Menten saturation curves yield the electron cooperativity number for deconvolution. Bioelectrochemistry 2012; 87:58-64. [DOI: 10.1016/j.bioelechem.2011.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/14/2011] [Accepted: 12/17/2011] [Indexed: 12/28/2022]
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7
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A theoretical investigation of the functional role of the axial methionine ligand of the Cu(A) site in cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1314-27. [PMID: 21745457 DOI: 10.1016/j.bbabio.2011.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/29/2011] [Accepted: 06/22/2011] [Indexed: 11/20/2022]
Abstract
The functional roles of the amino acid residues of the Cu(A) site in bovine cytochrome c oxidase (CcO) were investigated by utilizing hybrid quantum mechanics (QM)/molecular mechanics (MM) calculations. The energy levels of the molecular orbitals (MOs) involving Cu d(zx) orbitals unexpectedly increased, as compared with those found previously with a simplified model system lacking the axial Met residue (i.e., Cu(2)S(2)N(2)). This elevation of MO energies stemmed from the formation of the anti-bonding orbitals, which are generated by hybridization between the d(zx) orbitals of Cu ions and the p-orbitals of the S and O atoms of the axial ligands. To clarify the roles of the axial Met ligand, the inner-sphere reorganization energies of the Cu(A) site were computed, with the Met residue assigned to either the QM or MM region. The reorganization energy slightly increased when the Met residue was excluded from the QM region. The existing experimental data and the present structural modeling study also suggested that the axial Met residue moderately increased the redox potential of the Cu(A) site. Thus, the role of the Met may be to regulate the electron transfer rate through the fine modulation of the electronic structure of the Cu(A) "platform", created by two Cys/His residues coordinated to the Cu ions. This regulation would provide the optimum redox potential/reorganization energy of the Cu(A) site, and thereby facilitate the subsequent cooperative reactions, such as the proton pump and the enzymatic activity, of CcO. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.
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8
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Nöll T, Nöll G. Strategies for “wiring” redox-active proteins to electrodes and applications in biosensors, biofuel cells, and nanotechnology. Chem Soc Rev 2011; 40:3564-76. [DOI: 10.1039/c1cs15030h] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Zhang J, Gunner MR. Multiconformation continuum electrostatics analysis of the effects of a buried Asp introduced near heme a in Rhodobacter sphaeroides cytochrome c oxidase. Biochemistry 2010; 49:8043-52. [PMID: 20701325 DOI: 10.1021/bi100663u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c oxidase (CcO) reduces O(2) to water via a series of proton-coupled electron transfers, generating a transmembrane electrochemical gradient. Coupling electron and proton transfer requires changing the pK(a) values of buried residues at each stage in the reaction cycle. Heme a is a key cofactor in the CcO electron transfer chain. Mutation of Ser44 to Asp has been reported [Mills, D. A., et al. (2008) Biochemistry 47, 11499-11509], changing the hydrogen bond acceptor from His102, the heme a axial ligand in Rhodobactor sphaeroides CcO. This adds an acidic residue to the CcO interior. The electrochemical behavior of heme a in wild-type and S44D CcO is compared using the continuum electrostatics program MCCE. The introduced, deeply buried Asp remains ionized at physiological pH only when the nearby heme is oxidized. Heme a reduction is now calculated to be strongly coupled to Asp proton binding, while with Ser44, it is weakly coupled to small protonation shifts at multiple sites, increasing the pH dependence in the mutant. At pH 7, the partially ionized Asp 44 is calculated to lower the heme redox potential by 50 mV as expected given the thermodynamics of coupled electron and proton transfers. This highlights an curious finding in the experimental results where a low Asp pK(a) is found together with a stabilized reduced heme. The stabilization of a heme oxidation in a model complex by a hydrogen bond to the axial His ligand calculated with continuum electrostatics and with density functional theory were in good agreement.
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Affiliation(s)
- Jun Zhang
- Physics Department, J-419, City College of New York, 160 Convent Avenue, New York, New York 10031, USA
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10
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Smirnov AY, Mourokh LG, Nori F. Kinetics of proton pumping in cytochrome c oxidase. J Chem Phys 2009; 130:235105. [DOI: 10.1063/1.3155213] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Spaar A, Flöck D, Helms V. Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution. Biophys J 2009; 96:1721-32. [PMID: 19254533 DOI: 10.1016/j.bpj.2008.11.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 11/10/2008] [Indexed: 11/15/2022] Open
Abstract
Electron transfer between the water-soluble cytochrome c and the integral membrane protein cytochrome c oxidase (COX) is the terminal reaction in the respiratory chain. The first step in this reaction is the diffusional association of cytochrome c toward COX, and it is still not completely clear whether cytochrome c diffuses in the bulk solution while encountering COX, or whether it prefers to diffuse laterally on the membrane surface. This is a rather crucial question, since in the latter case the association would be strongly dependent on the lipid composition and the presence of additional membrane proteins. We applied Brownian dynamics simulations to investigate the effect of an atomistically modeled dipalmitoyl phosphatidylcholine membrane on the association behavior of cytochrome c toward COX from Paracoccus denitrificans. We studied the negatively charged, physiological electron-transfer partner of COX, cytochrome c(552), and the positively charged horse-heart cytochrome c. As expected, both cytochrome c species prefer diffusion in bulk solution while associating toward COX embedded in a membrane, where the partial charges of the lipids were switched off, and the corresponding optimal association pathways largely overlap with the association toward fully solvated COX. Remarkably, after switching on the lipid partial charges, both cytochrome c species were strongly attracted by the inhomogeneous charge distribution caused by the zwitterionic lipid headgroups. This effect is particularly enhanced for horse-heart cytochrome c and is stronger at lower ionic strength. We therefore conclude that in the presence of a polar or even a charged membrane, cytochrome c diffuses laterally rather than in three dimensions.
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Affiliation(s)
- Alexander Spaar
- Center for Bioinformatics, Saarland University, Im Stadtwald, Saarbrücken, Germany
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12
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Elucidation of Electron- Transfer Pathways in Copper and Iron Proteins by Pulse Radiolysis Experiments. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/9780470144428.ch1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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13
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Wiertz FGM, Richter OMH, Ludwig B, de Vries S. Kinetic Resolution of a Tryptophan-radical Intermediate in the Reaction Cycle of Paracoccus denitrificans Cytochrome c Oxidase. J Biol Chem 2007; 282:31580-91. [PMID: 17761680 DOI: 10.1074/jbc.m705520200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The catalytic mechanism, electron transfer coupled to proton pumping, of heme-copper oxidases is not yet fully understood. Microsecond freeze-hyperquenching single turnover experiments were carried out with fully reduced cytochrome aa(3) reacting with O(2) between 83 micros and 6 ms. Trapped intermediates were analyzed by low temperature UV-visible, X-band, and Q-band EPR spectroscopy, enabling determination of the oxidation-reduction kinetics of Cu(A), heme a, heme a(3), and of a recently detected tryptophan radical (Wiertz, F. G. M., Richter, O. M. H., Cherepanov, A. V., MacMillan, F., Ludwig, B., and de Vries, S. (2004) FEBS Lett. 575, 127-130). Cu(B) and heme a(3) were EPR silent during all stages of the reaction. Cu(A) and heme a are in electronic equilibrium acting as a redox pair. The reduction potential of Cu(A) is 4.5 mV lower than that of heme a. Both redox groups are oxidized in two phases with apparent half-lives of 57 micros and 1.2 ms together donating a single electron to the binuclear center in each phase. The formation of the heme a(3) oxoferryl species P(R) (maxima at 430 nm and 606 nm) was completed in approximately 130 micros, similar to the first oxidation phase of Cu(A) and heme a. The intermediate F (absorbance maximum at 571 nm) is formed from P(R) and decays to a hitherto undetected intermediate named F(W)(*). F(W)(*) harbors a tryptophan radical, identified by Q-band EPR spectroscopy as the tryptophan neutral radical of the strictly conserved Trp-272 (Trp-272(*)). The Trp-272(*) populates to 4-5% due to its relatively low rate of formation (t((1/2)) = 1.2 ms) and rapid rate of breakdown (t((1/2)) = 60 micros), which represents electron transfer from Cu(A)/heme a to Trp-272(*). The formation of the Trp-272(*) constitutes the major rate-determining step of the catalytic cycle. Our findings show that Trp-272 is a redox-active residue and is in this respect on an equal par to the metallocenters of the cytochrome c oxidase. Trp-272 is the direct reductant either to the heme a(3) oxoferryl species or to Cu (2+)(B). The potential role of Trp-272 in proton pumping is discussed.
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Affiliation(s)
- Frank G M Wiertz
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
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Wikström M, Verkhovsky MI. Mechanism and energetics of proton translocation by the respiratory heme-copper oxidases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1200-14. [PMID: 17689487 DOI: 10.1016/j.bbabio.2007.06.008] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 06/24/2007] [Accepted: 06/26/2007] [Indexed: 11/24/2022]
Abstract
Recent time-resolved optical and electrometric experiments have provided a sequence of events for the proton-translocating mechanism of cytochrome c oxidase. These data also set limits for the mechanistic, kinetic, and thermodynamic parameters of the proton pump, which are analysed here in some detail. The analysis yields limit values for the pK of the "pump site", its modulation during the proton-pumping process, and suggests its identity in the structure. Special emphasis is made on side-reactions that may short-circuit the pump, and the means by which these may be avoided. We will also discuss the most prominent proton pumping mechanisms proposed to date in relation to these data.
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Affiliation(s)
- Mårten Wikström
- Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, PB 65 (Viikinkaari 1), FI-00014 University of Helsinki, Finland.
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15
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Belevich I, Bloch DA, Belevich N, Wikström M, Verkhovsky MI. Exploring the proton pump mechanism of cytochrome c oxidase in real time. Proc Natl Acad Sci U S A 2007; 104:2685-90. [PMID: 17293458 PMCID: PMC1796784 DOI: 10.1073/pnas.0608794104] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase catalyzes most of the biological oxygen consumption on Earth, a process responsible for energy supply in aerobic organisms. This remarkable membrane-bound enzyme also converts free energy from O(2) reduction to an electrochemical proton gradient by functioning as a redox-linked proton pump. Although the structures of several oxidases are known, the molecular mechanism of redox-linked proton translocation has remained elusive. Here, correlated internal electron and proton transfer reactions were tracked in real time by spectroscopic and electrometric techniques after laser-activated electron injection into the oxidized enzyme. The observed kinetics establish the long-sought reaction sequence of the proton pump mechanism and describe some of its thermodynamic properties. The 10-micros electron transfer to heme a raises the pK(a) of a "pump site," which is loaded by a proton from the inside of the membrane in 150 micros. This loading increases the redox potentials of both hemes a and a(3), which allows electron equilibration between them at the same rate. Then, in 0.8 ms, another proton is transferred from the inside to the heme a(3)/Cu(B) center, and the electron is transferred to Cu(B). Finally, in 2.6 ms, the preloaded proton is released from the pump site to the opposite side of the membrane.
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Affiliation(s)
- Ilya Belevich
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Dmitry A. Bloch
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Nikolai Belevich
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Michael I. Verkhovsky
- Helsinki Bioenergetics Group, Program for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
- *To whom correspondence should be addressed at:
Institute of Biotechnology, University of Helsinki, Biocenter 3, P.O. Box 65, Viikinkaari 1, FI–00014, Helsinki, Finland. E-mail:
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Farver O, Hwang HJ, Lu Y, Pecht I. Reorganization Energy of the CuA Center in Purple Azurin: Impact of the Mixed Valence-to-Trapped Valence State Transition. J Phys Chem B 2007; 111:6690-4. [PMID: 17274649 DOI: 10.1021/jp0672555] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mixed valence (MV) coordination compounds play important roles in redox reactions in chemistry and biology. Details of the contribution of a mixed valence state to protein electron transfer (ET) reactivity such as reorganization energy, however, have not been experimentally defined. Herein we report measurements of reorganization energies of a binuclear CuA center engineered into Pseudomonas aeruginosa azurin that exhibits a reversible transition between a totally delocalized MV state at pH 8.0 and a trapped valence (TV) state at pH 4.0. The reorganization energy of a His120Ala variant of CuA azurin that displays a TV state at both the above pH values has also been determined. We found that the MV-to-TV state transition increases the reorganization energy by 0.18 eV, providing evidence that the MV state of the CuA center has lower reorganization energy than its TV counterpart. We have also shown that lowering the pH from 8.0 to 4.0 results in a similar (approximately 0.4 eV) decrease in reorganization energy for both blue (type 1) and purple (CuA) azurins, even though the reorganization energies of the two different copper centers are different at a given pH. These results suggest that the MV state plays only a secondary role in modulation of the ET reactivity via the reorganization energy, as compared to that of the driving force.
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Affiliation(s)
- Ole Farver
- Institute of Analytical and Pharmaceutical Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Farver O, Chen Y, Fee JA, Pecht I. Electron transfer among the CuA-, heme b- and a3-centers of Thermus thermophilus cytochrome ba3. FEBS Lett 2006; 580:3417-21. [PMID: 16712843 DOI: 10.1016/j.febslet.2006.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 04/27/2006] [Accepted: 05/03/2006] [Indexed: 10/24/2022]
Abstract
The 1-methyl-nicotinamide radical (MNA(*)), produced by pulse radiolysis has previously been shown to reduce the Cu(A)-site of cytochromes aa(3), a process followed by intramolecular electron transfer (ET) to the heme a but not to the heme a(3) [Farver, O., Grell, E., Ludwig, B., Michel, H. and Pecht, I. (2006) Rates and equilibrium of CuA to heme a electron transfer in Paracoccus denitrificans cytochrome c oxidase. Biophys. J. 90, 2131-2137]. Investigating this process in the cytochrome ba(3) of Thermus thermophilus (Tt), we now show that MNA(*) also reduces Cu(A) with a subsequent ET to the heme b and then to heme a(3), with first-order rate constants 11200 s(-1), and 770 s(-1), respectively. The results provide clear evidence for ET among the three spectroscopically distinguishable centers and indicate that the binuclear a(3)-Cu(B) center can be reduced in molecules containing a single reduction equivalent.
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Affiliation(s)
- Ole Farver
- Institute of Analytical Chemistry, The Danish University of Pharmaceutical Sciences, Copenhagen, Denmark
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