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Pirnia MM, Sarhangi SM, Singharoy A, Matyushov DV. Protein Medium Facilitates Electron Transfer in Photosynthetic Heliobacterial Reaction Center. J Phys Chem B 2024. [PMID: 39348290 DOI: 10.1021/acs.jpcb.4c04956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
Abstract
This computational study addresses the question of how large membrane-bound proteins of electron transport chains facilitate fast vector-based charge transport. We study electron transfer reactions following ultrafast initial charge separation induced by absorption of light by P800 primary pair and leading to the electron localization at the A0 cofactor. Two subsequent, much slower reactions, electron transfer to the iron-sulfur cluster Fx and reduction of the menaquinone (MQ) cofactor, are studied by combining molecular dynamics simulations, electronic structure calculations, and theoretical modeling. The low value of the electronic coupling between A0 and Fx brings this reaction to the microsecond time scale even at the zero activation barrier. In contrast, A0-MQ electron transfer occurs on a subnanosecond time scale and might become the preferred route for charge transport. We elucidate mechanistic properties of the protein medium allowing fast, vectorial charge transfer. The electric field is high and inhomogeneous inside the protein and is coupled to high polarizabilities of cofactors to significantly lower the reaction barrier. The A0-MQ separation puts this reaction at the edge between the plateau characterizing the reaction dynamical control and exponential falloff due to electronic tunneling. A strong separation in relaxation times of the medium dynamics for the forward and backward reactions promotes vectorial charge transfer.
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Affiliation(s)
- Mohammad Mehdi Pirnia
- School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
| | - Setare Mostajabi Sarhangi
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
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Abstract
The theory of electron transfer reactions establishes the conceptual foundation for redox solution chemistry, electrochemistry, and bioenergetics. Electron and proton transfer across the cellular membrane provide all energy of life gained through natural photosynthesis and mitochondrial respiration. Rates of biological charge transfer set kinetic bottlenecks for biological energy storage. The main system-specific parameter determining the activation barrier for a single electron-transfer hop is the reorganization energy of the medium. Both harvesting of light energy in natural and artificial photosynthesis and efficient electron transport in biological energy chains require reduction of the reorganization energy to allow fast transitions. This review article discusses mechanisms by which small values of the reorganization energy are achieved in protein electron transfer and how similar mechanisms can operate in other media, such as nonpolar and ionic liquids. One of the major mechanisms of reorganization energy reduction is through non-Gibbsian (nonergodic) sampling of the medium configurations on the reaction time. A number of alternative mechanisms, such as electrowetting of active sites of proteins, give rise to non-parabolic free energy surfaces of electron transfer. These mechanisms, and nonequilibrium population of donor-acceptor vibrations, lead to a universal phenomenology of separation between the Stokes shift and variance reorganization energies of electron transfer.
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Affiliation(s)
- Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA.
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3
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Faries KM, Kohout CE, Wang GX, Hanson DK, Holten D, Laible PD, Kirmaier C. Consequences of saturation mutagenesis of the protein ligand to the B-side monomeric bacteriochlorophyll in reaction centers from Rhodobacter capsulatus. PHOTOSYNTHESIS RESEARCH 2019; 141:273-290. [PMID: 30859455 DOI: 10.1007/s11120-019-00626-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
In bacterial reaction centers (RCs), photon-induced initial charge separation uses an A-side bacteriochlorophyll (BChl, BA) and bacteriopheophytin (BPh, HA), while the near-mirror image B-side BB and HB cofactors are inactive. Two new sets of Rhodobacter capsulatus RC mutants were designed, both bearing substitution of all amino acids for the native histidine M180 (M-polypeptide residue 180) ligand to the core Mg ion of BB. Residues are identified that largely result in retention of a BChl in the BB site (Asp, Ser, Pro, Gln, Asn, Gly, Cys, Lys, and Thr), ones that largely harbor the Mg-free BPh in the BB site (Leu and Ile), and ones for which isolated RCs are comprised of a substantial mixture of these two RC types (Ala, Glu, Val, Met and, in one set, Arg). No protein was isolated when M180 is Trp, Tyr, Phe, or (in one set) Arg. These findings are corroborated by ground state spectra, pigment extractions, ultrafast transient absorption studies, and the yields of B-side transmembrane charge separation. The changes in coordination chemistries did not reveal an RC with sufficiently precise poising of the redox properties of the BB-site cofactor to result in a high yield of B-side electron transfer to HB. Insights are gleaned into the amino acid properties that support BChl in the BB site and into the widely observed multi-exponential decay of the excited state of the primary electron donor. The results also have direct implications for tuning free energies of the charge-separated intermediates in RCs and mimetic systems.
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Affiliation(s)
- Kaitlyn M Faries
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Claire E Kohout
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Grace Xiyu Wang
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Deborah K Hanson
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Philip D Laible
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Christine Kirmaier
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA.
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Pan J, Saer R, Lin S, Beatty JT, Woodbury NW. Electron Transfer in Bacterial Reaction Centers with the Photoactive Bacteriopheophytin Replaced by a Bacteriochlorophyll through Coordinating Ligand Substitution. Biochemistry 2016; 55:4909-18. [DOI: 10.1021/acs.biochem.6b00317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jie Pan
- The
Biodesign Institute at Arizona State University, Arizona State University, Tempe, Arizona 85287-5201, United States
| | - Rafael Saer
- Department
of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Su Lin
- The
Biodesign Institute at Arizona State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - J. Thomas Beatty
- Department
of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Neal W. Woodbury
- The
Biodesign Institute at Arizona State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
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5
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Gibasiewicz K, Białek R, Pajzderska M, Karolczak J, Burdziński G, Jones MR, Brettel K. Weak temperature dependence of P (+) H A (-) recombination in mutant Rhodobacter sphaeroides reaction centers. PHOTOSYNTHESIS RESEARCH 2016; 128:243-258. [PMID: 26942583 PMCID: PMC4877430 DOI: 10.1007/s11120-016-0239-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/24/2016] [Indexed: 06/05/2023]
Abstract
In contrast with findings on the wild-type Rhodobacter sphaeroides reaction center, biexponential P (+) H A (-) → PH A charge recombination is shown to be weakly dependent on temperature between 78 and 298 K in three variants with single amino acids exchanged in the vicinity of primary electron acceptors. These mutated reaction centers have diverse overall kinetics of charge recombination, spanning an average lifetime from ~2 to ~20 ns. Despite these differences a protein relaxation model applied previously to wild-type reaction centers was successfully used to relate the observed kinetics to the temporal evolution of the free energy level of the state P (+) H A (-) relative to P (+) B A (-) . We conclude that the observed variety in the kinetics of charge recombination, together with their weak temperature dependence, is caused by a combination of factors that are each affected to a different extent by the point mutations in a particular mutant complex. These are as follows: (1) the initial free energy gap between the states P (+) B A (-) and P (+) H A (-) , (2) the intrinsic rate of P (+) B A (-) → PB A charge recombination, and (3) the rate of protein relaxation in response to the appearance of the charge separated states. In the case of a mutant which displays rapid P (+) H A (-) recombination (ELL), most of this recombination occurs in an unrelaxed protein in which P (+) B A (-) and P (+) H A (-) are almost isoenergetic. In contrast, in a mutant in which P (+) H A (-) recombination is relatively slow (GML), most of the recombination occurs in a relaxed protein in which P (+) H A (-) is much lower in energy than P (+) H A (-) . The weak temperature dependence in the ELL reaction center and a YLH mutant was modeled in two ways: (1) by assuming that the initial P (+) B A (-) and P (+) H A (-) states in an unrelaxed protein are isoenergetic, whereas the final free energy gap between these states following the protein relaxation is large (~250 meV or more), independent of temperature and (2) by assuming that the initial and final free energy gaps between P (+) B A (-) and P (+) H A (-) are moderate and temperature dependent. In the case of the GML mutant, it was concluded that the free energy gap between P (+) B A (-) and P (+) H A (-) is large at all times.
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Affiliation(s)
- Krzysztof Gibasiewicz
- Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614, Poznań, Poland.
| | - Rafał Białek
- Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614, Poznań, Poland
| | - Maria Pajzderska
- Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614, Poznań, Poland
| | - Jerzy Karolczak
- Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614, Poznań, Poland
- Center for Ultrafast Laser Spectroscopy, A. Mickiewicz University, ul. Umultowska 85, 61-614, Poznań, Poland
| | - Gotard Burdziński
- Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614, Poznań, Poland
| | - Michael R Jones
- School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Klaus Brettel
- Laboratoire Mécanismes Fondamentaux de la Bioénergétique, UMR 8221, CEA - iBiTec-S, CNRS, Université Paris Sud, 91191, Gif-Sur-Yvette, France
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6
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Pan J, Saer RG, Lin S, Guo Z, Beatty JT, Woodbury NW. The Protein Environment of the Bacteriopheophytin Anion Modulates Charge Separation and Charge Recombination in Bacterial Reaction Centers. J Phys Chem B 2013; 117:7179-89. [DOI: 10.1021/jp400132k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jie Pan
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
| | - Rafael G. Saer
- Department of Microbiology and
Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada
V6T 1Z3
| | - Su Lin
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- Department of Chemistry and
Biochemistry, Arizona State University,
Tempe, Arizona 85287-1604, United States
| | - Zhi Guo
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
| | - J. Thomas Beatty
- Department of Microbiology and
Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada
V6T 1Z3
| | - Neal W. Woodbury
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- Department of Chemistry and
Biochemistry, Arizona State University,
Tempe, Arizona 85287-1604, United States
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Guo Z, Woodbury NW, Pan J, Lin S. Protein dielectric environment modulates the electron-transfer pathway in photosynthetic reaction centers. Biophys J 2013. [PMID: 23199926 DOI: 10.1016/j.bpj.2012.09.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The replacement of tyrosine by aspartic acid at position M210 in the photosynthetic reaction center of Rhodobacter sphaeroides results in the generation of a fast charge recombination pathway that is not observed in the wild-type. Apparently, the initially formed charge-separated state (cation of the special pair, P, and anion of the A-side bacteriopheophytin, H(A)) can decay rapidly via recombination through the neighboring bacteriochlorophyll (B(A)) soon after formation. The charge-separated state then relaxes over tens of picoseconds and recombination slows to the hundreds-of-picoseconds or nanosecond timescale. This dielectric relaxation results in a time-dependent blue shift of B(A)(-) absorption, which can be monitored using transient absorbance measurements. Protein dynamics also appear to modulate the electron transfer between H(A) and the next electron carrier, Q(A) (a ubiquinone). The kinetics of this reaction are complex in the mutant, requiring two kinetic terms, and the spectra associated with the two terms are distinct; a red shift of the H(A) ground-state bleaching is observed between the shorter and longer H(A)-to-Q(A) electron-transfer phases. The kinetics appears to be pH-independent, suggesting a negligible contribution of static heterogeneity originating from protonation/deprotonation in the ground state. A dynamic model based on the energy levels of the two early charge-separated states, P(+)B(A)(-) and P(+)H(A)(-), has been developed in which the energetics of these states is modulated by fast protein dielectric relaxations and this in turn alters both the kinetic complexity of the reaction and the reaction pathway.
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Affiliation(s)
- Zhi Guo
- The Biodesign Institute at Arizona State University, Tempe, Arizona, USA
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8
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LeBard DN, Martin DR, Lin S, Woodbury NW, Matyushov DV. Protein dynamics to optimize and control bacterial photosynthesis. Chem Sci 2013. [DOI: 10.1039/c3sc51327k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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9
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Jones MR. Structural Plasticity of Reaction Centers from Purple Bacteria. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_16] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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10
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Parson WW, Warshel A. Dependence of Photosynthetic Electron-Transfer Kinetics on Temperature and Energy in a Density-Matrix Model. J Phys Chem B 2004. [DOI: 10.1021/jp0495904] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William W. Parson
- Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195-7350
| | - Arieh Warshel
- Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195-7350
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11
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Hucke O, Schmid R, Labahn A. Exploring the primary electron acceptor (QA)-site of the bacterial reaction center from Rhodobacter sphaeroides. Binding mode of vitamin K derivatives. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1096-108. [PMID: 11856340 DOI: 10.1046/j.0014-2956.2001.02699.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The functional replacement of the primary ubiquinone (QA) in the photosynthetic reaction center (RC) from Rhodobacter sphaeroides with synthetic vitamin K derivatives has provided a powerful tool to investigate the electron transfer mechanism. To investigate the binding mode of these quinones to the QA binding site we have determined the binding free energy and charge recombination rate from QA(-) to D+ (kAD) of 29 different 1,4-naphthoquinone derivatives with systematically altered structures. The most striking result was that none of the eight tested compounds carrying methyl groups in both positions 5 and 8 of the aromatic ring exhibited functional binding. To understand the binding properties of these quinones on a molecular level, the structures of the reaction center-naphthoquinone complexes were predicted with ligand docking calculations. All protein--ligand structures show hydrogen bonds between the carbonyl oxygens of the quinone and AlaM260 and HisM219 as found for the native ubiquinone-10 in the X-ray structure. The center-to-center distance between the naphthoquinones at QA and the native ubiquinone-10 at QB (the secondary electron acceptor) is essentially the same, compared to the native structure. A detailed analysis of the docking calculations reveals that 5,8-disubstitution prohibits binding due to steric clashes of the 5-methyl group with the backbone atoms of AlaM260 and AlaM249. The experimentally determined binding free energies were reproduced with an rmsd of approximately 4 kJ x mol(-1) in most cases providing a valuable tool for the design of new artificial electron acceptors and inhibitors.
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Affiliation(s)
- Oliver Hucke
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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13
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Kirmaier C, Cua A, He C, Holten D, Bocian DF. Probing M-Branch Electron Transfer and Cofactor Environment in the Bacterial Photosynthetic Reaction Center by Addition of a Hydrogen Bond to the M-Side Bacteriopheophytin. J Phys Chem B 2001. [DOI: 10.1021/jp012768r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christine Kirmaier
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, and Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Agnes Cua
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, and Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Chunyan He
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, and Department of Chemistry, University of California, Riverside, California 92521-0403
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, and Department of Chemistry, University of California, Riverside, California 92521-0403
| | - David F. Bocian
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, and Department of Chemistry, University of California, Riverside, California 92521-0403
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Zenkevich E, Willert A, Bachilo S, Rempel U, Kilin D, Shulga A, von Borczyskowski C. Competition between electron transfer and energy migration in self-assembled porphyrin triads. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2001. [DOI: 10.1016/s0928-4931(01)00376-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Arnaut LG, Formosinho SJ. Theory of electron transfer reactions in photosynthetic bacteria reaction centers. J Photochem Photobiol A Chem 1997. [DOI: 10.1016/s1010-6030(97)00225-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Heller BA, Holten D, Kirmaier C. Control of electron transfer between the L- and M-sides of photosynthetic reaction centers. Science 1995; 269:940-5. [PMID: 7638616 DOI: 10.1126/science.7638616] [Citation(s) in RCA: 170] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
An aspartic acid residue has been introduced near ring V of the L-side accessory bacteriochlorophyll (BCHlL) or the photosynthetic reaction center in a rhodobacter capsulatus mutant in which a His also replaces Leu 212 on the M-polypeptide. The initial stage of charge separation in the G(M201)D/L(M212)H double mutant yields approximately 70 percent electron transfer to the L-side cofactors, approximately 15 percent rapid deactivation to the ground state, and approximately 15 percent electron transfer to the so-called inactive M-side bacteriopheophytin (BPhM). It is suggested here that the Asp introduced at M201 modulates the reduction potential of BCHlL, thereby changing the energetics of charge separation. The results demonstrate that an individual amino acid residue can, through its influence on the free energies of the charge-separated states, effectively dictate the balance between the forward electron transfer reactions on the L-side of the RC, the charge-recombination processes, and electron transfer to the M-side chromophores.
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Affiliation(s)
- B A Heller
- Department of Chemistry, Washington University, St Louis, MO 63130, USA
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