Roles of proteins in the electron transfer in the photosynthetic reaction center ofRhodopseudomonas viridis: bacteriopheophytin to ubiquinone

Ito, Hiroyuki; Nakatsuji, Hiroshi

doi:10.1002/1096-987x(200102)22:3<265::aid-jcc1000>3.0.co;2-4

Cited by 17 publications

(45 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To our knowledge, a few combined studies [54][55][56][57][58] of ab initio QM methods with MD simulations have been conducted for fluctuating protein structures, as well as studies with ab initio QM methods for fixed protein structures. [59][60][61][62][63] Under this situation, the QM methods with specific algorithms aimed at large systems [64][65][66] have potential to overcome the difficulty in application of ab initio QM methods to biological ET systems. Among them, the fragment-based QM methods that have been developed actively and applied to various large systems [67][68][69][70][71][72][73][74][75][76][77][78][79] will be advantageous.…”

Section: Introductionmentioning

confidence: 99%

Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO–LCMO approach

Nishioka

Ando

2011

The Journal of Chemical Physics

View full text Add to dashboard Cite

By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling T(DA) of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate T(DA). Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable T(DA) for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix.

show abstract

Section: Introductionmentioning

confidence: 99%

Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO–LCMO approach

Nishioka

Ando

2011

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…34 The values of V AB from these studies are: 0.8 × 10 −4 eV, 5 3 × 10 −4 eV, 34 3.5 × 10 −4 eV for superexchange ET and 4.5 × 10 −7 eV for direct tunneling. 32 In addition, V AB between menaquinone at Q A site and ubiquinone at Q B site are: 1.3 × 10 −5 eV 31 ( Rhodopseudomonas viridis ) and 1.7 × 10 −4 eV 33 ( Blastochloris viridis ). The data from most recent calculations all reasonably agree with the experimental estimate, 34 V AB = 3 × 10 −4 eV, adopted in our calculations.…”

mentioning

confidence: 99%

Photosynthetic diode: electron transport rectification by wetting the quinone cofactor

Martin

Matyushov

2015

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

We report 11 μs of molecular dynamics simulations of the electron-transfer reaction between primary and secondary quinone cofactors in the bacterial reaction center. The main question addressed here is the mechanistic reason for unidirectional electron transfer between chemically identical cofactors. We find that electron is trapped at the secondary quinone by wetting of the protein pocket following electron transfer on the time-scale shorter than the backward transition. This mechanism provides effective rectification of the electron transport, making the reaction center a molecular diode operating by cyclic charge-induced electrowetting.

show abstract

“…The iron ligands have been proposed to play critical roles in the transfer of an electron from Qs to QB in proton-electron coupled mechanisms [45][46], in superexchange processes [47], and in serving as an intermediate electron acceptor [48]. In all cases investigated in this work, the RCs were found to be capable of performing all electron transfer reactions, with the rate of electron transfer from Q2" to QB ranging from 1200 to 4700 s -1 compared to 3700 s -1 for the wild type.…”

Section: Discussionmentioning

confidence: 99%

Changes in metal specificity due to iron ligand substitutions in reaction centers fromRhodobacter sphaeroides

et al. 2007

View full text Add to dashboard Cite

Bacterial reaction centers have a single nonheme iron that is located between two bound quinones, QA and Qn, which are the primary and secondary electron acceptors during photosynthesis, respectively. In Rhodobacter sphaeroides, the iron is coordinated by four nitrogen atoms, contributed by histidines at LI90, L230, M219, and M26£ and two oxygen atoms, contributed by Glu at M234. The roles of these ligands in determining the metal-binding specificity and electron transfer properties of the quinones were investigated by mutagenesis. Each of the four His ligands was changed to Glu, Gln, and Cys, whereas Glu was changed to His, Gln, Cys, and Asp. AII mutants supported photosynthetic growth except for those with substitutions of Glu or Cys at L190 or M219. The metal specificity of isolated mutant RCs was determined by measurements using atomic absorption and 35 GHz electron paramagnetic resonance spectroscopy. The M234 mutants had a lesser iron specificity than the wild type with a mole fraction of 0.7 to 0.8 iron but retained a total metal content of 1.0. AII His mutants had an even lower iron content with mole fractions of 0.04 to 0.16. The His to Cys at M266 mutant hada significantly greater amount of bound zinc that was further enhanced when the strain was grown in zinc-supplemented media. The charge recombination rates from Qff', which ranged from 0.5 to 1 s -~ in the mutants, were comparable to the 1 s -~ value for the wild type. Charge recombination from Q;" showed complex kinetics, with rates of 15 to 30 s -~ for the LI90, L230, and M234 mutants and 200 s -t for the M266 mutants compared with 8 s -t for the wild type. The faster rates in the mutants most likely reflected a smaller free energy difference between QA" and 9 ;, a nearby bacteriopheophytin, with the smaller energy difference facilitating indirect recombination. Al1 of the mutants transferred electrons to the secondary quinone, with rates (1200 to 4700 s -~) comparable to that of the native (3700 s-~). The data demonstrate that neither the ligands nor the bound metal playa critical tole in the electron transfer processes at the acceptor side.

show abstract

Roles of proteins in the electron transfer in the photosynthetic reaction center ofRhodopseudomonas viridis: bacteriopheophytin to ubiquinone

Cited by 17 publications

References 19 publications

Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO–LCMO approach

Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO–LCMO approach

Photosynthetic diode: electron transport rectification by wetting the quinone cofactor

Changes in metal specificity due to iron ligand substitutions in reaction centers fromRhodobacter sphaeroides

Contact Info

Product

Resources

About