Molecular dynamics study of the primary charge separation reactions in Photosystem I: Effect of the replacement of the axial ligands to the electron acceptor A0 |
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| Authors: | Georgy E. Milanovsky Vasily V. Ptushenko John H. Golbeck Alexey Yu. Semenov Dmitry A. Cherepanov |
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| Affiliation: | 1. A.N. Belozersky Institute of Physical–Chemical Biology, Moscow State University, Moscow, Russia;2. Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia;3. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA;4. Department of Chemistry, The Pennsylvania State University, University Park, PA, USA;5. A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia |
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| Abstract: | Molecular dynamics (MD) calculations, a semi-continuum (SC) approach, and quantum chemistry (QC) calculations were employed together to investigate the molecular mechanics of ultrafast charge separation reactions in Photosystem I (PS I) of Thermosynechococcus elongatus. A molecular model of PS I was developed with the aim to relate the atomic structure with electron transfer events in the two branches of cofactors. A structural flexibility map of PS I was constructed based on MD simulations, which demonstrated its rigid hydrophobic core and more flexible peripheral regions. The MD model permitted the study of atomic movements (dielectric polarization) in response to primary and secondary charge separations, while QC calculations were used to estimate the direct chemical effect of the A0A/A0B ligands (Met or Asn in the 688/668 position) on the redox potential of chlorophylls A0A/A0B and phylloquinones A1A/A1B. A combination of MD and SC approaches was used to estimate reorganization energies λ of the primary (λ1) and secondary (λ2) charge separation reactions, which were found to be independent of the active branch of electron transfer; in PS I from the wild type, λ1 was estimated to be 390 ± 20 mV, while λ2 was estimated to be higher at 445 ± 15 mV. MD and QC approaches were used to describe the effect of substituting Met688PsaA/Met668PsaB by Asn688PsaA/Asn668PsaB on the energetics of electron transfer. Unlike Met, which has limited degrees of freedom in the site, Asn was found to switch between two relatively stable conformations depending on cofactor charge. The introduction of Asn and its conformation flexibility significantly affected the reorganization energy of charge separation and the redox potentials of chlorophylls A0A/A0B and phylloquinones A1A/A1B, which may explain the experimentally observed slowdown of secondary electron transfer in the M688NPsaA variant. This article is part of a Special Issue entitled: Photosynthesis research for sustainability: Keys to produce clean energy. |
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| Keywords: | PS I, Photosystem I Chl, chlorophyll RC, reaction center P700, the primary electron donor in PS I A0, the primary chlorophyll electron acceptor in PS I A1, the secondary phylloquinone electron acceptor in PS I An, light-harvesting antenna chlorophyll Chl1A, Chl2A, Chl3A, Chl1B, Chl2B, Chl3B, chlorophyll molecules in PS I RC belonging to the A or B symmetric cofactor branches A1A, A1B, phylloquinone molecules in PS I RC belonging to the A or B symmetric cofactor branches N, A0&minus , A1&minus , neutral state of cofactor charging, primary charge separation state, secondary charge separation state MD, molecular dynamics SC, semi-continuum QC, quantum chemistry DFT, density functional theory |
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