The study of conformational changes in photosystem II during a charge separation
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ORIGINAL PAPER
The study of conformational changes in photosystem II during a charge separation Natalia Kulik 1 & Michal Kutý 1,2 & David Řeha 1 Received: 2 October 2019 / Accepted: 23 February 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Photosystem II (PSII) is a multi-subunit pigment-protein complex and is one of several protein assemblies that function cooperatively in photosynthesis in plants and cyanobacteria. As more structural data on PSII become available, new questions arise concerning the nature of the charge separation in PSII reaction center (RC). The crystal structure of PSII RC from cyanobacteria Thermosynechococcus vulcanus was selected for the computational study of conformational changes in photosystem II associated to the charge separation process. The parameterization of cofactors and lipids for classical MD simulation with Amber force field was performed. The parametrized complex of PSII was embedded in the lipid membrane for MD simulation with Amber in Gromacs. The conformational behavior of protein and the cofactors directly involved in the charge separation were studied by MD simulations and QM/MM calculations. This study identified the most likely mechanism of the proton-coupled reduction of plastoquinone QB. After the charge separation and the first electron transfer to QB, the system undergoes conformational change allowing the first proton transfer to QB− mediated via Ser264. After the second electron transfer to QBH, the system again adopts conformation allowing the second proton transfer to QBH−. The reduced QBH2 would then leave the binding pocket. Keywords MD simulations . Photosystem II reaction center . Proton-coupled reduction . Plastoquinone
Abbreviations PQ Plastoquinone PSII Photosystem II Pheo Pheophytin POPC 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine Chl Chlorophyll RC Reaction center Cyt Cytochrome QA Plastoquinone A QB Plastoquionone B
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00894-020-4332-9) contains supplementary material, which is available to authorized users. * David Řeha [email protected] 1
Center for Nanobiology and Structural Biology, Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 373 33 Nove Hrady, Czech Republic
2
Institute of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 1760, CZ-370 05 Ceske Budejovice, Czech Republic
DGDG SQDG MGDG PG uQ bRC
Digalactosyl-diacylglycerol Sulfoquinovosyl-diacylglycerol Monogalactosyl-diacylglycerol 1,2-Dipalmitoyl-phosphatidyl-glycerol Ubiquinone Bacterial reaction center
Introduction Photosystem II (PSII) is one of several protein assemblies that function cooperatively in the light-dependent stage of photosynthesis in cyanobacteria, and in chloroplasts of algae and green plants [1]. Briefly, PSII which is also called waterplastoquinone oxidoreductase takes light energy and drives electron transfer reactions resulting in charge separation across the membrane and leading to water oxidat
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