The study of conformational changes in photosystem II during a charge separation

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 Q_B. After the charge separation and the first electron transfer to Q_B, the system undergoes conformational change allowing the first proton transfer to Q_B^- mediated via Ser264. After the second electron transfer to Q_BH, the system again adopts conformation allowing the second proton transfer to Q_BH^-. The reduced Q_BH₂ would then leave the binding pocket.