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I. V. Dolgova, B. L. Grigorenko, A. V. Nemukhin, Yang Sun, Xi-Cheng Ai, Qi-Yuan Zhang

Modeling the mechanism of the proton transfer – coupled electron transfer reactions in the bacterial photosynthetic reaction centers: QM/MM simulations for the zinc-quinone complexes


The mechanism of the proton transfer – coupled electron transfer reactions in the bacterial photosynthetic reaction centers (BPRC) was studied by using the combined quantum mechanical – molecular mechanical (QM/MM) method. The molecular model was selected on the base of the experimental X-ray structure of the BPRC from Rhodobacter sphaeroides  (PDB ID: 1AIG), in which the iron ion was replaced by zinc. The quantum part consisted of ubiquinone molecules, the metal ion, side chains of five aminoacid residues (four His and GluM234) coordinated by the metal and a side chain of SerL223. The molecular mechanical part included hundreds of atoms of the nearest environment of the metal site from the protein. Optimization of geometry parameters was carried out by using the Hartree–Fock methods in the QM part and the AMBER force field parameters in the MM part. It was shown that oxidation of this zinc-quinone complex led to the stable electronic structure with an additional electron localized on the primary quinone QA. Addition of the second electron led to the electronically unstable structures in both singlet and triplet states of the complex. The reasons of such effect were attributed to the presence of unprotonated negatively charged residues GluL212 and AspL213 near the secondary quinone QB. As a consequence, the protons from SerL223 and HisL190 cannot be transferred to QB unless GluL212 and AspL213 are protonated. These data are consistent with the most recent experimental studies (Xu et al., Structure, 12, 703, 2004) revealing the key role of protonation of GluL212 and AspL213 in the course of proton transfers. After protonation of AspL213 the position of the proton from SerL223 should favor reduction of QB.
Moscow University Chemistry Bulletin.
2006, Vol. 47, No. 3, P. 159

Copyright (C) Chemistry Dept., Moscow State University, 2002
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