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