1Institute of Physical Biology, University of south Bohemia, Zámek 136, 373 33 Nové Hrady, Czech Republic
2Institute of Plant Molecular Biology, AS CR, Branišovská 31, 370 05 České Budějovice, Czech Republic
3Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 120 00 Prague, Czech Republic
4Institute of Landscape Ecology, AS CR, Zámek 136, 373 33 Nové Hrady, Czech Republic
Photosystem II (PSII) is a pigment-protein complex located in thylakoid membrane of cyanobacteria, algae and higher plants. It performs series of light driven reactions, which result in a separation of charge and subsequently in a reduction of an electron-transport chain and water oxidation. Primary site of the energy conversion is located in so-called reaction centre (RC).
Recently, structure of the PSII complex isolated from cyanobacteria Synechococcus elongatus has been presented at the resolution of 3.8A  and from Synechococcus vulkanus at 3.7 A . Also time constants of charge distribution and molecules involved in this process are already known, although X-ray and also spectroscopy methods are unfortunatelly not able to give us sufficient explanation of the charge-separation processes. Theoretical molecular modelling study could be such complementary method for a complex understanding of properties and function of the PSII RC pigments during a charge-separation process.
In our last study [3,4] we have combined the structural homology modelling based model proposed by Svensson et al.  (1DOP model), and the experimental structure presented by Zouni et al.  and succesfully calculated absorption and circular dichroism spectra using point-dipole approximations  and compared them with the experimental results in order to locate accumulated chlorophyll cation during a light treatment of Photosystem II reaction centre in presence of artificial electron acceptor silicomolybdate. Along with the spectra calculations the charge distribution on the primary electron acceptor pheophytine of the combined model in a ground and reduced state and its influence on the surrounding protein environment is studied by using quantum chemistry methods on a semiempirical (ZINDO-1), density functional (B3LYP) and ab initio (HF) levels.
Acknowledgments: This work is supported by grants MSMT LN00A141, MSM12310001, GACR 206/02/0942 and GACR 206/02/D177.
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