Excitonic interactions of Photosystem II reaction center studied by molecular modeling techniques


P. Palenčár1,2 and M. Kutý1,2


1Institute of Physical Biology, University of South Bohemia, Zámek 136, 37333 Nové Hrady, Czech Republic

2Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, Zámek 136, 37333 Nové Hrady, Czech Republic




Temperature dependent changes in excitonic interactions between pigments of photosystem II reaction center (PSII RC) from Thermosynechococcus elongatus upon reduction of primary acceptor pheophytin (D1-Pheo) have been studied by molecular modeling techniques. Six molecular dynamics (MD) simulations of so-called dark-adapted and light-adapted equilibrated PSII RC model in overall duration of ~20ns provided valuable information about structural changes in pigment and protein part of PSII RC complex at atomic level. In order to follow time and spatial distribution of structural changes in protein environment of D1-Pheo four protein layers in different distances from D1-Pheo were selected. Results from conformational analysis of all protein layers and eight core PSII RC pigments are presented and discussed. The major structural changes were detected for protein layers of D1 protein and for PSII RC pigments of active D1-branch. Absorption spectra calculated on equilibrated dynamic structures of PSII RC complex developed by performed MD simulations at 298K and 77K were in good accordance with experimental PSII RC absorption spectra [1, 2].


1.       F. Vácha, J. Pšenčík, M. Kutý, M. Durchan and P. Šiffel, Photosynthesis Research, 84, (2005), 297.

2.       F. Vácha, M. Durchan and P. Šiffel, Biochimica et Biophysica Acta, 1554, (2002), 147.




This work is supported by grants Institutional research concept MSM6007665808 of the Ministry of Education of the Czech Republic and Research Center LC06010 of Academy of Sciences of the Czech Republic.