Crystal structure of photosystem II from Thermosynechococcus elongatus refined by computational methods

Peter Palenčár¹, František Vácha^1,2, and Michal Kutý^1,2

¹Institute of Physical Biology, University of South Bohemia, Zámek 136, 37333 Nové Hrady, Czech Republic,
²Institute of Systems Biology and Ecology, AS CR,Zámek 136, 37333 Nové Hrady, Czech Republic

³Institute of Plant Molecular Biology, AS CR, Branišovská 31, 370 05 České Budějovice, Czech Republic

Keywords: photosynthetic proteins; conformational analysis; molecular modelling; crystal structure; photosystem 2

Crystal and NMR structures are essential and fundamental in performing almost all molecular modelling techniques. Three dimensions resolution of such structures is certainly one of the most crucial criteria of quality and credibility. Researchers made great effort to prepare crystals of photosystem II (PS II) from algae and higher plants in the last decades. However, till now there are only two experimental crystal structures resolved at adequate resolution. Both are from the same common organism Thermosynechococcus elongatus. First was obtained at 3.5 Å (PDB code: 1S5L) [1] and second at 3.2 Å (PDB code: 1W5C) [2] overall resolution. By performing series of molecular dynamics (MD) simulations at appropriate time scales also coupled partially with quantum-chemical calculations, it is possible to increase the model accuracy mainly in the regions, where the probability of spatial orientation of amino acid side chain lacks appropriate electron density or other sources of experimental data. We present here more natural-like, geometrically - optimised structures of extended reaction centre (RC) of PS II.

Recently, changes in excitonic interactions of PS II RC pigments upon light-induced oxidation of primary donor (P680) or reduction of primary acceptor pheophytin a (Phe a), were analysed using absorption and circular dichroism (CD) spectra [3, 4]. In contrast to the oxidation of primary donor, the light-induced change in the CD spectrum upon primary acceptor reduction was temperature-dependent. This suggests a hypothesis that at a room temperature the reduced Phe a induces conformational changes of the RC protein environment, which affects the excitonic interaction of the RC chlorophylls. Having optimised structural models of PS II RC we were able to elucidate and describe some of the details of these processes.

This research was supported by the Ministry of Education, Youth and Sports of the Czech Republic (MSM6007665808, LC06010) and by the Academy of Sciences of the Czech Republic (Institutional research concept AVOZ60870520).

[1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. – Science 303: 1831-1838, 2004.

[2] Biesiadka, J., Loll, B., Kern, J., Irrgang, K.-D., Zouni, A. – Phys. Chem. Chem. Phys. 6: 4733-4736, 2004.

[3] Vácha, F., Durchan, M., Šiffel, P. – Biochim. biophys. Acta. 1554: 147-152, 2002.

[4] Vácha, F., Pšenčík, J., Kutý, M., Durchan, M., Šiffel, P. – Photosynth. Res. 84: 297-302, 2005.