Crystal structure of photosystem II from Thermosynechococcus elongatus refined and studied by molecular dynamics


P. Palenčár1, F. Vácha1,3, 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

3Institute of Plant Molecular Biology, Academy of Sciences of the Czech Republic,

Branišovská 31, 370 05 České Budějovice, Czech Republic



Crystal or 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 elongates. 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.

First, we constructed truncated models of PS II considering protein subunits and pigment molecules from and around the RC, keeping also functionally and structurally important spatial subunits. These structures were then used as starting structural models for MD simulation runs. Force field (FF) [3] parameters (charge distribution and force constants) and topology for PS II RC pigment molecules [4] were developed for the Yamber2 FF [5, 6] by performing quantum chemical calculations and by modifying and extending Ceccarelli [7] studies concerning bacterial type a pigments. Geometry optimisation of PS II RC pigment molecules and development of new FF parameters was performed at RHF/6-31G* level of quantum chemical theory using Gaussian 98 [8]. Calculation of RESP atomic charges following AMBER FF developing scheme [9] was done using Gaussian 98, R.E.D, antechamber, and resp subroutines. Complete FF parameters and topology for the PS II RC pigment molecules were developed and introduced to YASARA [5]. Several MD simulation runs, taking into account different pigment oxidation states and various solvent properties, were performed in order to check the quality of new FF parameters for the PS II RC pigments. Subsequently, by further optimising overall geometry of new structural models using MD simulation runs with small time step of 1.0 fs, we obtained final models of PS II RC complex. Detailed analysis of new FF parameters showed realistic dynamic behaviour of pigment molecules and typical electrostatic interactions with the surrounding protein environment.

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 [10, 11]. 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 (Chls). Having optimised structural models of PS II RC we were able to elucidate and describe some of the details of these processes.


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This research was supported by the Ministry of Education, Youth and Sports of the Czech Republic (MSM6007665808, GACR206/02/D177) and by the Academy of Sciences of the Czech Republic (Institutional research concept AVOZ60870520 and AV0Z50510513).