Thylakoid membrane and Photosystem II, structure and molecular dynamics simulations
Michal Kutý1,2, Žofie Sovova1,2 and Rudiger Ettrich2
1Institute of Physical Biology, University of South Bohemia CB, Nové Hrady, Czech Republic
2Institute of Systems Biology and Ecology, AS CR, Nove Hrady, Czech Republic
Photosynthetical membrane is the most abundant membrane in the nature and differs from other membranes by the foremost glycolipid composition. The mebrane lipid composition is dependent on the organism species and its living conditions. In our previous computational study of the PSII Reaction Centre pigment-protein complex, the thylakoid membrane as the protein natural environment was replaced by assembly of octane molecules due to the lack of electron density for lipid components and computationally demanding geometry optimization of lipid-protein complexes.
Using the most common force field (FF) for membrane modelling, OPLS (Optimized Potential for Liquid Simulations) and GROMOS, the monolipid mebrane model of size 8x8 glycolipids was relaxed in the presence of water and then pressed to fit „area per lipid“ and bilayer diameter to correspond with the experimental data and than again relaxed to be in equilibrium.
The complex model of PSII RC embedded into the natural environment (glycolipid membrane) will be finally involved in theoretical study of photosynthetic processes, like excitonic interaction and charge separation in PSII RC and behavior of some external parts of membrane protein subunits.
Grants Kontakt ME09062, MSM6007665808, LC06010, AV0Z60870520, INT03-09049 are acknowledged