In thylakoids of cyanobacteria and other photosynthetic organisms, the light-induced production of molecular oxygen is catalyzed by the lipid-pigment-protein complex called photosystem II (PSII). The oxygen-evolving complex (manganese cluster) is located deep in luminal site of PSII, therefore water molecules to reach the active site, and oxygen molecules to release from active site of enzyme, need to pass through the protein environment. Previous studies aimed at finding oxygen and water channels in PSII were based on analysis cavities in static structure or experiments with penetration molecules of noble gas into PSII crystals under pressure. It allowed describe some possible exiting pathways of molecules and static positions of molecular oxygen. In this work movement of water and oxygen molecules in PSII transport network is simulated by molecular dynamics method. Program for automation process of analysis molecular dynamics movement trajectory in PSII was created and criteria were offered.
photosystem II, molecular dynamics
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