All-Atom Molecular Dynamics Simulation of Photosystem II Embedded in Thylakoid Membrane

The molecular dynamics simulation
is reported. The latest data
on photosystem II structure, a thylakoid membrane model with the same
lipid class distribution and fatty acid composition as the native
thylakoid membrane, are used. The results indicate that the transfer
of water, oxygen and protons has different pathways. The root mean
square (rms)-fluctuation analysis of trajectory revealed that the
residues surrounding the oxygen-evolving center (OEC) show small fluctuations
and that most of the water molecules there show large fluctuation
and are on proposed pathways for water and oxygen transfer. The water
molecules near the OEC having small fluctuation could be involved
in proton transfer. We assume that each kind of pathway characterized
in this study plays a role in photosynthesis.