Investigation of a Pathway for Water Delivery in Photosystem II Protein by Molecular Dynamics Simulation

To understand the
mechanism of the water-splitting reaction in photosynthesis, the dynamics
of water molecules surrounding the oxygen evolution center (OEC) involving
the Mn4O5Ca cluster in photosystem II (PSII)
is investigated using molecular dynamics (MD) simulation. During the
simulation, the surrounding interspace around the Mn4O5Ca cluster was filled with numerous water molecules. The traffic
of water molecules in the bidirectional pathway between the Mn4O5Ca cluster and outside of PSII is investigated
by analyzing MD trajectories. The result of this simulation suggests
that water delivery to the Mn4O5Ca cluster in
PSII is driven by self-diffusion of water molecules coupled with the
synchronized motion of the residues surrounding the Mn4O5Ca cluster. By tracing these water molecules, we find
that the water molecules predominantly take five water pathways to
enter into and leave from PSII. In these pathways, the water molecules
move being strongly affected by the structure and dynamics of PSII.
Nevertheless, the directions of each water molecule in these pathways
are nearly random. In contrast, the principal component analysis for
Cα atoms in the PSII complex revealed that the residues surrounding
the OEC showed the collective and continuing motion. In an attempt
to assess the validity, the MD simulation of the D1-D61A mutant is
performed, comparing the distribution of water molecules near the
Mn4O5Ca cluster. The results show that the change
in the water distribution by the D1-D61A mutant is responsible for
the experimentally observed decrease in the activLity of PSII. The
details of the pathways for water delivery provide important information
about the water-splitting reaction.