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

• Published in: The journal of physical chemistry. B 2019-08, Vol.123 (30), p.6444-6452
• Main Authors: Ogata, Koji, Hatakeyama, Makoto, Sakamoto, Yuki, Nakamura, Shinichiro
• Format: Article
• Language: English
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.9b04838

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.