Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics SimulationsClick to copy article linkArticle link copied!
- Divya Kaur*Divya Kaur*Email: [email protected]Department of Chemistry, Brock University, 500 Glenridge Avenue, St. Catharines L2S 3A1, Ontario, CanadaMore by Divya Kaur
- Krystle ReissKrystle ReissDepartment of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United StatesMore by Krystle Reiss
- Jimin WangJimin WangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United StatesMore by Jimin Wang
- Victor S. BatistaVictor S. BatistaDepartment of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United StatesMore by Victor S. Batista
- Gary W. BrudvigGary W. BrudvigDepartment of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United StatesMore by Gary W. Brudvig
- M. R. GunnerM. R. GunnerDepartment of Physics, City College of New York New York, New York 10031, United StatesMore by M. R. Gunner
Abstract
![Abstract Image](/cms/10.1021/acs.jpcb.3c05367/asset/images/medium/jp3c05367_0007.gif)
At room temperature and neutral pH, the oxygen-evolving center (OEC) of photosystem II (PSII) catalyzes water oxidation. During this process, oxygen is released from the OEC, while substrate waters are delivered to the OEC and protons are passed from the OEC to the lumen through water channels known as the narrow or the O4 channel, broad or the Cl1 channel, and large or the O1 channel. Protein residues lining the surfaces of these channels play a critical role in stabilizing the hydrogen-bonding networks that assist in the process. We carried out an occupancy analysis to better understand the structural and possible substrate water dynamics in full PSII monomer molecular dynamics (MD) trajectories in both the S1 and S2 states. We find that the equilibrated positions of water molecules derived from MD-derived electron density maps largely match the experimentally observed positions in crystallography. Furthermore, the occupancy reduction in MD simulations of some water molecules inside the single-filed narrow channel also correlates well with the crystallographic data during a structural transition when the S1 state of the OEC advances to the S2 state. The overall reduced occupancies of water molecules are the source of their “vacancy-hopping” dynamic nature inside these channels, unlike water molecules inside an ice lattice where all water molecules have a fixed unit occupancy. We propose on the basis of findings in our structural and molecular dynamics analysis that the water molecule occupying a pocket formed by D1-D61, D1-S169, and O4 of the OEC could be the last steppingstone to enter into the OEC and that the broad channel may be favored for proton transfer.
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This article is cited by 3 publications.
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, 1538-1549. https://doi.org/10.1021/acs.accounts.4c00148
- Richard J. Debus, Paul H. Oyala. Independent Mutation of Two Bridging Carboxylate Ligands Stabilizes Alternate Conformers of the Photosynthetic O2-Evolving Mn4CaO5 Cluster in Photosystem II. The Journal of Physical Chemistry B 2024, 128
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, 3870-3884. https://doi.org/10.1021/acs.jpcb.4c00829
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