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Abstract
The photosystem II PsbS protein triggers the photo-protective mechanism of plants – nonphotochemical quenching (NPQ) – by sensing the acidification of the thylakoid lumen. A popular model of the NPQ activation involves the monomerization of the PsbS dimer. However, a clear connection between the PsbS pH-dependent structural changes and the dimer stability is still missing. Here, we apply a multiscale computational workflow including constant pH coarse grained (CG) and all-atom (AA) molecular dynamics simulations to investigate the structural response of the PsbS dimer to the pH variation. We find that most of the Glu residues undergo significant pKa shifts, in line with previous predictions for the monomeric state. Protonation of the key Glu173 residue induces the movement of an amphipathic helix, located at the dimeric interface, from the membrane to the aqueous environment, providing the first atomistic model of the PsbS dimer in its neutral pH conformation. Moreover, free energy profiles for the monomerization process, obtained with metadynamics simulations at the CG level, reveal that in the neutral pH conformation, where the network of H-bond interactions at the dimeric interface is destroyed, the protein-protein interaction is weaker. Taken together, our results show how the pH-dependent conformations of PsbS affect their dimerization propensity, which is at the basis of the NPQ mechanism.
Supplementary materials
Title
pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer
Description
It includes computational details for the system setup, all-atom MD, standard and constant pH CG Martini simulations and CG MTD simulations; schematic overview of the simulation workflow (Figure S1), structural analysis of the MD and CG simulation (Figure S2, S3); schematic representation of Glu titratable bead with the model system titration curve (Figure S4); titration curves for Glu residues not shown in the main text (Figure S5), secondary structure analysis of the all-atom simulations (Figure S6); analysis of tilt angle (Figure S7); pairwise RMSD and clustering of the CG simulation at pH 5 (Figure S8); convergence of the free energy profiles for MTD simulations presented in this work (Figure S9), full list of the performed simulations (Table S1) and pKa values (Table S2).
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