Protein–protein interactions within photosystem II under photoprotection: the synergy between CP29 minor antenna, subunit S (PsbS) and zeaxanthin at all-atom resolution

The assembly and disassembly of protein complexes within cells are crucial life-sustaining processes. In photosystem II (PSII) of higher plants, there is a delicate yet obscure balance between light harvesting and photo-protection under fluctuating light conditions, that involves protein–protein complexes. Recent breakthroughs in molecular dynamics (MD) simulations are combined with new approaches herein to provide structural and energetic insight into such a complex between the CP29 minor antenna and the PSII subunit S (PsbS). The microscopic model involves extensive sampling of bound and dissociated states at atomic resolution in the presence of photo-protective zeaxanthin (Zea), and reveals well defined protein–protein cross-sections. The complex is placed within PSII, and macroscopic connections are emerging (PsbS–CP29–CP24–CP47) along the energy transfer pathways from the antenna to the PSII core. These connections explain macroscopic observations in the literature, while the previously obscured atomic scale details are now revealed. The implications of these findings are discussed in the context of the Non-Photochemical Quenching (NPQ) of chlorophyll fluorescence, the down-regulatory mechanism of photosynthesis, that enables the protection of PSII against excess excitation load. Zea is found at the PsbS–CP29 cross-section and a pH-dependent equilibrium between PsbS dimer/monomers and the PsbS–CP29 dissociation/association is identified as the target for engineering tolerant plants with increased crop and biomass yields. Finally, the new MD based approaches can be used to probe protein–protein interactions in general, and the PSII structure provided can initiate large scale molecular simulations of the photosynthetic apparatus, under NPQ conditions.