How the pH controls photoprotection in the light-harvesting complex of mosses

12 January 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


In response to varying light conditions, light-harvesting complexes (LHCs) switch from a light-harvesting to a quenched state to protect the photosynthetic organism from excessive light irradiation, in a strategy known as nonphotochemical quenching (NPQ). NPQ is activated by an acidification of the thylakoid lumen which is sensed directly or indirectly by the LHC, resulting in a conformational change of the complex that leads to the quenched state. The conformational changes responsible for NPQ activation and their connection to specific quenching mechanisms are still unknown. Here, we investigate the pH-triggered conformational changes in the light-harvesting complex stress-related (LHCSR) of mosses. By combining constant-pH molecular dynamics and enhanced sampling techniques, we find that the pH sensitivity of the complex is driven by the coupled protonation of three residues modulating the conformation of the short amphipathic helix placed at lumen side of the embedding membrane. Combining these results with quantum mechanics/molecular mechanics calculations, we show that the quenching mechanism sensitive to the pH goes through a charge-transfer between a carotenoid and an excited chlorophyll which is controlled by the protein conformation.


Molecular Dynamics
Nonphotochemical quenching (NPQ)
light-harvesting complexes (LHCs)
light-harvesting complex stress-related (LHCSR)

Supplementary materials

Supporting Information
Details on molecular dynamics simulations; Details on the fitting of CpHMD titration curves for pKa estimation; Protonation fraction of eight target ionizable residues; Details about the protonation state transition analysis; Raw data of acceleration parameters and free-energy reweighting for each GaMD replica; Details on tICA construction and clustering; Coulomb couplings of selected Chls a with L1-Lut S1 state; L1-Lut BLA and S1 energy of each cluster; Raw data of the driving forces and reorganization energies for charge-separation; Comparison between the L1 site of LHCSR1, LHCII and CP29; Supplementary figures.


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