Simulated pH-difference infrared spectra: Application to the PsbS monomer

In strong sunlight, plants prevent photooxidation by dissipating excess energy absorbed. PsbS, a membrane protein that responds to light-induced pH changes in the thylakoid lumen, initiates this energy quenching. Recent molecular dynamics simulations predicted the structures and protonation states of the monomeric PsbS at different pH values. In this paper, we present a simulation protocol for predicting the pH-difference spectra starting from molecular dynamics simulations. We use it to simulate the infrared spectroscopy of the low-and neutral-pH structures of the PsbS monomers previously predicted and analyze the origin of the spectral changes. Comparison with the experimental spectra of PsbS suggests that dimer formation may change the structure and spectroscopy significantly. Analysis of the simulated infrared difference spectra demonstrates that the response to the pH change in the monomer is rather global and the largest change arises from the transmembrane helices.