Atomistic Structural Insights into the M Intermediate of the Blue Proteorhodopsin Photocycle via Equilibrium Molecular Dynamics Simulation

Abstract

Increased interest in optogenetics has illuminated the necessity to understand the structure-function relationships of microbial rhodopsin proteins at the atomic level. This class of integral membrane proteins utilize a retinal chromophore that is covalently bound to the transmembrane helical bundle by a Schiff base linkage for photoactivation, leading to exquisite control of ion concentrations within the cell. Photoactivation is triggered by absorption of a photon, leading to an all-trans to 13-cis photoisomerization of retinal that propagates large-scale conformational changes in the protein. The photocycle of microbial rhodopsins has been studied spectroscopically, but the majority of rhodopsins lack X-ray crystal structures beyond the ground state of the photocycle. We present a model of the M intermediate of blue proteorhodopsin (PR) that was obtained by isomerization of retinal from a PR structure in the dark state (PDB 4JQ6) and simulated for over 20 us using equilibrium molecular dynamics (MD) simulations. Compared to the dark and K Intermediates previously simulated, the M intermediate of PR shows higher concentration of water in the internal channel of the protein, due to the rearrangement of side chains in accommodation of the all-trans retinal. Furthermore, differences in contacts between residues and hydrogen bonding networks contribute to the marked shift in the conformation of PR compared to the dark state. These results highlight our continued efforts to elucidate the photocycle of PR, which add to our fundamental understanding of how this protein plays a critical role in stability of the marine carbon cycle.