Proteorhodopsin Activation Captured by Molecular Dynamics Simulations

Abstract

Proteorhodopsin, a light-activated proton pump, is widely distributed among marine bacteria and has promising applications in areas such as optogenetics. Proteorhodopsin activation and proton pumping is triggered by the photoisomerization of the covalently bond ligand retinal. Similar to other retinal proteins, protein structural changes along with the rearrangement of internal water molecules are expected to take place during the proton pumping photocycle. However, little experimental information regarding the structures of the photointermediates is known and the underpinning mechanism of proton pumping remains largely elusive. We have conducted molecular dynamics simulations to investigate the initial stages of proteorhodopsin activation at the atomistic level of detail. A series of µs-long simulations of the K state of proteorhodopsin were performed with in silico isomerization of all-trans to 13-cis retinal and were compared with simulations of the inactive state starting from the X-ray crystal structure of blue proteorhodopsin. Each of the amino acid residues known to be implicated in proton pumping were found to be well-hydrated. Our simulations revealed formation of a hydrogen bond between the color tuning switch Q105 and the protonated Schiff base after retinal isomerization, supporting a previous FTIR difference spectrum study of K state structural changes [1]. Another significant phenomenon in the K state was that an increase in water flux occurred connecting the proton release group, a conserved arginine residue, and the retinal binding pocket. Transient water channel formation in the interior of the protein was also discovered, potentially facilitating distal proton transfer among active sites. Altogether these results provide suggestions for the molecular mechanism of protonation switches and proton relay which are key to our understanding of proton pumping in PR and activation of retinal proteins in general. [1] Amdsden, J.J. (2008) Biochemistry 47:11490.