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Protonation–state‐Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins
Author(s) -
Bondar AnaNicoleta,
Smith Jeremy C.
Publication year - 2017
Publication title -
photochemistry and photobiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.818
H-Index - 131
eISSN - 1751-1097
pISSN - 0031-8655
DOI - 10.1111/php.12790
Subject(s) - bacteriorhodopsin , rhodopsin , chemistry , protonation , chromophore , channelrhodopsin , biophysics , structural biology , ion channel , molecular dynamics , proton transport , optogenetics , membrane , retinal , ion , computational chemistry , biochemistry , photochemistry , biology , receptor , organic chemistry , neuroscience
Channel and pump rhodopsins use energy from light absorbed by a covalently bound retinal chromophore to transport ions across membranes of microbial cells. Ion transfer steps, including proton transfer, can couple to changes in protein conformational dynamics and water positions. Although general principles of how microbial rhodopsins function are largely understood, key issues pertaining to reaction mechanisms remain unclear. In this review, we compare the protonation‐coupled dynamics of pump and channelrhodopsins, highlighting the roles that water dynamics, protein electrostatics and protein flexibility can have in ion transport mechanisms. We discuss observations supporting important functional roles of inter‐ and intra‐helical carboxylate/hydroxyl hydrogen‐bonding motifs. As specific examples, we use the proton pump bacteriorhodopsin, the sodium pump KR2, channelrhodopsins and Anabaena sensory rhodopsin. We outline the usefulness of theoretic biophysics approaches to the study of retinal proteins, challenges in studying the hydrogen‐bond dynamics of rhodopsin active sites, and implications for conformational coupling in membrane transporters.