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Title: Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins

Abstract

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. Here, 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. Specifically, 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.

Authors:
 [1]; ORCiD logo [2]
+ Show Author Affiliations
  1. Freie Univ., Berlin (Germany). Dept. of Physics
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Molecular Biophysics; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Biochemistry, Cellular and Molecular Biology
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1394768
Grant/Contract Number:  
AC05-00OR22725; SFB 1078; bec00063
Resource Type:
Accepted Manuscript
Journal Name:
Photochemistry and Photobiology
Additional Journal Information:
Journal Volume: 93; Journal Issue: 6; Journal ID: ISSN 0031-8655
Publisher:
The American Society of Photobiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Bondar, Ana-Nicoleta, and Smith, Jeremy C. Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins. United States: N. p., 2017. Web. doi:10.1111/php.12790.
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Bondar, Ana-Nicoleta, & Smith, Jeremy C. Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins. United States. https://doi.org/10.1111/php.12790
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Bondar, Ana-Nicoleta, and Smith, Jeremy C. Tue . "Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins". United States. https://doi.org/10.1111/php.12790. https://www.osti.gov/servlets/purl/1394768.
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@article{osti_1394768,
title = {Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins},
author = {Bondar, Ana-Nicoleta and Smith, Jeremy C.},
abstractNote = {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. Here, 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. Specifically, 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.},
doi = {10.1111/php.12790},
journal = {Photochemistry and Photobiology},
number = 6,
volume = 93,
place = {United States},
year = {Tue Jul 25 00:00:00 EDT 2017},
month = {Tue Jul 25 00:00:00 EDT 2017}
}
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https://doi.org/10.1111/php.12790
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