Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin

View ORCID ProfileZhong Ren
doi: https://doi.org/10.1101/2021.09.16.460656
Zhong Ren
Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA Renz Research, Inc., Westmont, IL 60559, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Zhong Ren
  • For correspondence: zren@uic.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Photoisomerization of retinoids inside a confined protein pocket represents a critical chemical event in many important biological processes from animal vision, non-visual light effects, to bacterial light sensing and harvesting. Light driven proton pumping in bacteriorhodopsin entails exquisite electronic and conformational reconfigurations during its photocycle. However, it has been a major challenge to delineate transient molecular events preceding and following the photoisomerization of the retinal from noisy electron density maps when varying populations of intermediates coexist and evolve as a function of time. Here I report several distinct early photoproducts deconvoluted from the recently observed mixtures in time-resolved serial crystallography. This deconvolution substantially improves the quality of the electron density maps hence demonstrates that the all-trans retinal undergoes extensive isomerization sampling before it proceeds to the productive 13-cis configuration. Upon light absorption, the chromophore attempts to perform trans-to-cis isomerization at every double bond coupled with the stalled anti-to-syn rotations at multiple single bonds along its polyene chain. Such isomerization sampling pushes all seven transmembrane helices to bend outward, resulting in a transient expansion of the retinal binding pocket, and later, a contraction due to recoiling. These ultrafast responses observed at the atomic resolution support that the productive photoreaction in bacteriorhodopsin is initiated by light-induced charge separation in the prosthetic chromophore yet governed by stereoselectivity of its protein pocket. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

Significance Statement Photoisomerization of retinal is a critical rearrangement reaction in many important biological processes from animal vision, non-visual light effects, to bacterial light sensing and harvesting. It has been a major challenge to visualize rapid molecular events preceding and following photoisomerization so that many protein functions depending on such reaction remain vaguely understood. Here I report a direct observation of the stereoselectivity of bacteriorhodopsin hence delineate the structural mechanism of isomerization. Upon a light-induced charge separation, the retinal in a straight conformation attempts to perform double bond isomerization and single bond rotation everywhere along its polyene chain before it proceeds to the productive configuration. This observation improves our understanding on how a non-specific attraction force could drive a specific isomerization.

Competing Interest Statement

ZR is the founder of Renz Research, Inc. that currently holds the copyright of the computer software dynamiX.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted December 21, 2021.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin
Zhong Ren
bioRxiv 2021.09.16.460656; doi: https://doi.org/10.1101/2021.09.16.460656
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Photoinduced Isomerization Sampling of Retinal in Bacteriorhodopsin
Zhong Ren
bioRxiv 2021.09.16.460656; doi: https://doi.org/10.1101/2021.09.16.460656

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biochemistry
Subject Areas
All Articles
  • Animal Behavior and Cognition (4237)
  • Biochemistry (9155)
  • Bioengineering (6797)
  • Bioinformatics (24052)
  • Biophysics (12149)
  • Cancer Biology (9562)
  • Cell Biology (13814)
  • Clinical Trials (138)
  • Developmental Biology (7653)
  • Ecology (11729)
  • Epidemiology (2066)
  • Evolutionary Biology (15534)
  • Genetics (10663)
  • Genomics (14346)
  • Immunology (9502)
  • Microbiology (22876)
  • Molecular Biology (9113)
  • Neuroscience (49080)
  • Paleontology (357)
  • Pathology (1487)
  • Pharmacology and Toxicology (2576)
  • Physiology (3851)
  • Plant Biology (8347)
  • Scientific Communication and Education (1473)
  • Synthetic Biology (2299)
  • Systems Biology (6202)
  • Zoology (1302)