Literature DB >> 19072155

Bicycle-pedal isomerization in a rhodopsin chromophore model.

Igor Schapiro1, Oliver Weingart, Volker Buss.   

Abstract

Probing the isomerization of a retinal chromophore model we have found the first ab initio realization of the so-called "bicycle-pedal mechanism". In an ensemble of 47 starting geometries generated by ground-state zero-point-energy sampling one single trajectory followed the aforementioned reaction mode which was proposed by Warshel in 1976. Furthermore restrained optimization of synchronous rotation mode shows that two-double-bond isomerization is barrierless for the conrotatory and disrotatory pathway.

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Year:  2009        PMID: 19072155     DOI: 10.1021/ja805586z

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  12 in total

1.  Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping.

Authors:  Piero Altoè; Alessandro Cembran; Massimo Olivucci; Marco Garavelli
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-03       Impact factor: 11.205

2.  Light activation of the isomerization and deprotonation of the protonated Schiff base retinal.

Authors:  Carlos Kubli-Garfias; Karim Salazar-Salinas; Emily C Perez-Angel; Jorge M Seminario
Journal:  J Mol Model       Date:  2011-01-05       Impact factor: 1.810

Review 3.  Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins.

Authors:  Mikhail N Ryazantsev; Dmitrii M Nikolaev; Andrey V Struts; Michael F Brown
Journal:  J Membr Biol       Date:  2019-09-30       Impact factor: 1.843

4.  QM/MM study of the structure, energy storage, and origin of the bathochromic shift in vertebrate and invertebrate bathorhodopsins.

Authors:  Sivakumar Sekharan; Keiji Morokuma
Journal:  J Am Chem Soc       Date:  2011-03-10       Impact factor: 15.419

5.  Retinal conformation governs pKa of protonated Schiff base in rhodopsin activation.

Authors:  Shengshuang Zhu; Michael F Brown; Scott E Feller
Journal:  J Am Chem Soc       Date:  2013-06-11       Impact factor: 15.419

6.  Reaction dynamics of the chimeric channelrhodopsin C1C2.

Authors:  Yusaku Hontani; Marco Marazzi; Katja Stehfest; Tilo Mathes; Ivo H M van Stokkum; Marcus Elstner; Peter Hegemann; John T M Kennis
Journal:  Sci Rep       Date:  2017-08-03       Impact factor: 4.379

7.  Direct evidence for hula twist and single-bond rotation photoproducts.

Authors:  Aaron Gerwien; Monika Schildhauer; Stefan Thumser; Peter Mayer; Henry Dube
Journal:  Nat Commun       Date:  2018-06-28       Impact factor: 14.919

8.  Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins.

Authors:  Silvia Rinaldi; Federico Melaccio; Samer Gozem; Francesca Fanelli; Massimo Olivucci
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-21       Impact factor: 11.205

9.  Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography.

Authors:  Yang Ouk Jung; Jae Hyuk Lee; Joonghan Kim; Marius Schmidt; Keith Moffat; Vukica Srajer; Hyotcherl Ihee
Journal:  Nat Chem       Date:  2013-02-03       Impact factor: 24.427

10.  Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin.

Authors:  Madushanka Manathunga; Adam J Jenkins; Yoelvis Orozco-Gonzalez; Alireza Ghanbarpour; Babak Borhan; James H Geiger; Delmar S Larsen; Massimo Olivucci
Journal:  J Phys Chem Lett       Date:  2020-05-13       Impact factor: 6.888

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