Literature DB >> 15604139

Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level.

Tadeusz Andruniów1, Nicolas Ferré, Massimo Olivucci.   

Abstract

We demonstrate that a "brute force" quantum chemical calculation based on an ab initio multiconfigurational second order perturbation theory approach implemented in a quantum mechanics/molecular mechanics strategy can be applied to the investigation of the excited state of the visual pigment rhodopsin (Rh) with a computational error <5 kcal.mol(-1). As a consequence, the simulation of the absorption and fluorescence of Rh and its retinal chromophore in solution allows for a nearly quantitative analysis of the factors determining the properties of the protein environment. More specifically, we demonstrate that the Rh environment is more similar to the "gas phase" than to the solution environment and that the so-called "opsin shift" originates from the inability of the solvent to effectively "shield" the chromophore from its counterion. The same strategy is used to investigate three transient structures involved in the photoisomerization of Rh under the assumption that the protein cavity does not change shape during the reaction. Accordingly, the analysis of the initially relaxed excited-state structure, the conical intersection driving the excited-state decay, and the primary isolable bathorhodopsin intermediate supports a mechanism where the photoisomerization coordinate involves a "motion" reminiscent of the so-called bicycle-pedal reaction coordinate. Most importantly, it is shown that the mechanism of the approximately 30 kcal.mol(-1) photon energy storage observed for Rh is not consistent with a model based exclusively on the change of the electrostatic interaction of the chromophore with the protein/counterion environment.

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Year:  2004        PMID: 15604139      PMCID: PMC539762          DOI: 10.1073/pnas.0407997101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  21 in total

Review 1.  Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs).

Authors:  D C Teller; T Okada; C A Behnke; K Palczewski; R E Stenkamp
Journal:  Biochemistry       Date:  2001-07-03       Impact factor: 3.162

2.  QM/MM study of energy storage and molecular rearrangements due to the primary event in vision.

Authors:  Jose A Gascon; Victor S Batista
Journal:  Biophys J       Date:  2004-08-31       Impact factor: 4.033

3.  Bicycle-pedal model for the first step in the vision process.

Authors:  A Warshel
Journal:  Nature       Date:  1976-04-22       Impact factor: 49.962

4.  Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore.

Authors:  Shigehiko Hayashi; Emad Tajkhorshid; Klaus Schulten
Journal:  Biophys J       Date:  2003-09       Impact factor: 4.033

5.  11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore.

Authors:  Minoru Sugihara; Volker Buss; Peter Entel; Marcus Elstner; Thomas Frauenheim
Journal:  Biochemistry       Date:  2002-12-24       Impact factor: 3.162

6.  Dependency of photon density on primary process of cattle rhodopsin.

Authors:  H Kandori; S Matuoka; Y Shichida; T Yoshizawa
Journal:  Photochem Photobiol       Date:  1989-02       Impact factor: 3.421

7.  Energy storage in the primary photochemical events of rhodopsin and isorhodopsin.

Authors:  G A Schick; T M Cooper; R A Holloway; L P Murray; R R Birge
Journal:  Biochemistry       Date:  1987-05-05       Impact factor: 3.162

8.  Computational evidence in favor of a two-state, two-mode model of the retinal chromophore photoisomerization.

Authors:  R González-Luque; M Garavelli; F Bernardi; M Merchán; M A Robb; M Olivucci
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-15       Impact factor: 11.205

9.  Time-resolved resonance Raman analysis of chromophore structural changes in the formation and decay of rhodopsin's BSI intermediate.

Authors:  Duohai Pan; Ziad Ganim; Judy E Kim; Michiel A Verhoeven; Johan Lugtenburg; Richard A Mathies
Journal:  J Am Chem Soc       Date:  2002-05-01       Impact factor: 15.419

10.  Deuterium NMR structure of retinal in the ground state of rhodopsin.

Authors:  Gilmar F J Salgado; Andrey V Struts; Katsunori Tanaka; Naoko Fujioka; Koji Nakanishi; Michael F Brown
Journal:  Biochemistry       Date:  2004-10-12       Impact factor: 3.162

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  37 in total

1.  A large geometric distortion in the first photointermediate of rhodopsin, determined by double-quantum solid-state NMR.

Authors:  Maria Concistrè; Ole G Johannessen; Neville McLean; Petra H M Bovee-Geurts; Richard C D Brown; Willem J Degrip; Malcolm H Levitt
Journal:  J Biomol NMR       Date:  2012-05-26       Impact factor: 2.835

2.  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

3.  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

4.  Molecular bases for the selection of the chromophore of animal rhodopsins.

Authors:  Hoi Ling Luk; Federico Melaccio; Silvia Rinaldi; Samer Gozem; Massimo Olivucci
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-25       Impact factor: 11.205

5.  Bond torsion affects the product distribution in the photoreaction of retinal model chromophores.

Authors:  Oliver Weingart; Igor Schapiro; Volker Buss
Journal:  J Mol Model       Date:  2005-11-10       Impact factor: 1.810

6.  The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution.

Authors:  Pedro B Coto; Angela Strambi; Nicolas Ferré; Massimo Olivucci
Journal:  Proc Natl Acad Sci U S A       Date:  2006-11-07       Impact factor: 11.205

7.  Vibrational analysis of a solvated green fluorescent protein chromophore.

Authors:  Tadeusz Andruniów
Journal:  J Mol Model       Date:  2007-03-23       Impact factor: 1.810

8.  Anabaena sensory rhodopsin is a light-driven unidirectional rotor.

Authors:  Angela Strambi; Bo Durbeej; Nicolas Ferré; Massimo Olivucci
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-22       Impact factor: 11.205

Review 9.  Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins.

Authors:  Ahmet Altun; Shozo Yokoyama; Keiji Morokuma
Journal:  Photochem Photobiol       Date:  2008-03-07       Impact factor: 3.421

10.  Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry.

Authors:  Luis Manuel Frutos; Tadeusz Andruniów; Fabrizio Santoro; Nicolas Ferré; Massimo Olivucci
Journal:  Proc Natl Acad Sci U S A       Date:  2007-04-30       Impact factor: 11.205

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