101
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Kubli-Garfias C, Salazar-Salinas K, Perez-Angel EC, Seminario JM. Light activation of the isomerization and deprotonation of the protonated Schiff base retinal. J Mol Model 2011; 17:2539-47. [PMID: 21207087 DOI: 10.1007/s00894-010-0927-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 11/29/2010] [Indexed: 11/29/2022]
Abstract
We perform an ab initio analysis of the photoisomerization of the protonated Schiff base of retinal (PSB-retinal) from 11-cis to 11-trans rotating the C10-C11=C12-C13 dihedral angle from 0° (cis) to -180° (trans). We find that the retinal molecule shows the lowest rotational barrier (0.22 eV) when its charge state is zero as compared to the barrier for the protonated molecule which is ∼0.89 eV. We conclude that rotation most likely takes place in the excited state of the deprotonated retinal. The addition of a proton creates a much larger barrier implying a switching behavior of retinal that might be useful for several applications in molecular electronics. All conformations of the retinal compound absorb in the green region with small shifts following the dihedral angle rotation; however, the Schiff base of retinal (SB-retinal) at trans-conformation absorbs in the violet region. The rotation of the dihedral angle around the C11=C12 π-bond affects the absorption energy of the retinal and the binding energy of the SB-retinal with the proton at the N-Schiff; the binding energy is slightly lower at the trans-SB-retinal than at other conformations of the retinal.
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Affiliation(s)
- Carlos Kubli-Garfias
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
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102
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Bernini C, Pogni R, Ruiz-Dueñas FJ, Martínez AT, Basosi R, Sinicropi A. EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level. Phys Chem Chem Phys 2011; 13:5078-98. [DOI: 10.1039/c0cp02151b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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103
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Frähmcke JS, Wanko M, Phatak P, Mroginski MA, Elstner M. The protonation state of Glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations. J Phys Chem B 2010; 114:11338-52. [PMID: 20698519 DOI: 10.1021/jp104537w] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structure and spectroscopy of rhodopsin have been intensely studied in the past decade both experimentally and theoretically; however, important issues still remain unresolved. Of central interest is the protonation state of Glu181, where controversial and contradictory experimental evidence has appeared. While FTIR measurements indicate this residue to be unprotonated, preresonance Raman and UV-vis spectra have been interpreted in favor of a protonated Glu181. Previous computational approaches were not able to resolve this issue, providing contradicting data as well. Here, we perform hybrid QM/MM calculations using DFT methods for the electronic ground state, MRCI methods for the electronically excited states, and a polarization model for the MM part in order to investigate this issue systematically. We constructed various active-site models for protonated as well as unprotonated Glu181, which were evaluated by computing NMR, IR, Raman, and UV-vis spectroscopic data. The resulting differences in the UV-vis and Raman spectra between protonated and unprotonated models are very subtle, which has two major consequences. First, the common interpretation of prior Raman and UV-vis experiments in favor of a neutral Glu181 appears questionable, as it is based on the assumption that a charge at the Glu181 location would have a sizable impact. Second, also theoretical results should be interpreted with care. Spectroscopic differences between the structural models must be related to modeling uncertainties and intrinsic methodological errors. Despite a detailed comparison of various rhodopsins and mutants and consistently favorite results with charged Glu181 models, we find merely weak evidence from UV-vis and Raman calculations. On the contrary, difference FTIR and NMR chemical shift measurements on Rh mutants are indicative of the protonation state of Glu181. Supported by our results, they provide strong and independent evidence for a charged Glu181.
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Affiliation(s)
- Jan S Frähmcke
- Institute for Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Str. 10, D-38106 Braunschweig, Germany
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104
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Abstract
The implementation of multiconfigurational quantum chemistry methods into a quantum-mechanics/molecular-mechanics protocol has allowed the construction of a realistic computer model for the sensory rhodopsin of the cyanobacterium Anabaena PCC 7120. The model, which reproduces the absorption spectra of both the all-trans and 13-cis forms of the protein and their associated K and L intermediates, is employed to investigate the light-driven steps of the photochromic cycle exhibited by the protein. It is found that the photoisomerizations of the all-trans and 13-cis retinal chromophores occur through unidirectional, counterclockwise 180° rotations of the =C14-C15= moiety with respect to the Lys210-linked end of the chromophore axis. Thus, the sequential interconversions of the all-trans and 13-cis forms during a single photochromic cycle yield a complete (360°) unidirectional rotation of the =C14-C15= moiety. This finding implies that Anabaena sensory rhodopsin is a biological realization of a light-driven molecular rotor.
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105
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Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping. Proc Natl Acad Sci U S A 2010; 107:20172-7. [PMID: 21048087 DOI: 10.1073/pnas.1007000107] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantum mechanics/molecular mechanics calculations based on ab initio multiconfigurational second order perturbation theory are employed to construct a computer model of Bacteriorhodopsin that reproduces the observed static and transient electronic spectra, the dipole moment changes, and the energy stored in the photocycle intermediate K. The computed reaction coordinate indicates that the isomerization of the retinal chromophore occurs via a complex motion accounting for three distinct regimes: (i) production of the excited state intermediate I, (ii) evolution of I toward a conical intersection between the excited state and the ground state, and (iii) formation of K. We show that, during stage ii, a space-saving mechanism dominated by an asynchronous double bicycle-pedal deformation of the C10═C11─C12═C13─C14═N moiety of the chromophore dominates the isomerization. On this same stage a N─H/water hydrogen bond is weakened and initiates a breaking process that is completed during stage iii.
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106
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Melloni A, Rossi Paccani R, Donati D, Zanirato V, Sinicropi A, Parisi ML, Martin E, Ryazantsev M, Ding WJ, Frutos LM, Basosi R, Fusi S, Latterini L, Ferré N, Olivucci M. Modeling, preparation, and characterization of a dipole moment switch driven by Z/E photoisomerization. J Am Chem Soc 2010; 132:9310-9. [PMID: 20568762 DOI: 10.1021/ja906733q] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the results of a multidisciplinary research effort where the methods of computational photochemistry and retrosynthetic analysis/synthesis have contributed to the preparation of a novel N-alkylated indanylidene-pyrroline Schiff base featuring an exocyclic double bond and a permanent zwitterionic head. We show that, due to its large dipole moment and efficient photoisomerization, such a system may constitute the prototype of a novel generation of electrostatic switches achieving a reversible light-induced dipole moment change on the order of 30 D. The modeling of a peptide fragment incorporating the zwitterionic head into a conformationally rigid side chain shows that the switch can effectively modulate the fluorescence of a tryptophan probe.
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Affiliation(s)
- Alfonso Melloni
- Dipartimento di Chimica, Università degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy
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107
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Tsutsui K, Shichida Y. Multiple functions of Schiff base counterion in rhodopsins. Photochem Photobiol Sci 2010; 9:1426-34. [PMID: 20842311 DOI: 10.1039/c0pp00134a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In rhodopsins, visible-light absorption is achieved by the protonation of the chromophore Schiff base. The Schiff base proton is stabilized by the negative charge of an amino acid residue called the Schiff base counterion. Since E113 was identified as the counterion in bovine rhodopsin, there has been growing evidence that the counterion has multiple functions besides proton stabilization. Here, we first introduce generally accepted findings as well as some controversial theories about the identity of the Schiff base counterion in the dark and in intermediate states and then review multiple functions of the counterion in vertebrate visual pigments. Special focus is placed on the recently demonstrated role in photoisomerization efficiency. Finally, differences in the position of the counterion between vertebrate visual pigments and other opsins and its relevance to the molecular evolution of opsins are discussed.
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Affiliation(s)
- Kei Tsutsui
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
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108
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Rostov IV, Amos RD, Kobayashi R, Scalmani G, Frisch MJ. Studies of the ground and excited-state surfaces of the retinal chromophore using CAM-B3LYP. J Phys Chem B 2010; 114:5547-55. [PMID: 20369810 DOI: 10.1021/jp911329g] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.
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Affiliation(s)
- Ivan V Rostov
- Australian National University Supercomputer Facility, Mills Road, Canberra, ACT 0200, Australia
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109
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110
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Khrenova MG, Bochenkova AV, Nemukhin AV. Modeling reaction routes from rhodopsin to bathorhodopsin. Proteins 2010; 78:614-22. [PMID: 19787771 DOI: 10.1002/prot.22590] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The quantum mechanical-molecular mechanical (QM/MM) theory was applied to calculate accurate structural parameters, vibrational and optical spectra of bathorhodopsin (BATHO), one of the primary photoproducts of the functional cycle of the visual pigment rhodopsin (RHO), and to characterize reaction routes from RHO to BATHO. The recently resolved crystal structure of BATHO (PDBID: 2G87) served as an initial source of coordinates of heavy atoms. Protein structures in the ground electronic state and vibrational frequencies were determined by using the density functional theory in the PBE0/cc-pVDZ approximation for the QM part and the AMBER force field parameters in the MM part. Calculated and assigned vibrational spectra of both model protein systems, BATHO and RHO, cover three main regions referring to the hydrogen-out-of-plan (HOOP) motion, the C==C ethylenic stretches, and the C--C single-bond stretches. The S(0)-S(1) electronic excitation energies of the QM part, including the chromophore group in the field of the protein matrix, were estimated by using the advanced quantum chemistry methods. The computed structural parameters as well as the spectral bands match perfectly the experimental findings. A structure of the transition state on the S(0) potential energy surface for the ground electronic state rearrangement from RHO to BATHO was located proving a possible route of the thermal protein activation to the primary photoproduct.
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Affiliation(s)
- M G Khrenova
- Department of Chemistry, MV Lomonosov Moscow State University, Moscow 119991, Russian Federation
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111
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Valsson O, Filippi C. Photoisomerization of Model Retinal Chromophores: Insight from Quantum Monte Carlo and Multiconfigurational Perturbation Theory. J Chem Theory Comput 2010. [DOI: 10.1021/ct900692y] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Omar Valsson
- Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Claudia Filippi
- Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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112
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Altun A, Yokoyama S, Morokuma K. Color tuning in short wavelength-sensitive human and mouse visual pigments: ab initio quantum mechanics/molecular mechanics studies. J Phys Chem A 2010; 113:11685-92. [PMID: 19630373 DOI: 10.1021/jp902754p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated the protonation state and photoabsorption spectrum of Schiff-base (SB) nitrogen bound 11-cis-retinal in human blue and mouse UV cone visual pigments as well as in bovine rhodopsin by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. We have employed both multireference (MRCISD+Q, MR-SORCI+Q, and MR-DDCI2+Q) and single reference (TD-B3LYP and RI-CC2) QM methods. The calculated ground-state and vertical excitation energies show that UV-sensitive pigments have deprotonated SB nitrogen, while violet-sensitive pigments have protonated SB nitrogen, in agreement with some indirect experimental evidence. A significant blue shift of the absorption maxima of violet-sensitive pigments relative to rhodopsins arises from the increase in bond length alternation of the polyene chain of 11-cis-retinal induced by polarizing fields of these pigments. The main counterion is Glu113 in both violet-sensitive vertebrate pigments and bovine rhodopsin. Neither Glu113 nor the remaining pigment has a significant influence on the first excitation energy of 11-cis-retinal in the UV-sensitive pigments that have deprotonated SB nitrogen. There is no charge transfer between the SB and beta-ionone terminals of 11-cis-retinal in the ground and first excited states.
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Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
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113
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Watanabe HC, Mori Y, Tada T, Yokoyama S, Yamato T. Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin. Biophysics (Nagoya-shi) 2010; 6:67-68. [PMID: 21297892 PMCID: PMC3032607 DOI: 10.2142/biophysics.6.67] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The synergetic effects of multiple rhodopsin mutations on color tuning need to be completely elucidated. Systematic genetic studies and spectroscopy have demonstrated an interesting example of synergetic color tuning between two amino acid residues in conger rhodopsin's ancestral pigment (p501): -a double mutation at one nearby and one distant residue led to a significant λ(max) blue shift of 13 nm, whereas neither of the single mutations at these two sites led to meaningful shifts.To analyze the molecular mechanisms of this synergetic color tuning, we performed homology modeling, molecular simulations, and electronic state calculations. For the double mutant, N195A/A292S, in silico mutation analysis demonstrated conspicuous structural changes in the retinal chromophore, whereas that of the single mutant, A292S, was almost unchanged. Using statistical ensembles of QM/MM optimized structures, the excitation energy of retinal chromophore was evaluated for the three visual pigments. As a result, the λ(max) shift of double mutant (DM) from p501 was -8 nm, while that of single mutant (SM) from p501 was +1 nm. Molecular dynamics simulation for DM demonstrated frequent isomerization between 6-s-cis and 6-s-trans conformers. Unexpectedly, however, the two conformers exhibited almost identical excitation energy, whereas principal component analysis (PCA) identified the retinal-counterion cooperative change of BLA (bond length alternation) and retinal-counterion interaction lead to the shift.
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Affiliation(s)
- Hiroshi C Watanabe
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
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114
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Neugebauer J. Subsystem-Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies. Chemphyschem 2009; 10:3148-73. [DOI: 10.1002/cphc.200900538] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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115
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Andruniów T, Olivucci M. How Does the Relocation of Internal Water Affect Resonance Raman Spectra of Rhodopsin? An Insight from CASSCF/Amber Calculations. J Chem Theory Comput 2009; 5:3096-104. [DOI: 10.1021/ct900071c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tadeusz Andruniów
- Quantum Chemistry and Molecular Modelling Lab, Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, 53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403
| | - Massimo Olivucci
- Quantum Chemistry and Molecular Modelling Lab, Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, 53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403
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116
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Brown MF, Salgado GFJ, Struts AV. Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:177-93. [PMID: 19716801 DOI: 10.1016/j.bbamem.2009.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/25/2009] [Accepted: 08/12/2009] [Indexed: 11/28/2022]
Abstract
Rhodopsin is a canonical member of class A of the G protein-coupled receptors (GPCRs) that are implicated in many of the drug interventions in humans and are of great pharmaceutical interest. The molecular mechanism of rhodopsin activation remains unknown as atomistic structural information for the active metarhodopsin II state is currently lacking. Solid-state (2)H NMR constitutes a powerful approach to study atomic-level dynamics of membrane proteins. In the present application, we describe how information is obtained about interactions of the retinal cofactor with rhodopsin that change with light activation of the photoreceptor. The retinal methyl groups play an important role in rhodopsin function by directing conformational changes upon transition into the active state. Site-specific (2)H labels have been introduced into the methyl groups of retinal and solid-state (2)H NMR methods applied to obtain order parameters and correlation times that quantify the mobility of the cofactor in the inactive dark state, as well as the cryotrapped metarhodopsin I and metarhodopsin II states. Analysis of the angular-dependent (2)H NMR line shapes for selectively deuterated methyl groups of rhodopsin in aligned membranes enables determination of the average ligand conformation within the binding pocket. The relaxation data suggest that the beta-ionone ring is not expelled from its hydrophobic pocket in the transition from the pre-activated metarhodopsin I to the active metarhodopsin II state. Rather, the major structural changes of the retinal cofactor occur already at the metarhodopsin I state in the activation process. The metarhodopsin I to metarhodopsin II transition involves mainly conformational changes of the protein within the membrane lipid bilayer rather than the ligand. The dynamics of the retinylidene methyl groups upon isomerization are explained by an activation mechanism involving cooperative rearrangements of extracellular loop E2 together with transmembrane helices H5 and H6. These activating movements are triggered by steric clashes of the isomerized all-trans retinal with the beta4 strand of the E2 loop and the side chains of Glu(122) and Trp(265) within the binding pocket. The solid-state (2)H NMR data are discussed with regard to the pathway of the energy flow in the receptor activation mechanism.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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117
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Szymczak JJ, Barbatti M, Lischka H. Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process? J Phys Chem A 2009; 113:11907-18. [DOI: 10.1021/jp903329j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jaroslaw J. Szymczak
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090, Vienna, Austria, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090, Vienna, Austria, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090, Vienna, Austria, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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118
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Epifanovsky E, Polyakov I, Grigorenko B, Nemukhin A, Krylov AI. Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore. 1. Electronically Excited and Ionized States of the Anionic Chromophore in the Gas Phase. J Chem Theory Comput 2009; 5:1895-906. [DOI: 10.1021/ct900143j] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Evgeny Epifanovsky
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Igor Polyakov
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Bella Grigorenko
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alexander Nemukhin
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
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119
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Tomasello G, Olaso-González G, Altoè P, Stenta M, Serrano-Andrés L, Merchán M, Orlandi G, Bottoni A, Garavelli M. Electrostatic control of the photoisomerization efficiency and optical properties in visual pigments: on the role of counterion quenching. J Am Chem Soc 2009; 131:5172-86. [PMID: 19309158 DOI: 10.1021/ja808424b] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hybrid QM(CASPT2//CASSCF/6-31G*)/MM(Amber) computations have been used to map the photoisomerization path of the retinal chromophore in Rhodopsin and explore the reasons behind the photoactivity efficiency and spectral control in the visual pigments. It is shown that while the electrostatic environment plays a central role in properly tuning the optical properties of the chromophore, it is also critical in biasing the ultrafast photochemical event: it controls the slope of the photoisomerization channel as well as the accessibility of the S(1)/S(0) crossing space triggering the ultrafast decay. The roles of the E113 counterion, the E181 residue, and the other amino acids of the protein pocket are explicitly analyzed: it appears that counterion quenching by the protein environment plays a key role in setting up the chromophore's optical properties and its photochemical efficiency. A unified scenario is presented that discloses the relationship between spectroscopic and mechanistic properties in rhodopsins and allows us to draw a solid mechanism for spectral tuning in color vision pigments: a tunable counterion shielding appears as the elective mechanism for L<-->M spectral modulation, while a retinal conformational control must dictate S absorption. Finally, it is suggested that this model may contribute to shed new light into mutations-related vision deficiencies that opens innovative perspectives for experimental biomolecular investigations in this field.
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Affiliation(s)
- Gaia Tomasello
- Dipartimento di Chimica G. Ciamician, Università di Bologna, via Selmi 2, Bologna I-40126, Italy
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120
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Sumita M, Ryazantsev MN, Saito K. Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane motion: theoretical study on a model system of retinal protonated Schiff base. Phys Chem Chem Phys 2009; 11:6406-14. [PMID: 19809672 DOI: 10.1039/b900882a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the result of comparison between two reaction coordinates [on the potential energy surface of the first excited state (S(1))] produced by CASSCF and these energies recalculated by MRMP2 in the Z to E photoisomerization of penta-2,4-dieniminium (PDI) as the minimal model of the retinal protonated Schiff base (RPSB). One coordinate is the S(1) state minimum-energy-path (MEP) in mass-weighted coordinates from the S(1) vertically excited point, where a strong hydrogen-out-of plane (HOOP) motion is not exhibited. The energy profile of the S(1) MEP at the MRMP2//CASSCF level shows a barrier for the rotation around the reactive C-C and hits the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by 65 degrees . The other coordinate is an S(1) coordinate obtained by the relaxed scan strategy. The relaxed coordinate along the central C-C-C-C dihedral angle, which we call the HOOP coordinate, shows strong HOOP motion. According to the MRMP2//CASSCF calculation, there is no barrier on the HOOP coordinate. Furthermore, the S(1) to S(0) transition may be possible without the large skeletal deformation by HOOP motion because the HOOP coordinate encounters the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by only 40 degrees . Consequently, if PDI is a suitable model molecule for the RPSB as often assumed, the 11-cis to all-trans photoisomerization is predicted to be accelerated by the HOOP motion.
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Affiliation(s)
- Masato Sumita
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, 305-8571, Japan
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121
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Rivado-Casas L, Sampedro D, Campos PJ, Fusi S, Zanirato V, Olivucci M. Fluorenylidene−Pyrroline Biomimetic Light-Driven Molecular Switches. J Org Chem 2009; 74:4666-74. [DOI: 10.1021/jo802792j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laura Rivado-Casas
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Diego Sampedro
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Pedro J. Campos
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Stefania Fusi
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Vinicio Zanirato
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Massimo Olivucci
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
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122
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Keal TW, Wanko M, Thiel W. Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0546-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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123
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Hayashi S, Tajkhorshid E, Schulten K. Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. Biophys J 2009; 96:403-16. [PMID: 19167292 DOI: 10.1016/j.bpj.2008.09.049] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 09/26/2008] [Indexed: 11/19/2022] Open
Abstract
The photoisomerization reaction dynamics of a retinal chromophore in the visual receptor rhodopsin was investigated by means of hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. The photoisomerization reaction of retinal constitutes the primary step of vision and is known as one of the fastest reactions in nature. To elucidate the molecular mechanism of the high efficiency of the reaction, we carried out hybrid ab initio QM/MM MD simulations of the complete reaction process from the vertically excited state to the photoproduct via electronic transition in the entire chromophore-protein complex. An ensemble of reaction trajectories reveal that the excited-state dynamics is dynamically homogeneous and synchronous even in the presence of thermal fluctuation of the protein, giving rise to the very fast formation of the photoproduct. The synchronous nature of the reaction dynamics in rhodopsin is found to originate from weak perturbation of the protein surroundings and from dynamic regulation of volume-conserving motions of the chromophore. The simulations also provide a detailed view of time-dependent modulations of hydrogen-out-of-plane vibrations during the reaction process, and identify molecular motions underlying the experimentally observed dynamic spectral modulations.
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Affiliation(s)
- Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
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124
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Sinicropi A, Bernini C, Basosi R, Olivucci M. A novel biomimetic photochemical switch at work: design of a photomodulable peptide. Photochem Photobiol Sci 2009; 8:1639-49. [DOI: 10.1039/b906271h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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125
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Schapiro I, Weingart O, Buss V. Bicycle-Pedal Isomerization in a Rhodopsin Chromophore Model. J Am Chem Soc 2008; 131:16-7. [DOI: 10.1021/ja805586z] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Igor Schapiro
- Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Oliver Weingart
- Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Volker Buss
- Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
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126
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Altun A, Yokoyama S, Morokuma K. Mechanism of Spectral Tuning Going from Retinal in Vacuo to Bovine Rhodopsin and its Mutants: Multireference ab Initio Quantum Mechanics/Molecular Mechanics Studies. J Phys Chem B 2008; 112:16883-90. [DOI: 10.1021/jp807172h] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, and Department of Biology, Rollins Research Center, Emory University, Atlanta, Georgia 30322, USA and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Shozo Yokoyama
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, and Department of Biology, Rollins Research Center, Emory University, Atlanta, Georgia 30322, USA and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Keiji Morokuma
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, and Department of Biology, Rollins Research Center, Emory University, Atlanta, Georgia 30322, USA and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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127
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Sinicropi A, Martin E, Ryazantsev M, Helbing J, Briand J, Sharma D, Léonard J, Haacke S, Cannizzo A, Chergui M, Zanirato V, Fusi S, Santoro F, Basosi R, Ferré N, Olivucci M. An artificial molecular switch that mimics the visual pigment and completes its photocycle in picoseconds. Proc Natl Acad Sci U S A 2008; 105:17642-7. [PMID: 19004797 PMCID: PMC2584735 DOI: 10.1073/pnas.0802376105] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Indexed: 11/18/2022] Open
Abstract
Single molecules that act as light-energy transducers (e.g., converting the energy of a photon into atomic-level mechanical motion) are examples of minimal molecular devices. Here, we focus on a molecular switch designed by merging a conformationally locked diarylidene skeleton with a retinal-like Schiff base and capable of mimicking, in solution, different aspects of the transduction of the visual pigment Rhodopsin. Complementary ab initio multiconfigurational quantum chemistry-based computations and time-resolved spectroscopy are used to follow the light-induced isomerization of the switch in methanol. The results show that, similar to rhodopsin, the isomerization occurs on a 0.3-ps time scale and is followed by <10-ps cooling and solvation. The entire (2-photon-powered) switch cycle was traced by following the evolution of its infrared spectrum. These measurements indicate that a full cycle can be completed within 20 ps.
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Affiliation(s)
- Adalgisa Sinicropi
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Elena Martin
- Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avenida de Elvas s/n 06071 Badajoz, Spain
| | - Mikhail Ryazantsev
- Chemistry Department, Bowling Green State University, Bowling Green, OH 43403
| | - Jan Helbing
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Julien Briand
- Institut de Physique et Chimie des Matériaux de Strasbourg–Group of Nonlinear Optics, Unité Mixte de la Recherche 7504, Centre National de la Recherche Scientifique, Université Louis Pasteur, 23 Rue du Loess, 67034 Strasbourg Cédex, France
| | - Divya Sharma
- Institut de Physique et Chimie des Matériaux de Strasbourg–Group of Nonlinear Optics, Unité Mixte de la Recherche 7504, Centre National de la Recherche Scientifique, Université Louis Pasteur, 23 Rue du Loess, 67034 Strasbourg Cédex, France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg–Group of Nonlinear Optics, Unité Mixte de la Recherche 7504, Centre National de la Recherche Scientifique, Université Louis Pasteur, 23 Rue du Loess, 67034 Strasbourg Cédex, France
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg–Group of Nonlinear Optics, Unité Mixte de la Recherche 7504, Centre National de la Recherche Scientifique, Université Louis Pasteur, 23 Rue du Loess, 67034 Strasbourg Cédex, France
| | - Andrea Cannizzo
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne-Dorigny, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne-Dorigny, Switzerland
| | - Vinicio Zanirato
- Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy
| | - Stefania Fusi
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Fabrizio Santoro
- Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche, Via Moruzzi 1, I-56124 Pisa, Italy; and
| | - Riccardo Basosi
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Nicolas Ferré
- Laboratoire de Chimie Théorique et de Modélisation Moléculaire, Unité Mixte de la Recherche 6517, Centre National de la Recherche Scientifique Université de Provence, Case 521–Faculté de Saint-Jérôme, Av. Esc. Normandie Niemen, 13397 Marseille Cedex 20, France
| | - Massimo Olivucci
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Bowling Green, OH 43403
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128
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Three-Layer ONIOM Studies of the Dark State of Rhodopsin: The Protonation State of Glu181. J Mol Biol 2008; 383:106-21. [DOI: 10.1016/j.jmb.2008.08.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 07/29/2008] [Accepted: 08/01/2008] [Indexed: 11/18/2022]
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129
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Bravaya KB, Bochenkova AV, Granovsky AA, Savitsky AP, Nemukhin AV. Modeling Photoabsorption of the asFP595 Chromophore. J Phys Chem A 2008; 112:8804-10. [DOI: 10.1021/jp804183w] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
| | - Anastasia V. Bochenkova
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
| | - Alexander A. Granovsky
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
| | - Alexander P. Savitsky
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
| | - Alexander V. Nemukhin
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
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130
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Muñoz-Losa A, Fdez. Galván I, Aguilar MA, Martín ME. Retinal Models: Comparison of Electronic Absorption Spectra in the Gas Phase and in Methanol Solution. J Phys Chem B 2008; 112:8815-23. [DOI: 10.1021/jp800244h] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aurora Muñoz-Losa
- Química Física, Universidad de Extremadura, Avenida de Elvas s/n, 06071 Badajoz, Spain
| | - Ignacio Fdez. Galván
- Química Física, Universidad de Extremadura, Avenida de Elvas s/n, 06071 Badajoz, Spain
| | - Manuel A. Aguilar
- Química Física, Universidad de Extremadura, Avenida de Elvas s/n, 06071 Badajoz, Spain
| | - M. Elena Martín
- Química Física, Universidad de Extremadura, Avenida de Elvas s/n, 06071 Badajoz, Spain
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131
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Simonson T. Dielectric relaxation in proteins: the computational perspective. PHOTOSYNTHESIS RESEARCH 2008; 97:21-32. [PMID: 18443919 DOI: 10.1007/s11120-008-9293-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 02/18/2008] [Indexed: 05/26/2023]
Abstract
In photoexcitation and electron transfer, a new dipole or charge is introduced, and the structure is adjusted. This adjustment represents dielectric relaxation, which is the focus of this review. We concentrate on a few selected topics. We discuss linear response theory, as a unifying framework and a tool to describe non-equilibrium states. We review recent, molecular dynamics simulation studies that illustrate the calculation of dynamic and thermodynamic properties, such as Stokes shifts or reorganization free energies. We then turn to the macroscopic, continuum electrostatic view. We recall the physical definition of a dielectric constant and revisit the decomposition of the free energy into a reorganization and a static term. We review some illustrative continuum studies and discuss some difficulties that can arise with the continuum approach. In conclusion, we consider recent developments that will increase the accuracy and broaden the scope of all these methods.
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Affiliation(s)
- Thomas Simonson
- Laboratoire de Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.
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132
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Coto PB, Martí S, Oliva M, Olivucci M, Merchán M, Andrés J. Origin of the Absorption Maxima of the Photoactive Yellow Protein Resolved via Ab Initio Multiconfigurational Methods. J Phys Chem B 2008; 112:7153-6. [DOI: 10.1021/jp711396b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pedro B. Coto
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Sergio Martí
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Mónica Oliva
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Massimo Olivucci
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Manuela Merchán
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Juan Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
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133
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Altun A, Yokoyama S, Morokuma K. Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants. J Phys Chem B 2008; 112:6814-27. [PMID: 18473437 DOI: 10.1021/jp709730b] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.
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Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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134
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Effect of opsin on the shape of the potential energy surfaces at the conical intersection of the Rhodopsin chromophore. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.03.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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135
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Pescitelli G, Sreerama N, Salvadori P, Nakanishi K, Berova N, Woody RW. Inherent Chirality Dominates the Visible/Near-Ultraviolet CD Spectrum of Rhodopsin. J Am Chem Soc 2008; 130:6170-81. [DOI: 10.1021/ja711009y] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, and Department of Chemistry, Columbia University, 3000 Broadway, MC 3114, New York 10027
| | - Narasimha Sreerama
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, and Department of Chemistry, Columbia University, 3000 Broadway, MC 3114, New York 10027
| | - Piero Salvadori
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, and Department of Chemistry, Columbia University, 3000 Broadway, MC 3114, New York 10027
| | - Koji Nakanishi
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, and Department of Chemistry, Columbia University, 3000 Broadway, MC 3114, New York 10027
| | - Nina Berova
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, and Department of Chemistry, Columbia University, 3000 Broadway, MC 3114, New York 10027
| | - Robert W. Woody
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, via Risorgimento 35, I-56126 Pisa, Italy, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, and Department of Chemistry, Columbia University, 3000 Broadway, MC 3114, New York 10027
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136
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Sinicropi A, Basosi R, Olivucci M. Recent applications of a QM/MM scheme at the CASPT2//CASSCF/AMBER (or CHARMM) level of theory in photochemistry and photobiology. ACTA ACUST UNITED AC 2008. [DOI: 10.1088/1742-6596/101/1/012001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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137
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Altun A, Yokoyama S, Morokuma K. Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins. Photochem Photobiol 2008; 84:845-54. [PMID: 18331400 DOI: 10.1111/j.1751-1097.2008.00308.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants.
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Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, GA, USA
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138
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Strambi A, Coto PB, Frutos LM, Ferré N, Olivucci M. Relationship between the Excited State Relaxation Paths of Rhodopsin and Isorhodopsin. J Am Chem Soc 2008; 130:3382-8. [DOI: 10.1021/ja0749082] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Angela Strambi
- Dipartimento di Chimica, Università di Siena, via Aldo Moro I-53100 Siena, Italy, Instituto de Ciencia Molecular (ICMOL) Universidad de Valencia, Institutos de Paterna, 22085, ES-46071, Valencia, Spain, Laboratoire de Chimie Théorique et de Modélisation Moléculaire, UMR 6517- CNRS Université de Provence, Case 521 − Faculté de Saint-Jérôme, Av. Esc. Normandie Niemen, 13397 Marseille Cedex 20, France, and Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403
| | - Pedro B. Coto
- Dipartimento di Chimica, Università di Siena, via Aldo Moro I-53100 Siena, Italy, Instituto de Ciencia Molecular (ICMOL) Universidad de Valencia, Institutos de Paterna, 22085, ES-46071, Valencia, Spain, Laboratoire de Chimie Théorique et de Modélisation Moléculaire, UMR 6517- CNRS Université de Provence, Case 521 − Faculté de Saint-Jérôme, Av. Esc. Normandie Niemen, 13397 Marseille Cedex 20, France, and Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403
| | - Luis Manuel Frutos
- Dipartimento di Chimica, Università di Siena, via Aldo Moro I-53100 Siena, Italy, Instituto de Ciencia Molecular (ICMOL) Universidad de Valencia, Institutos de Paterna, 22085, ES-46071, Valencia, Spain, Laboratoire de Chimie Théorique et de Modélisation Moléculaire, UMR 6517- CNRS Université de Provence, Case 521 − Faculté de Saint-Jérôme, Av. Esc. Normandie Niemen, 13397 Marseille Cedex 20, France, and Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403
| | - Nicolas Ferré
- Dipartimento di Chimica, Università di Siena, via Aldo Moro I-53100 Siena, Italy, Instituto de Ciencia Molecular (ICMOL) Universidad de Valencia, Institutos de Paterna, 22085, ES-46071, Valencia, Spain, Laboratoire de Chimie Théorique et de Modélisation Moléculaire, UMR 6517- CNRS Université de Provence, Case 521 − Faculté de Saint-Jérôme, Av. Esc. Normandie Niemen, 13397 Marseille Cedex 20, France, and Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403
| | - Massimo Olivucci
- Dipartimento di Chimica, Università di Siena, via Aldo Moro I-53100 Siena, Italy, Instituto de Ciencia Molecular (ICMOL) Universidad de Valencia, Institutos de Paterna, 22085, ES-46071, Valencia, Spain, Laboratoire de Chimie Théorique et de Modélisation Moléculaire, UMR 6517- CNRS Université de Provence, Case 521 − Faculté de Saint-Jérôme, Av. Esc. Normandie Niemen, 13397 Marseille Cedex 20, France, and Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403
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139
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Röhrig UF, Sebastiani D. NMR Chemical Shifts of the Rhodopsin Chromophore in the Dark State and in Bathorhodopsin: A Hybrid QM/MM Molecular Dynamics Study. J Phys Chem B 2008; 112:1267-74. [DOI: 10.1021/jp075662q] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ute F. Röhrig
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Sebastiani
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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140
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Hasegawa JY, Nakatsuji H. Exploring Photobiology and Biospectroscopy with the Sac-Ci (Symmetry-Adapted Cluster-Configuration Interaction) Method. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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141
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Yamato T, Ishikura T, Kakitani T, Kawaguchi K, Watanabe H. Spectral tuning of photoactive yellow protein. Photochem Photobiol 2007; 83:323-7. [PMID: 17017845 DOI: 10.1562/2006-06-16-ra-930] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We report a theoretical study on the optical properties of a small, water-soluble photosensory receptor, photoactive yellow protein (PYP). A hierarchical ab initio molecular orbital calculation accurately evaluated the optical absorption maximum of the wild-type, as well as the lambda(max) values of 12 mutants. Electronic excitation of the chromophore directly affects the electronic state of nearby atoms in the protein environment. This effect is explicitly considered in the present study. Furthermore, the spectral tuning mechanism of PYP was investigated at the atomic level. The static disorder of a protein molecule is intimately related to the complex nature of its energy landscape. By using molecular dynamics simulation and quantum mechanical structure optimization, we obtained multiple minimum energy conformations of PYP. The statistical distribution of electronic excitation energies of these minima was compared with the hole-burning experiment (Masciangioli, T. [2000] Photochem. Photobiol. 72, 639), a direct observation of the distribution of excitation energies.
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Affiliation(s)
- T Yamato
- Graduate School of Science, Nagoya University, Nagoya, Japan.
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142
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Bravaya K, Bochenkova A, Granovsky A, Nemukhin A. An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase. J Am Chem Soc 2007; 129:13035-42. [PMID: 17924622 DOI: 10.1021/ja0732126] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We considered a series of model systems for treating the photoabsorption of the 11-cis retinal chromophore in the protonated Schiff-base form in vacuum, solutions, and the protein environment. A high computational level, including the quantum mechanical-molecular mechanical (QM/MM) approach for solution and protein was utilized in simulations. The S0-S1 excitation energies in quantum subsystems were evaluated by means of an augmented version of the multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) with the ground-state geometry parameters optimized in the density functional theory PBE0/cc-pVDZ approximation. The computed positions of absorption bands lambdamax, 599(g), 448(s), and 515(p) nm for the gas phase, solution, and protein, respectively, are in excellent agreement with the corresponding experimental data, 610(g), 445(s), and 500(p) nm. Such consistency provides a support for the formulated qualitative conclusions on the role of the chromophore geometry, environmental electrostatic field, and the counterion in different media. An essentially nonplanar geometry conformation of the chromophore group in the region of the C14-C15 bond was obtained for the protein, in particular, owing to the presence of the neighboring charged amino acid residue Glu181. Nonplanarity of the C14-C15 bond region along with the influence of the negatively charged counterions Glu181 and Glu113 are found to be important to reproduce the spectroscopic features of retinal chromophore inside the Rh cavity. Furthermore, the protein field is responsible for the largest bond-order decrease at the C11-C12 double bond upon excitation, which may be the reason for the 11-cis photoisomerization specificity.
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Affiliation(s)
- Ksenia Bravaya
- Department of Chemistry, M.V. Lomonosov Moscow State University, 1/3, Leninskie Gory, Moscow 119992, Russian Federation
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143
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Send R, Sundholm D. Stairway to the conical intersection: a computational study of the retinal isomerization. J Phys Chem A 2007; 111:8766-73. [PMID: 17713894 DOI: 10.1021/jp073908l] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order Møller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.
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Affiliation(s)
- Robert Send
- Institut für Physikalische Chemie, Universität Karlsruhe, Kaiserstrasse 12, D-76128 Karlsruhe, Germany
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144
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Substituent-controlled photoisomerization in retinal chromophore models: Fluorinated and methoxy-substituted protonated Schiff bases. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2006.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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145
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Frutos LM, Andruniów T, Santoro F, Ferré N, Olivucci M. Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry. Proc Natl Acad Sci U S A 2007; 104:7764-9. [PMID: 17470789 PMCID: PMC1876521 DOI: 10.1073/pnas.0701732104] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2007] [Indexed: 11/18/2022] Open
Abstract
The primary event that initiates vision is the photoinduced isomerization of retinal in the visual pigment rhodopsin (Rh). Here, we use a scaled quantum mechanics/molecular mechanics potential that reproduces the isomerization path determined with multiconfigurational perturbation theory to follow the excited-state evolution of bovine Rh. The analysis of a 140-fs trajectory provides a description of the electronic and geometrical changes that prepare the system for decay to the ground state. The data uncover a complex change of the retinal backbone that, at approximately 60-fs delay, initiates a space saving "asynchronous bicycle-pedal or crankshaft" motion, leading to a conical intersection on a 110-fs time scale. It is shown that the twisted structure achieved at decay features a momentum that provides a natural route toward the photoRh structure recently resolved by using femtosecond-stimulated Raman spectroscopy.
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Affiliation(s)
- Luis Manuel Frutos
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Tadeusz Andruniów
- Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 27 Wyb. Wyspianskiego, 50-370, Wroclaw, Poland
| | - Fabrizio Santoro
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Via Moruzzi 1, I-56124 Pisa, Italy; and
| | - Nicolas Ferré
- Laboratoire de Chimie Théorique et de Modélisation Moléculaire, Unité Mixte de Recherche 6517, Centre National de la Recherche Scientifique, Université de Provence, Case 521, Faculté de Saint-Jérôme, Avenue Esc. Normandie Niemen, 13397 Marseille Cedex 20, France
| | - Massimo Olivucci
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403
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146
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Abstract
Femtosecond stimulated Raman spectroscopy (FSRS) is a new ultrafast spectroscopic technique that provides vibrational structural information with high temporal (50-fs) and spectral (10-cm(1)) resolution. As a result of these unique capabilities, FSRS studies of chemical and biochemical reaction dynamics are expected to grow rapidly, giving previously unattainable insight into the structural dynamics of reactively evolving systems with atomic spatial and femtosecond temporal resolution. This review discusses the experimental and theoretical concepts behind FSRS, with an emphasis on the origins of its unique temporal and spectral capabilities. We illustrate these capabilities with vibrational studies of ultrafast electronic dynamics, as well as the direct structural observation of nonstationary vibrational wave-packet motion in small molecules and in complex biochemical reaction dynamics.
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Affiliation(s)
- Philipp Kukura
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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147
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Altoè P, Stenta M, Bottoni A, Garavelli M. A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0275-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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148
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Strambi A, Coto PB, Ferré N, Olivucci M. Effects of water re-location and cavity trimming on the CASPT2//CASSCF/AMBER excitation energy of Rhodopsin. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0273-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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149
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Struts AV, Salgado GFJ, Tanaka K, Krane S, Nakanishi K, Brown MF. Structural analysis and dynamics of retinal chromophore in dark and meta I states of rhodopsin from 2H NMR of aligned membranes. J Mol Biol 2007; 372:50-66. [PMID: 17640664 PMCID: PMC5233725 DOI: 10.1016/j.jmb.2007.03.046] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 03/02/2007] [Accepted: 03/19/2007] [Indexed: 11/29/2022]
Abstract
Rhodopsin is a prototype for G protein-coupled receptors (GPCRs) that are implicated in many biological responses in humans. A site-directed (2)H NMR approach was used for structural analysis of retinal within its binding cavity in the dark and pre-activated meta I states. Retinal was labeled with (2)H at the C5, C9, or C13 methyl groups by total synthesis, and was used to regenerate the opsin apoprotein. Solid-state (2)H NMR spectra were acquired for aligned membranes in the low-temperature lipid gel phase versus the tilt angle to the magnetic field. Data reduction assumed a static uniaxial distribution, and gave the retinylidene methyl bond orientations plus the alignment disorder (mosaic spread). The dark-state (2)H NMR structure of 11-cis-retinal shows torsional twisting of the polyene chain and the beta-ionone ring. The ligand undergoes restricted motion, as evinced by order parameters of approximately 0.9 for the spinning C-C(2)H(3) groups, with off-axial fluctuations of approximately 15 degrees . Retinal is accommodated within the rhodopsin binding pocket with a negative pre-twist about the C11=C12 double bond that explains its rapid photochemistry and the trajectory of 11-cis to trans isomerization. In the cryo-trapped meta I state, the (2)H NMR structure shows a reduction of the polyene strain, while torsional twisting of the beta-ionone ring is maintained. Distortion of the retinal conformation is interpreted through substituent control of receptor activation. Steric hindrance between trans retinal and Trp265 can trigger formation of the subsequent activated meta II state. Our results are pertinent to quantum and molecular mechanics simulations of ligands bound to GPCRs, and illustrate how (2)H NMR can be applied to study their biological mechanisms of action.
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Affiliation(s)
- Andrey V. Struts
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Gilmar F. J. Salgado
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
| | - Katsunori Tanaka
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Sonja Krane
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Koji Nakanishi
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Michael F. Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
- Department of Physics, University of Arizona, Tucson, Arizona 85721, USA
- Corresponding author:
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150
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Weingart O, Schapiro I, Buss V. Photochemistry of Visual Pigment Chromophore Models by Ab Initio Molecular Dynamics. J Phys Chem B 2007; 111:3782-8. [PMID: 17388554 DOI: 10.1021/jp0683216] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ab initio excited-state molecular dynamics calculations have been performed to study the effect of methyl substitution and chromophore distortion on the photoreaction of different four-double-bond retinal model chromophores. Randomly distributed starting geometries were generated by zero-point energy sampling; after Franck-Condon excitation the reaction was followed on the S1 surface. For determining the photoproduct and its configuration, a simplified approach--torsion angle following--is discussed and applied. We find that chromophore distortion significantly affects the outcome of the photoreaction: with dihedral angles taken from the rhodopsin-embedded 11-cis-retinal chromophore, the reaction rate of the model chromophore is increased by a factor of 3 compared to that of the relaxed chromophore. Also, the reaction proceeds in a completely stereoselective manner involving only the cis double bond and with a minimum quantum yield of 72%. Bond torsion is more effective than methyl substitution for fast and selective photochemistry, which is in agreement with photophysical measurements on rhodopsin analogues. We conclude that apart from the geometric distortions caused by the protein pocket it is not necessary to postulate other specific interactions between the protein and the chromophore to effect the selective and ultrafast photoreaction in rhodopsin.
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Affiliation(s)
- Oliver Weingart
- Department of Chemistry, University of Duisburg-Essen, 47048 Duisburg, Germany
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