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Ostrovsky MA, Nadtochenko VA. Femtochemistry of Rhodopsins. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2021. [DOI: 10.1134/s1990793121020226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
The review considers the spectral kinetic data obtained by us by femtosecond absorption laser spectroscopy for the photochromic reaction of retinal isomerization in animal rhodopsin (type II), namely, bovine visual rhodopsin and microbial rhodopsins (type I), such as Exiguobacterium sibiricum rhodopsin and Halobacterium salinarum bacteriorhodopsin. It is shown that the elementary act of the photoreaction of retinal isomerization in type I and type II rhodopsins can be interpreted as a transition through a conical intersection with retention of the coherence of the vibrational wave packets generated during excitation. The coherent nature of the reaction is most pronounced in visual rhodopsin as a result of the barrier-free movement along the excited surface of potential energy, which also leads to an extremely high rate of retinal isomerization compared to microbial rhodopsins. Differences in the dynamics of photochemical reactions of type I and type II rhodopsins can be related to both differences in the initial isomeric forms of their chromophores (all-trans and 11-cis retinal, respectively), as well as with the effect of the protein environment on the chromophore. Despite the practically identical values of the quantum yields of the direct photoreaction of visual rhodopsin and bacteriorhodopsin, the reverse photoreaction of visual rhodopsin is much less effective (φ = 0.15) than in the case of bacteriorhodopsin (φ = 0.81). It can be assumed that the photobiological mechanism for converting light into an information process in the evolutionarily younger visual rhodopsins (type II rhodopsins) should be more reliable than the mechanism for converting light into a photoenergetic process in the evolutionarily more ancient microbial rhodopsins (type I rhodopsins). The low value of the quantum yield of the reverse reaction of visual rhodopsin can be considered as an increase in the reliability of the forward reaction, which triggers the process of phototransduction.
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Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
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Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
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Kaduk B, Tsuchimochi T, Van Voorhis T. Analytic energy gradients for constrained DFT-configuration interaction. J Chem Phys 2014; 140:18A503. [DOI: 10.1063/1.4862497] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Zhou P, Liu J, Han K, He G. The photoisomerization of 11-cis-retinal protonated schiff base in gas phase: Insight from spin-flip density functional theory. J Comput Chem 2013; 35:109-20. [DOI: 10.1002/jcc.23463] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/12/2013] [Accepted: 09/24/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Guozhong He
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
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Muñoz-Losa A, Martín ME, Galván IF, Sánchez ML, Aguilar MA. Solvent Effects on the Radiative and Nonradiative Decay of a Model of the Rhodopsin Chromophore. J Chem Theory Comput 2011; 7:4050-9. [DOI: 10.1021/ct200295r] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [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, Avda. de Elvas s/n 06071 Badajoz, Spain
| | - M. Elena Martín
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
| | - Ignacio Fdez. Galván
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
| | - M. Luz Sánchez
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
| | - Manuel A. Aguilar
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
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Schapiro I, Ryazantsev MN, Frutos LM, Ferré N, Lindh R, Olivucci M. The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects. J Am Chem Soc 2011; 133:3354-64. [DOI: 10.1021/ja1056196] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Igor Schapiro
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Luis Manuel Frutos
- Departamento de Química Física, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Nicolas Ferré
- Laboratoire Chimie Provence UMR 6264, Université de Provence, Campus Saint Jérôme Case 521, 13397 Marseille Cedex 20, France
| | - Roland Lindh
- Department of Quantum Chemistry, Ångströmlab, Lägerhyddsv. 1, Box 518, 751 20 Uppsala University, Sweden
| | - Massimo Olivucci
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Chimica, Università degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy
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Bovee-Geurts PHM, Fernández Fernández I, Liu RSH, Mathies RA, Lugtenburg J, DeGrip WJ. Fluoro Derivatives of Retinal Illuminate the Decisive Role of the C12-H Element in Photoisomerization and Rhodopsin Activation. J Am Chem Soc 2009; 131:17933-42. [DOI: 10.1021/ja907577p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Petra H. M. Bovee-Geurts
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Isabelle Fernández Fernández
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Robert S. H. Liu
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Richard A. Mathies
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Johan Lugtenburg
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Willem J. DeGrip
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
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Coto PB, Roca-Sanjuán D, Serrano-Andrés L, Martín-Pendás A, Martí S, Andrés J. Toward Understanding the Photochemistry of Photoactive Yellow Protein: A CASPT2/CASSCF and Quantum Theory of Atoms in Molecules Combined Study of a Model Chromophore in Vacuo. J Chem Theory Comput 2009; 5:3032-8. [DOI: 10.1021/ct900401z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. B. Coto
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - D. Roca-Sanjuán
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - L. Serrano-Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - A. Martín-Pendás
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - S. Martí
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - J. Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
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González-Navarrete P, Coto PB, Polo V, Andrés J. A theoretical study on the thermal ring opening rearrangement of 1H-bicyclo[3.1.0]hexa-3,5-dien-2-one: a case of two state reactivity. Phys Chem Chem Phys 2009; 11:7189-96. [DOI: 10.1039/b906404d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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