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Gordeliy V, Kovalev K, Bamberg E, Rodriguez-Valera F, Zinovev E, Zabelskii D, Alekseev A, Rosselli R, Gushchin I, Okhrimenko I. Microbial Rhodopsins. Methods Mol Biol 2022; 2501:1-52. [PMID: 35857221 DOI: 10.1007/978-1-0716-2329-9_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The first microbial rhodopsin, a light-driven proton pump bacteriorhodopsin from Halobacterium salinarum (HsBR), was discovered in 1971. Since then, this seven-α-helical protein, comprising a retinal molecule as a cofactor, became a major driver of groundbreaking developments in membrane protein research. However, until 1999 only a few archaeal rhodopsins, acting as light-driven proton and chloride pumps and also photosensors, were known. A new microbial rhodopsin era started in 2000 when the first bacterial rhodopsin, a proton pump, was discovered. Later it became clear that there are unexpectedly many rhodopsins, and they are present in all the domains of life and even in viruses. It turned out that they execute such a diversity of functions while being "nearly the same." The incredible evolution of the research area of rhodopsins and the scientific and technological potential of the proteins is described in the review with a focus on their function-structure relationships.
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Affiliation(s)
- Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Egor Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Dmitrii Zabelskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Riccardo Rosselli
- Departamento de Fisiología, Genetica y Microbiología. Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
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Kusochek PA, Scherbinin AV, Bochenkova AV. Insights into the Early-Time Excited-State Dynamics of Structurally Inhomogeneous Rhodopsin KR2. J Phys Chem Lett 2021; 12:8664-8671. [PMID: 34472871 DOI: 10.1021/acs.jpclett.1c02312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The light-driven sodium-pump rhodopsin KR2 exhibits ultrafast photoisomerization dynamics of its all-trans protonated Schiff-base retinal (PSBR). However, the excited-state decay of KR2 also shows slow picosecond time constants, which are attributed to nonreactive states. The mechanism that produces long-lived states is unclear. Here, by using molecular dynamics simulations and large-scale XMCQDPT2-based QM/MM modeling, we explore the origin of reactive and nonreactive states in KR2. By calculating the S0-S1 vibronic band shapes, we gain insight into the early-time excited-state dynamics of PSBR and show that the protein environment can significantly alter vibrational modes that are active upon photoexcitation, thus facilitating photoisomerization from all-trans to 13-cis PSBR. Importantly, we reveal structural heterogeneity of the retinal-binding pocket of KR2, characterized by three distinct conformations, and conclude that the formation of a strong hydrogen bond between the retinal Schiff base and its counterion is essential for the ultrafast reaction dynamics.
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Affiliation(s)
- Pavel A Kusochek
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andrei V Scherbinin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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Rokitskaya TI, Maliar N, Kovalev KV, Volkov O, Gordeliy VI, Antonenko YN. Rhodopsin Channel Activity Can Be Evaluated by Measuring the Photocurrent Voltage Dependence in Planar Bilayer Lipid Membranes. BIOCHEMISTRY (MOSCOW) 2021; 86:409-419. [PMID: 33941063 DOI: 10.1134/s0006297921040039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The studies of the functional properties of retinal-containing proteins often include experiments in model membrane systems, e.g., measurements of electric current through planar bilayer lipid membranes (BLMs) with proteoliposomes adsorbed on one of the membrane surfaces. However, the possibilities of this method have not been fully explored yet. We demonstrated that the voltage dependence of stationary photocurrents for two light-sensitive proteins, bacteriorhodopsin (bR) and channelrhodopsin 2 (ChR2), in the presence of protonophore had very different characteristics. In the case of the bR (proton pump), the photocurrent through the BLM did not change direction when the polarity of the applied voltage was switched. In the case of the photosensitive channel protein ChR2, the photocurrent increased with the increase in voltage and the current polarity changed with the change in the voltage polarity. The protonophore 4,5,6,7-tetrachloro-2-trifluoromethyl benzimidazole (TTFB) was more efficient in the maximizing stationary photocurrents. In the presence of carbonyl cyanide-m-chlorophenylhydrazone (CCCP), the amplitude of the measured photocurrents for bR significantly decreased, while in the case of ChR2, the photocurrents virtually disappeared. The difference between the effects of TTFB and CCCP was apparently due to the fact that, in contrast to TTFB, CCCP transfers protons across the liposome membranes with a higher rate than through the decane-containing BLM used as a surface for the proteoliposome adsorption.
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Affiliation(s)
- Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Nina Maliar
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Kirill V Kovalev
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, 38044, France
| | - Oleksandr Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Juelich, 52425, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Juelich, 52425, Germany
| | - Valentin I Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, 38044, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Juelich, 52425, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Juelich, 52425, Germany
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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