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Kuroi K, Tsukamoto T, Honda N, Sudo Y, Furutani Y. Concerted primary proton transfer reactions in a thermophilic rhodopsin studied by time-resolved infrared spectroscopy at high temperature. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148980. [PMID: 37080329 DOI: 10.1016/j.bbabio.2023.148980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/22/2023]
Abstract
The primary proton transfer reactions of thermophilic rhodopsin, which was first discovered in an extreme thermophile, Thermus thermophilus JL-18, were investigated using time-resolved Fourier transform infrared spectroscopy at various temperatures ranging from 298 to 343 K (25 to 70 °C) and proton transport activity analysis. The analyses were performed using counterion (D95E, D95N, D229E, and D229N) and proton donor mutants (E106D and E106Q) as well. First, the initial proton transfer from the protonated retinal Schiff base (PRSB) to D95 was identified. The temperature dependency showed that the proton transfer reaction in the intermediate states dramatically changed above 318 K (45 °C). In addition, the proton transfer reaction correlated well with the structural change from turn to β-strand in the protein moiety, suggesting that this step may be regulated by the rigidity of the loop region. We also elucidated that the proton transfer reaction from proton donor E106 to the retinal Schiff base occurred synchronously with the primary proton transfer from the PRSB to D95. Surprisingly, we discovered that the direction of proton transfer was regulated by the secondary counterion, D229. Comparative analysis of Gloeobacter rhodopsin from the mesophile, Gloeobacter violaceus, highlighted that the primary proton transfer reactions in thermophilic rhodopsin were optimized at high temperatures partly due to the specific turn to β-strand structural change. This was not observed in Gloeobacter rhodopsin and other related proteins such as bacteriorhodopsin.
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Affiliation(s)
- Kunisato Kuroi
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Takashi Tsukamoto
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan; Faculty of Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Naoya Honda
- Faculty of Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan; Faculty of Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan.
| | - Yuji Furutani
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan; Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.
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Furutani Y, Yang CS. Ion-transporting mechanism in microbial rhodopsins: Mini-review relating to the session 5 at the 19th International Conference on Retinal Proteins. Biophys Physicobiol 2023; 20:e201005. [PMID: 38362333 PMCID: PMC10865854 DOI: 10.2142/biophysico.bppb-v20.s005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Affiliation(s)
- Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Chii-Shen Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
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Yamamoto T, Yasuda S, Kasai RS, Nakano R, Hikiri S, Sugaya K, Hayashi T, Ogasawara S, Shiroishi M, Fujiwara TK, Kinoshita M, Murata T. A methodology for creating mutants of G-protein coupled receptors stabilized in active state by combining statistical thermodynamics and evolutionary molecular engineering. Protein Sci 2022; 31:e4425. [PMID: 36173170 PMCID: PMC9490800 DOI: 10.1002/pro.4425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 09/28/2023]
Abstract
We challenged the stabilization of a G-protein coupled receptor (GPCR) in the active state solely by multiple amino-acid mutations without the agonist binding. For many GPCRs, the free energy of the active state is higher than that of the inactive state. When the inactive state is stabilized through the lowering of its free energy, the apparent midpoint temperature of thermal denaturation Tm exhibits a significant increase. However, this is not always the case for the stabilization of the active state. We constructed a modified version of our methodology combining statistical thermodynamics and evolutionary molecular engineering, which was recently developed for the inactive state. First, several residues to be mutated are determined using our statistical-thermodynamics theory. Second, a gene (mutant) library is constructed using Escherichia coli cells to efficiently explore most of the mutational space. Third, for the mutant screening, the mutants prepared in accordance with the library are expressed in engineered Saccharomyces cerevisiae YB14 cells which can grow only when a GPCR mutant stabilized in the active state has signaling function. For the adenosine A2A receptor tested, the methodology enabled us to sort out two triple mutants and a double mutant. It was experimentally corroborated that all the mutants exhibit much higher binding affinity for G protein than the wild type. Analyses indicated that the mutations make the structural characteristics shift toward those of the active state. However, only slight increases in Tm resulted from the mutations, suggesting the unsuitability of Tm to the stability measure for the active state.
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Affiliation(s)
- Taisei Yamamoto
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
| | - Rinshi S. Kasai
- Institute for Glyco‐core Research (iGCORE)Gifu UniversityGifuJapan
- Institute for Life and Medical SciencesKyoto UniversityKyotoJapan
| | - Ryosuke Nakano
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Simon Hikiri
- Graduate School of Engineering ScienceOsaka UniversityOsakaJapan
| | - Kanna Sugaya
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of EngineeringNiigata UniversityNiigataJapan
- Institute of Advanced EnergyKyoto UniversityKyotoJapan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
- Institute for Advanced Academic ResearchChiba UniversityChibaJapan
| | - Mitsunori Shiroishi
- Department of Biological Science and TechnologyTokyo University of ScienceTokyoJapan
| | - Takahiro K. Fujiwara
- Institute for Integrated Cell‐Material Sciences (WPI‐iCeMS)Kyoto UniversityKyotoJapan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Institute of Advanced EnergyKyoto UniversityKyotoJapan
- Center for the Promotion of Interdisciplinary Education and ResearchKyoto UniversityKyoto‐shiJapan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
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Sugaya K, Yasuda S, Sato S, Sisi C, Yamamoto T, Umeno D, Matsuura T, Hayashi T, Ogasawara S, Kinoshita M, Murata T. A methodology for creating thermostabilized mutants of G‐protein coupled receptors by combining statistical thermodynamics and evolutionary molecular engineering. Protein Sci 2022. [DOI: 10.1002/pro.4404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kanna Sugaya
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
| | - Shingo Sato
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Chen Sisi
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
| | - Taisei Yamamoto
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Daisuke Umeno
- Department of Applied Chemistry Waseda University Tokyo Japan
| | - Tomoaki Matsuura
- Earth‐Life Science Institute Tokyo Institute of Technology Tokyo Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering Niigata University Niigata Japan
- Institute of Advanced Energy Kyoto University Kyoto Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
- Institute for Advanced Academic Research Chiba University Chiba Japan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Institute of Advanced Energy Kyoto University Kyoto Japan
- Center for the Promotion of Interdisciplinary Education and Research Kyoto University Kyoto‐shi Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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