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Kandori H. Structure/Function Study of Photoreceptive Proteins by FTIR Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200109] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry & OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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2
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Nomura Y, Ito S, Teranishi M, Ono H, Inoue K, Kandori H. Low-temperature FTIR spectroscopy provides evidence for protein-bound water molecules in eubacterial light-driven ion pumps. Phys Chem Chem Phys 2018; 20:3165-3171. [DOI: 10.1039/c7cp05674e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The present FTIR study showed that eubacterial light-driven H+, Na+ and Cl− pump rhodopsins contain strongly hydrogen-bonded water molecule, the functional determinant of light-driven proton pump. This explains well the asymmetric functional conversions of light-driven ion pumps.
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Affiliation(s)
- Yurika Nomura
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Miwako Teranishi
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Hikaru Ono
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
- OptoBioTechnology Research Center
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
- OptoBioTechnology Research Center
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Koua FHM, Kandori H. Light-induced structural changes during early photo-intermediates of the eubacterial Cl−pump Fulvimarina rhodopsin observed by FTIR difference spectroscopy. RSC Adv 2016. [DOI: 10.1039/c5ra19363j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Fulvimarina pelagirhodopsin (FR) is a member of inward eubacterial light-activated Cl−translocating rhodopsins (ClR) that were found recently in marine bacteria.
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Affiliation(s)
| | - Hideki Kandori
- OptoBioTechnology Research Center
- Nagoya Institute of Technology
- 466-8555 Nagoya
- Japan
- Department of Frontier Materials
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Sudo Y, Mizuno M, Wei Z, Takeuchi S, Tahara T, Mizutani Y. The Early Steps in the Photocycle of a Photosensor Protein Sensory Rhodopsin I from Salinibacter ruber. J Phys Chem B 2014; 118:1510-8. [DOI: 10.1021/jp4112662] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yuki Sudo
- Division
of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
- Department
of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Misao Mizuno
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Zhengrong Wei
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Satoshi Takeuchi
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yasuhisa Mizutani
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Fukuda T, Muroda K, Kandori H. Detection of a protein-bound water vibration of halorhodopsin in aqueous solution. Biophysics (Nagoya-shi) 2013; 9:167-72. [PMID: 27493555 PMCID: PMC4629683 DOI: 10.2142/biophysics.9.167] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/04/2013] [Indexed: 01/14/2023] Open
Abstract
Protein-bound water molecules play crucial roles in their structure and function, but their detection is an experimental challenge, particularly in aqueous solution at room temperature. By applying attenuated total reflection (ATR) Fourier-transform infrared (FTIR) spectroscopy to a light-driven Cl(-) pump pharaonis halorhodopsin (pHR), here we detected an O-H stretching vibration of protein-bound water molecules in the active center. The pHR(Cl(-)) minus pHR(Br(-)) ATR-FTIR spectra show random fluctuation at 3600-3000 cm(-1), frequency window of water vibration, which can be interpreted in terms of dynamical fluctuation of aqueous water at room temperature. On the other hand, we observed a reproducible spectral feature at 3617 (+)/3630 (-) cm(-1) in the pHR(Cl(-)) minus pHR(Br(-)) spectrum, which is absent in the pHR(Cl(-)) minus pHR(Cl(-)) and in the pHR(Br(-)) minus pHR(Br(-)) spectra. The water O-H stretching vibrations of pHR(Cl(-)) and pHR(Br(-)) at 3617 and 3630 cm(-1), respectively, are confirmed by light-induced difference FTIR spectra in isotope water (H2 (18)O) at 77 K. The observed water molecule presumably binds to the active center of pHR, and alter its hydrogen bond during the Cl(-) pumping photocycle.
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Affiliation(s)
- Tetsuya Fukuda
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kosuke Muroda
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Muroda K, Nakashima K, Shibata M, Demura M, Kandori H. Protein-bound water as the determinant of asymmetric functional conversion between light-driven proton and chloride pumps. Biochemistry 2012; 51:4677-84. [PMID: 22583333 DOI: 10.1021/bi300485r] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacteriorhodopsin (BR) and halorhodopsin (HR) are light-driven outward proton and inward chloride pumps, respectively. They have similar protein architecture, being composed of seven-transmembrane helices that bind an all-trans-retinal. BR can be converted into a chloride pump by a single amino acid replacement at position 85, suggesting that BR and HR share a common transport mechanism, and the ionic specificity is determined by the amino acid at that position. However, HR cannot be converted into a proton pump by the corresponding reverse mutation. Here we mutated 6 and 10 amino acids of HR into BR-like, whereas such multiple HR mutants never pump protons. Light-induced Fourier transform infrared spectroscopy revealed that hydrogen bonds of the retinal Schiff base and water are both strong for BR and both weak for HR. Multiple HR mutants exhibit strong hydrogen bonds of the Schiff base, but the hydrogen bond of water is still weak. We concluded that the cause of nonfunctional conversion of HR is the lack of strongly hydrogen-bonded water, the functional determinant of the proton pump.
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Affiliation(s)
- Kosuke Muroda
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
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Hashimoto K, Choi AR, Furutani Y, Jung KH, Kandori H. Low-Temperature FTIR Study of Gloeobacter Rhodopsin: Presence of Strongly Hydrogen-Bonded Water and Long-Range Structural Protein Perturbation upon Retinal Photoisomerization. Biochemistry 2010; 49:3343-50. [DOI: 10.1021/bi100184k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kyohei Hashimoto
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Ah Reum Choi
- Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea
| | - Yuji Furutani
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kwang-Hwan Jung
- Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Zgrablić G, Ricci M, Novello AM, Parmigiani F. Dependence of Photochemical Reactivity of the All-trans Retinal Protonated Schiff Base on the Solvent and the Excitation Wavelength. Photochem Photobiol 2010; 86:507-12. [DOI: 10.1111/j.1751-1097.2009.00697.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sobotta C, Braun M, Tittor J, Oesterhelt D, Zinth W. Influence of the charge at D85 on the initial steps in the photocycle of bacteriorhodopsin. Biophys J 2009; 97:267-76. [PMID: 19580764 DOI: 10.1016/j.bpj.2009.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 03/25/2009] [Accepted: 04/06/2009] [Indexed: 10/20/2022] Open
Abstract
Studies have shown that trans-cis isomerization of retinal is the primary photoreaction in the photocycle of the light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum, as well as in the photocycle of the chloride pump halorhodopsin (HR). The transmembrane proteins HR and BR show extensive structural similarities, but differ in the electrostatic surroundings of the retinal chromophore near the protonated Schiff base. Point mutation of BR of the negatively charged aspartate D85 to a threonine T (D85T) in combination with variation of the pH value and anion concentration is used to study the ultrafast photoisomerization of BR and HR for well-defined electrostatic surroundings of the retinal chromophore. Variations of the pH value and salt concentration allow a switch in the isomerization dynamics of the BR mutant D85T between BR-like and HR-like behaviors. At low salt concentrations or a high pH value (pH 8), the mutant D85T shows a biexponential initial reaction similar to that of HR. The combination of high salt concentration and a low pH value (pH 6) leads to a subpopulation of 25% of the mutant D85T whose stationary and dynamic absorption properties are similar to those of native BR. In this sample, the combination of low pH and high salt concentration reestablishes the electrostatic surroundings originally present in native BR, but only a minor fraction of the D85T molecules have the charge located exactly at the position required for the BR-like fast isomerization reaction. The results suggest that the electrostatics in the native BR protein is optimized by evolution. The accurate location of the fixed charge at the aspartate D85 near the Schiff base in BR is essential for the high efficiency of the primary reaction.
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Affiliation(s)
- Constanze Sobotta
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
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Nakashima K, Nakamura T, Takeuchi S, Shibata M, Demura M, Tahara T, Kandori H. Properties of the Anion-Binding Site of pharaonis Halorhodopsin Studied by Ultrafast Pump−Probe Spectroscopy and Low-Temperature FTIR Spectroscopy. J Phys Chem B 2009; 113:8429-34. [DOI: 10.1021/jp902596k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Keisuke Nakashima
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Takumi Nakamura
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Satoshi Takeuchi
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Mikihiro Shibata
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Makoto Demura
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Tahei Tahara
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
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Ito M, Sudo Y, Furutani Y, Okitsu T, Wada A, Homma M, Spudich JL, Kandori H. Steric constraint in the primary photoproduct of sensory rhodopsin II is a prerequisite for light-signal transfer to HtrII. Biochemistry 2008; 47:6208-15. [PMID: 18479149 DOI: 10.1021/bi8003507] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sensory rhodopsin II (SRII, also called pharaonis phoborhodopsin, ppR) is responsible for negative phototaxis in Natronomonas pharaonis. Photoisomerization of the retinal chromophore from all- trans to 13- cis initiates conformational changes in the protein, leading to activation of the cognate transducer protein (HtrII). We previously observed enhancement of the C 14-D stretching vibration of the retinal chromophore at 2244 cm (-1) upon formation of the K state and interpreted that a steric constraint occurs at the C 14D group in SRII K. Here, we identify the counterpart of the C 14D group as Thr204, because the C 14-D stretching signal disappeared in T204A, T204S, and T204C mutants as well as a C 14-HOOP (hydrogen out-of-plane) vibration at 864 cm (-1). Although the K state of the wild-type bacteriorhodopsin (BR), a light-driven proton pump, possesses neither 2244 nor 864 cm (-1) bands, both signals appeared for the K state of a triple mutant of BR that functions as a light sensor (P200T/V210Y/A215T). We found a positive correlation between these vibrational amplitudes of the C 14 atom at 77 K and the physiological phototaxis response. These observations strongly suggest that the steric constraint between the C 14 group of retinal and Thr204 of the protein is a prerequisite for light-signal transduction by SRII.
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Affiliation(s)
- Motohiro Ito
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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