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Hashimoto M, Miyagawa K, Singh M, Katayama K, Shoji M, Furutani Y, Shigeta Y, Kandori H. Specific zinc binding to heliorhodopsin. Phys Chem Chem Phys 2023; 25:3535-3543. [PMID: 36637167 DOI: 10.1039/d2cp04718g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Heliorhodopsins (HeRs), a recently discovered family of rhodopsins, have an inverted membrane topology compared to animal and microbial rhodopsins. The slow photocycle of HeRs suggests a light-sensor function, although the actual function remains unknown. Although HeRs exhibit no specific binding of monovalent cations or anions, recent ATR-FTIR spectroscopy studies have demonstrated the binding of Zn2+ to HeR from Thermoplasmatales archaeon (TaHeR) and 48C12. Even though ion-specific FTIR spectra were observed for many divalent cations, only helical structural perturbations were observed for Zn2+-binding, suggesting a possible modification of the HeR function by Zn2+. The present study shows that Zn2+-binding lowers the thermal stability of TaHeR, and slows back proton transfer to the retinal Schiff base (M decay) during its photocycle. Zn2+-binding was similarly observed for a TaHeR opsin that lacks the retinal chromophore. We then studied the Zn2+-binding site by means of the ATR-FTIR spectroscopy of site-directed mutants. Among five and four mutants of His and Asp/Glu, respectively, only E150Q exhibited a completely different spectral feature of the α-helix (amide-I) in ATR-FTIR spectroscopy, suggesting that E150 is responsible for Zn2+-binding. Molecular dynamics (MD) simulations built a coordination structure of Zn2+-bound TaHeR, where E150 and protein bound water molecules participate in direct coordination. It was concluded that the specific binding site of Zn2+ is located at the cytoplasmic side of TaHeR, and that Zn2+-binding affects the structure and structural dynamics, possibly modifying the unknown function of TaHeR.
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Affiliation(s)
- Masanori Hashimoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan. .,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,JST-PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan. .,JST-PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan. .,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan. .,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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Sakajiri Y, Sugano E, Watanabe Y, Sakajiri T, Tabata K, Kikuchi T, Tomita H. Natronomonas pharaonis halorhodopsin Ser81 plays a role in maintaining chloride ions near the Schiff base. Biochem Biophys Res Commun 2018; 503:2326-2332. [PMID: 29964009 DOI: 10.1016/j.bbrc.2018.06.156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 06/27/2018] [Indexed: 02/02/2023]
Abstract
Optogenetic technologies have often been used as tools for neuronal activation or silencing by light. Natronomonas pharaonis halorhodopsin (NpHR) is a light-driven chloride ion pump. Upon light absorption, a chloride ion passes through the cell membrane, which is accompanied by the temporary binding of a chloride ion with Thr126 at binding site-1 (BS1) near the protonated Schiff base in NpHR. However, the mechanism of stabilization of the binding state between a chloride ion and BS1 has not been investigated. Therefore, to identify a key component of the chloride ion transport pathway as well as to acquire dynamic information about the chloride ion-BS1 binding state, we performed a rough analysis of the chloride ion pathway shape followed by molecular dynamics (MD) simulations for both wild-type and mutant NpHR structures. The MD simulations showed that the hydrogen bond between Thr126 and the chloride ion was retained in the wild-type protein, while the chloride ion could not be retained at and tended to leave BS1 in the S81A mutant. We found that the direction of the Thr126 side chain was fixed by a hydroxyl group of Ser81 through a hydrogen bond and that Thr126 bound to a chloride ion in the wild-type protein, while this interaction was lost in the S81A mutant, resulting in rotation of the Thr126 side chain and reduction in the interaction between Thr126 and a chloride ion. To confirm the role of S81, patch clamp recordings were performed using cells expressing NpHR S81A mutant protein. Considered together with the results that the NpHR S81A-expressing cells did not undergo hyperpolarization under light stimulation, our results indicate that Ser81 plays a key role in chloride migration. Our findings might be relevant to ongoing clinical trials using optogenetic gene therapy in blind patients.
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Affiliation(s)
- Yuko Sakajiri
- The United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan.
| | - Eriko Sugano
- The United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan; Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan.
| | - Yoshito Watanabe
- Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan.
| | - Tetsuya Sakajiri
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.
| | - Kitako Tabata
- Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan.
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu Shiga, 525-8577, Japan.
| | - Hiroshi Tomita
- The United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan; Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan; Clinical Research, Innovation and Education Center, Tohoku University Hospital, 1-1 Seiryo, Aoba, Sendai, Miyagi, 980-8574, Japan.
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Iwaki M, Takeshita K, Kondo HX, Kinoshita K, Okamura Y, Takano Y, Nakagawa A, Kandori H. Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP. J Phys Chem B 2018; 122:9076-9080. [DOI: 10.1021/acs.jpcb.8b04890] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Hiroko X. Kondo
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, 565-0874, Japan
| | - Kengo Kinoshita
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seityo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryocho, Aoba-ku, Sendai, 980-8575, Japan
| | | | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
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Katayama K, Furutani Y, Iwaki M, Fukuda T, Imai H, Kandori H. “In situ” observation of the role of chloride ion binding to monkey green sensitive visual pigment by ATR-FTIR spectroscopy. Phys Chem Chem Phys 2018; 20:3381-3387. [DOI: 10.1039/c7cp07277e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ATR-FTIR spectroscopic study elucidates the novel role of Cl−-binding in primate long-wavelength-sensitive (LWS) visual pigment.
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Affiliation(s)
- Kota Katayama
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Yuji Furutani
- Department of Life and Coordination-Complex Molecular Science
- Institute for Molecular Science
- Okazaki 444-8585
- Japan
| | - Masayo Iwaki
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Tetsuya Fukuda
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Hiroo Imai
- Primate Research Institute
- Kyoto University
- Inuyama 484-8506
- Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBio Technology Research Center
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Ito S, Iwaki M, Sugita S, Abe-Yoshizumi R, Iwata T, Inoue K, Kandori H. Unique Hydrogen Bonds in Membrane Protein Monitored by Whole Mid-IR ATR Spectroscopy in Aqueous Solution. J Phys Chem B 2017; 122:165-170. [PMID: 29215887 DOI: 10.1021/acs.jpcb.7b11064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein function is coupled to its structural changes, for which stimulus-induced difference Fourier-transform infrared (FTIR) spectroscopy is a powerful method. By optimizing the attenuated total reflection (ATR)-FTIR analysis on sodium-pumping rhodopsin KR2 in aqueous solution, we first measured the accurate difference spectra upon sodium binding in the whole IR region (4000-1000 cm-1). The new spectral window allows the analysis of not only the fingerprint region (1800-1000 cm-1) but also the hydrogen-bonding donor region (4000-1800 cm-1), revealing an unusually strong hydrogen bond of Tyr located in the sodium binding site of KR2. Progress in ATR-FTIR difference spectroscopy provides an approach to investigating stimulus-induced structural changes of membrane proteins under physiological aqueous conditions.
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Affiliation(s)
| | | | | | | | | | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Kandori H, Furutani Y, Murata T. Infrared spectroscopic studies on the V-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:134-41. [PMID: 25111748 DOI: 10.1016/j.bbabio.2014.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 11/27/2022]
Abstract
V-ATPase is an ATP-driven rotary motor that vectorially transports ions. Together with F-ATPase, a homologous protein, several models on the ion transport have been proposed, but their molecular mechanisms are yet unknown. V-ATPase from Enterococcus hirae forms a large supramolecular protein complex (total molecular weight: ~700,000) and physiologically transports Na⁺ and Li⁺ across a hydrophobic lipid bilayer. Stabilization of these cations in the binding site has been discussed on the basis of X-ray crystal structures of a membrane-embedded domain, the K-ring (Na⁺ and Li⁺ bound forms). Sodium or lithium ion binding-induced difference FTIR spectra of the intact E. hirae V-ATPase have been measured in aqueous solution at physiological temperature. The results suggest that sodium or lithium ion binding induces the deprotonation of Glu139, a hydrogen-bonding change in the tyrosine residue and rigid α-helical structures. Identical difference FTIR spectra between the entire V-ATPase complex and K-ring strongly suggest that protein interaction with the I subunit does not cause large structural changes in the K-ring. This result supports the previously proposed Na⁺ transport mechanism by V-ATPase stating that a flip-flop movement of a carboxylate group of Glu139 without large conformational changes in the K-ring accelerates the replacement of a Na⁺ ion in the binding site. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, 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 Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Takeshi Murata
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
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