1
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Nakamura T, Shinozaki Y, Otomo A, Urui T, Mizuno M, Abe-Yoshizumi R, Hashimoto M, Kojima K, Sudo Y, Kandori H, Mizutani Y. Unusual Vibrational Coupling of the Schiff Base in the Retinal Chromophore of Sodium Ion-Pumping Rhodopsins. J Phys Chem B 2024; 128:7813-7821. [PMID: 39090991 DOI: 10.1021/acs.jpcb.4c04466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
A Schiff base in the retinal chromophore of microbial rhodopsin is crucial to its ion transport mechanism. Here, we discovered an unprecedented isotope effect on the C═N stretching frequency of the Schiff base in sodium ion-pumping rhodopsins, showing an unusual interaction of the Schiff base. No amino acid residue attributable to the unprecedented isotope effect was identified, suggesting that the H-O-H bending vibration of a water molecule near the Schiff base was coupled with the C═N stretching vibration. A twist in the polyene chain in the chromophore for the sodium ion-pumping rhodopsins enabled this unusual interaction of the Schiff base. The present discovery provides new insights into the interaction network of the retinal chromophore in microbial rhodopsins.
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Affiliation(s)
- Taiki Nakamura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuka Shinozaki
- Department of Chemistry, School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akihiro Otomo
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Manami Hashimoto
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Keiichi Kojima
- Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Wijesiri K, Gascón JA. Structural Models of the First Molecular Events in the Heliorhodopsin Photocycle. J Phys Chem B 2024; 128:5966-5972. [PMID: 38877606 DOI: 10.1021/acs.jpcb.4c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Retinylidene conformations and rearrangements of the hydrogen-bond network in the vicinity of the protonated Schiff base (PSB) play a key role in the proton transfer process in the Heliorhodopsin photocycle. Photoisomerization of the retinylidene chromophore and the formation of photoproducts corresponding to the early intermediates were modeled using a combination of molecular dynamics simulations and quantum mechanical/molecular mechanics calculations. The resulting structures were refined, and the respective excitation energies were calculated. Aided by metadynamics simulations, we constructed a photoisomerized intermediate where the 13-cis retinylidene chromophore is rotated about a parallel pair of double bonds at C13=C14 and C15=NZ double bonds. We demonstrate how the deprotonation of the Schiff base and the concomitant protonation of the Glu107 counterion are only favored because of these rearrangements.
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Affiliation(s)
- Kithmini Wijesiri
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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3
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Urui T, Shionoya T, Mizuno M, Inoue K, Kandori H, Mizutani Y. Chromophore-Protein Interactions Affecting the Polyene Twist and π-π* Energy Gap of the Retinal Chromophore in Schizorhodopsins. J Phys Chem B 2024; 128:2389-2397. [PMID: 38433395 DOI: 10.1021/acs.jpcb.3c08465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
The properties of a prosthetic group are broadened by interactions with its neighboring residues in proteins. The retinal chromophore in rhodopsins absorbs light, undergoes structural changes, and drives functionally important structural changes in proteins during the photocycle. It is therefore crucial to understand how chromophore-protein interactions regulate the molecular structure and electronic state of chromophores in rhodopsins. Schizorhodopsin is a newly discovered subfamily of rhodopsins found in the genomes of Asgard archaea, which are extant prokaryotes closest to the last common ancestor of eukaryotes and of other microbial species. Here, we report the effects of a hydrogen bond between a retinal Schiff base and its counterion on the twist of the polyene chain and the color of the retinal chromophore. Correlations between spectral features revealed the unexpected fact that the twist of the polyene chain is reduced as the hydrogen bond becomes stronger, suggesting that the twist is caused by tight atomic contacts between the chromophore and nearby residues. In addition, the strength of the hydrogen bond is the primary factor affecting the color-tuning of the retinal chromophore in schizorhodopsins. The findings of this study are valuable for manipulating the molecular structure and electronic state of the chromophore by controlling chromophore-protein interactions.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tomomi Shionoya
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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4
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Singh M, Hashimoto M, Katayama K, Furutani Y, Kandori H. Internal Proton Transfer in the Activation of Heliorhodopsin. J Mol Biol 2024; 436:168273. [PMID: 37709010 DOI: 10.1016/j.jmb.2023.168273] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Heliorhodopsin (HeR), a recently discovered new rhodopsin family, contains a single counterion of the protonated Schiff base, E108 in HeR from Thermoplasmatales archaeon SG8-52-1 (TaHeR). Upon light absorption, the M and O intermediates form in HeRs, as well as type-1 microbial rhodopsins, indicating that the proton transfer from the Schiff base leads to the activation of HeRs. The present flash photolysis study of TaHeR in the presence of a pH-sensitive dye showed that TaHeR contains a proton-accepting group (PAG) inside protein. Comprehensive mutation study of TaHeR found the E108D mutant abolishing the M formation, which is not only at pH 8, but also at pH 9 and 10. The lack of M observation does not originate from the short lifetime of the M intermediate in E108D, as FTIR spectroscopy revealed that a red-shifted K-like intermediate is long lived in E108D. It is likely that the K-like intermediate returns to the unphotolyzed state without internal proton transfer in E108D. E108 and D108 are the Schiff base counterions of the wild-type and E108D mutant TaHeR, respectively, whereas small difference in length of side chains determine internal proton transfer reaction from the Schiff base. Based on the present finding, we propose that the internal water cluster (four water molecules) constitutes PAG in the M intermediate of TaHeR. In the wild type TaHeR, a protonated water cluster is stabilized by forming a salt bridge with E108. In contrast, slightly shortened counterion (D108) cannot stabilize the protonated water cluster in E108D, and thus impairs internal proton transfer from the Schiff base.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Masanori Hashimoto
- 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; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, 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
| | - 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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5
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Urui T, Hayashi K, Mizuno M, Inoue K, Kandori H, Mizutani Y. Cis- Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping. J Phys Chem B 2024; 128:744-754. [PMID: 38204413 DOI: 10.1021/acs.jpcb.3c07510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The creation of unidirectional ion transporters across membranes represents one of the greatest challenges in chemistry. Proton-pumping rhodopsins are composed of seven transmembrane helices with a retinal chromophore bound to a lysine side chain via a Schiff base linkage and provide valuable insights for designing such transporters. What makes these transporters particularly intriguing is the discovery of both outward and inward proton-pumping rhodopsins. Surprisingly, despite sharing identical overall structures and membrane topologies, these proteins facilitate proton transport in opposite directions, implying an underlying rational mechanism that can transport protons in different directions within similar protein structures. In this study, we unraveled this mechanism by examining the chromophore structures of deprotonated intermediates in schizorhodopsins, a recently discovered subfamily of inward proton-pumping rhodopsins, using time-resolved resonance Raman spectroscopy. The photocycle of schizorhodopsins revealed the cis-trans thermal isomerization that precedes reprotonation at the Schiff base of the retinal chromophore. Notably, this order has not been observed in other proton-pumping rhodopsins, but here, it was observed in all seven schizorhodopsins studied across the archaeal domain, strongly suggesting that cis-trans thermal isomerization preceding reprotonation is a universal feature of the schizorhodopsin family. Based on these findings, we propose a structural basis for the remarkable order of events crucial for facilitating inward proton transport. The mechanism underlying inward proton transport by schizorhodopsins is straightforward and rational. The insights obtained from this study hold great promise for the design of transmembrane unidirectional ion transporters.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kouhei Hayashi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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6
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Li Z, Mizuno M, Ejiri T, Hayashi S, Kandori H, Mizutani Y. Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins. J Phys Chem B 2023; 127:9873-9886. [PMID: 37940604 DOI: 10.1021/acs.jpcb.3c02146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.
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Affiliation(s)
- Zixuan Li
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Tomo Ejiri
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
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7
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Tomida S, Wada A, Furutani Y. Protonation of Asp116 and distortion of the all-trans retinal chromophore in Krokinobacter eikastus rhodopsin 2 causes a redshift in absorption maximum upon dehydration. Photochem Photobiol Sci 2023; 22:2499-2517. [PMID: 37498510 DOI: 10.1007/s43630-023-00464-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
Water is usually indispensable for protein function. For ion-pumping rhodopsins, water molecules inside the proteins play an important role in ion transportation. In addition to amino acid residues, water molecules regulate the colors of retinal proteins. It was reported that a sodium-pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2), showed a color change from red to purple upon dehydration under crystalline conditions. Here, we applied comprehensive visible and IR absorption spectroscopy and resonance Raman spectroscopy to KR2 in liposomes under hydration-controlled conditions. A large increase in the hydrogen-out-of-plane (HOOP) vibration at 947 (H-C11=C12-H Au mode) and moderate increases at 893 (C7-H and C10-H) and 808 (C14-H) cm-1 were observed under dehydrated conditions, which were assigned by using systematically deuterated retinal. Moreover, the Asn variant at Asp116, which functions as a counter ion for the protonated retinal Schiff base (PRSB), caused a large redshift in the absorption maximum and constitutive increase in the HOOP modes under hydrated and dehydrated conditions. The protonation of a counter ion at Asp116 clearly causes a redshift in the absorption maximum as the all-trans retinal chromophore twists upon dehydration. Namely, the results strongly suggested that water molecules are important for maintaining the hydrogen-bonding network at the PRSB and deprotonation state of Asp116 in KR2.
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Affiliation(s)
- Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Higashinada-ku, Kobe, 658-8558, 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.
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8
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Chang CF, Konno M, Inoue K, Tahara T. Effects of the Unique Chromophore-Protein Interactions on the Primary Photoreaction of Schizorhodopsin. J Phys Chem Lett 2023; 14:7083-7091. [PMID: 37527812 PMCID: PMC10424672 DOI: 10.1021/acs.jpclett.3c01133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Schizorhodopsin (SzR) is a newly discovered microbial rhodopsin subfamily, functioning as an unusual inward-proton (H+) pump upon absorbing light. Two major protein structural differences around the chromophore have been found, resulting in unique chromophore-protein interactions that may be responsible for its unusual function. Therefore, it is important to elucidate how such a difference affects the primary photoreaction dynamics. We study the primary dynamics of SzR and its C75S mutant by femtosecond time-resolved absorption (TA) spectroscopy. The obtained TA data revealed that the photoisomerization in SzR proceeds more slowly and less efficiently than typical outward H+-pumping rhodopsins and that it further slows in the C75S mutant. We performed impulsive stimulated Raman measurements to clarify the effect of the cysteine residue on the retinal chromophore and found that interactions with Cys75 flatten the retinal chromophore of wild-type SzR. We discuss the effect of the unique chromophore-cysteine interaction on the retinal isomerization dynamics and structure of SzR.
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Affiliation(s)
- Chun-Fu Chang
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Masae Konno
- The
Institute for Solid State Physics, The University
of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- PRESTO, Japan
Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Inoue
- The
Institute for Solid State Physics, The University
of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
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9
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Mizuno M, Sato K, Yamashita T, Sakai K, Imamoto Y, Yamano Y, Wada A, Ohuchi H, Shichida Y, Mizutani Y. Chromophore Structure in an Inactive State of a Novel Photosensor Protein Opn5L1: Resonance Raman Evidence for the Formation of a Deprotonated Adduct at the 11th Carbon Atom. J Phys Chem B 2023; 127:2169-2176. [PMID: 36857774 DOI: 10.1021/acs.jpcb.2c08780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Opsins are photosensitive G protein-coupled receptor proteins and are classified into visual and nonvisual receptors. Opn5L1 is a nonvisual opsin that binds all-trans retinal as a chromophore. A unique feature of Opn5L1 is that the protein exhibits a photocyclic reaction upon photoexcitation. Determining the chromophore structures of intermediates in the photocycle is essential for understanding the functional mechanism of Opn5L1. A previous study revealed that a long-lived intermediate in the photocycle cannot activate the G protein and forms a covalent bond between the retinal chromophore and a nearby cysteine residue. However, the position of this covalent bond in the chromophore remains undetermined. Here, we report a resonance Raman study on isotopically labeled samples in combination with density functional theory calculations and reveal that the 11th carbon atom of the chromophore of the intermediate forms a covalent linkage to the cysteine residue. Furthermore, vibrational assignments based on the isotopic substitutions and density functional theory calculations suggested that the Schiff base of the intermediate is deprotonated. The chromophore structure determined in the present study well explains the mechanism of the photocyclic reaction, which is crucial to the photobiological function of Opn5L1.
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Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Keita Sato
- Department of Cytology and Histology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama 700-8558, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazumi Sakai
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yasushi Imamoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yumiko Yamano
- Comprehensive Education and Research Center, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-cho, Higashinada, Kobe, Hyogo 658-8558, Japan
| | - Hideyo Ohuchi
- Department of Cytology and Histology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama 700-8558, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Research Organization for Science and Technology, Ritsumeikan University, Shiga 525-8577, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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10
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Suzuki S, Kumagai S, Nagashima T, Yamazaki T, Okitsu T, Wada A, Naito A, Katayama K, Inoue K, Kandori H, Kawamura I. Characterization of retinal chromophore and protonated Schiff base in Thermoplasmatales archaeon heliorhodopsin using solid-state NMR spectroscopy. Biophys Chem 2023; 296:106991. [PMID: 36905840 DOI: 10.1016/j.bpc.2023.106991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Heliorhodopsin (HeR) is a seven-helical transmembrane protein with a retinal chromophore that corresponds to a new rhodopsin family. HeR from the archaebacterium Thermoplasmatales archaeon (TaHeR) exhibits unique features, such as the inverted protein orientation in the membrane compared to other rhodopsins and a long photocycle. Here, we used solid-state nuclear magnetic resonance (NMR) spectroscopy to investigate the 13C and 15N NMR signals of the retinal chromophore and protonated Schiff base (RPSB) in TaHeR embedded in POPE/POPG membrane. Although the 14- and 20-13C retinal signals indicated 13-trans/15-anti (all-trans) configurations, the 20-13C chemical shift value was different from that of other microbial rhodopsins, indicating weakly steric hinderance between Phe203 and the C20 methyl group. 15N RPSB/λmax plot deviated from the linear correlation based on retinylidene-halide model compounds. Furthermore, 15N chemical shift anisotropy (CSA) suggested that Ser112 and Ser234 polar residues distinguish the electronic environment tendencies of RPSB from those of other microbial rhodopsins. Our NMR results revealed that the retinal chromophore and the RPSB in TaHeR exhibit unique electronic environments.
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Affiliation(s)
- Shibuki Suzuki
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, Japan
| | - Sari Kumagai
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, Japan
| | - Toshio Nagashima
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Toshio Yamazaki
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Takashi Okitsu
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan; Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Akira Naito
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, 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
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, 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
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Yokohama 240-8501, Japan.
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11
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Urui T, Das I, Mizuno M, Sheves M, Mizutani Y. Origin of a Double-Band Feature in the Ethylenic C═C Stretching Modes of the Retinal Chromophore in Heliorhodopsins. J Phys Chem B 2022; 126:8680-8688. [PMID: 36281583 DOI: 10.1021/acs.jpcb.2c04883] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Photoreceptor proteins play a critical role in light utilization for energy conversion and environmental sensing. Rhodopsin is a prototypical photoreceptor protein containing a retinal group that functions as a light-receptive site. It is essential to characterize the structure of the retinal chromophore because the chromophore structure, along with retinal-protein interactions, regulates which wavelengths of light are absorbed. Resonance Raman spectroscopy is a powerful tool to characterize chromophore structures in proteins. The resonance Raman spectra of heliorhodopsins, a recently discovered rhodopsin family, were previously reported to exhibit two intense ethylenic C═C stretching bands never observed for type-1 rhodopsins. Here, we show that the double-band feature in the ethylenic C═C stretching modes is not due to structural inhomogeneity but rather to the retinal polyene chain's linear structure. It contrasts with bent all-trans chromophore in type-1 rhodopsins. The linear structure of the chromophore results from weak atomic contacts between the 13-methyl group and a nearby Trp side chain, which can slow thermal reisomerization in the photocycle. It is possible that the deceleration of reisomerization increases the lifetime of the signaling intermediate for photosensory function.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76305, Israel
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76305, Israel
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
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12
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Besaw JE, Reichenwallner J, De Guzman P, Tucs A, Kuo A, Morizumi T, Tsuda K, Sljoka A, Miller RJD, Ernst OP. Low pH structure of heliorhodopsin reveals chloride binding site and intramolecular signaling pathway. Sci Rep 2022; 12:13955. [PMID: 35977989 PMCID: PMC9385722 DOI: 10.1038/s41598-022-17716-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022] Open
Abstract
Within the microbial rhodopsin family, heliorhodopsins (HeRs) form a phylogenetically distinct group of light-harvesting retinal proteins with largely unknown functions. We have determined the 1.97 Å resolution X-ray crystal structure of Thermoplasmatales archaeon SG8-52-1 heliorhodopsin (TaHeR) in the presence of NaCl under acidic conditions (pH 4.5), which complements the known 2.4 Å TaHeR structure acquired at pH 8.0. The low pH structure revealed that the hydrophilic Schiff base cavity (SBC) accommodates a chloride anion to stabilize the protonated retinal Schiff base when its primary counterion (Glu-108) is neutralized. Comparison of the two structures at different pH revealed conformational changes connecting the SBC and the extracellular loop linking helices A-B. We corroborated this intramolecular signaling transduction pathway with computational studies, which revealed allosteric network changes propagating from the perturbed SBC to the intracellular and extracellular space, suggesting TaHeR may function as a sensory rhodopsin. This intramolecular signaling mechanism may be conserved among HeRs, as similar changes were observed for HeR 48C12 between its pH 8.8 and pH 4.3 structures. We additionally performed DEER experiments, which suggests that TaHeR forms possible dimer-of-dimer associations which may be integral to its putative functionality as a light sensor in binding a transducer protein.
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Affiliation(s)
- Jessica E Besaw
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jörg Reichenwallner
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Paolo De Guzman
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Andrejs Tucs
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Anling Kuo
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Koji Tsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
- RIKEN Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo, 103-0027, Japan
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba, Ibaraki, 305-0047, Japan
| | - Adnan Sljoka
- RIKEN Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo, 103-0027, Japan.
- Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada.
| | - R J Dwayne Miller
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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13
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Fujisawa T, Kinoue K, Seike R, Kikukawa T, Unno M. Reisomerization of retinal represents a molecular switch mediating Na + uptake and release by a bacterial sodium-pumping rhodopsin. J Biol Chem 2022; 298:102366. [PMID: 35963435 PMCID: PMC9483557 DOI: 10.1016/j.jbc.2022.102366] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/27/2022] Open
Abstract
Sodium-pumping rhodopsins (NaRs) are membrane transporters that utilize light energy to pump Na+ across the cellular membrane. Within the NaRs, the retinal Schiff base chromophore absorbs light, and a photochemically induced transient state, referred to as the “O intermediate”, performs both the uptake and release of Na+. However, the structure of the O intermediate remains unclear. Here, we used time-resolved cryo-Raman spectroscopy under preresonance conditions to study the structure of the retinal chromophore in the O intermediate of an NaR from the bacterium Indibacter alkaliphilus. We observed two O intermediates, termed O1 and O2, having distinct chromophore structures. We show O1 displays a distorted 13-cis chromophore, while O2 contains a distorted all-trans structure. This finding indicated that the uptake and release of Na+ are achieved not by a single O intermediate but by two sequential O intermediates that are toggled via isomerization of the retinal chromophore. These results provide crucial structural insight into the unidirectional Na+ transport mediated by the chromophore-binding pocket of NaRs.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan.
| | - Kouta Kinoue
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Ryouhei Seike
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sappo-ro 060-0810, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan.
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14
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Wijesiri K, Gascón JA. Microsolvation Effects in the Spectral Tuning of Heliorhodopsin. J Phys Chem B 2022; 126:5803-5809. [PMID: 35894868 DOI: 10.1021/acs.jpcb.2c03672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heliorhodopsins (HeR) are a new category of heptahelical transmembrane photoactive proteins with a covalently linked all-trans retinal. The protonated Schiff base (PSB) nitrogen in the retinal is stabilized by a negatively charged counterion. It is well-known that stronger or weaker electrostatic interactions with the counterion cause a significant spectral blue- or red-shift, respectively, in both microbial and animal rhodopsins. In HeR, however, while Glu107 acts as the counterion, mutations of this residue are not directly correlated with a spectral shift. A molecular dynamics analysis revealed that a water cluster pocket produces a microsolvation effect on the Schiff base, compensating to various extents the replacement of the native counterion. Using a combination of molecular dynamics and quantum mechanical/molecular mechanics (QM/MM), we study this microsolvation effect on the electronic absorption of the retinylidene Schiff base chromophore of HeR.
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Affiliation(s)
- Kithmini Wijesiri
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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15
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Abstract
Vibrational spectroscopy such as FTIR and Raman spectroscopy is a powerful, sensitive, and informative method for studying protein structural changes in rhodopsins during their functions. The usefulness has been historically proven for the study of bacteriorhodopsin and bovine rhodopsin before their structural determination of rhodopsins. We now have atomic structures of many animal and microbial rhodopsins, and it is now important to know the structural dynamics of rhodopsins for function. FTIR and Raman spectroscopy provides useful information for this aim. In this chapter, we introduce the methods of FTIR and resonance Raman spectroscopy applied to rhodopsins. These vibrational methods offer deeper understanding on the mechanism how rhodopsins change their structures for function.
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Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
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16
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Shionoya T, Singh M, Mizuno M, Kandori H, Mizutani Y. Strongly Hydrogen-Bonded Schiff Base and Adjoining Polyene Twisting in the Retinal Chromophore of Schizorhodopsins. Biochemistry 2021; 60:3050-3057. [PMID: 34601881 DOI: 10.1021/acs.biochem.1c00529] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A transmembrane proton gradient is generated and maintained by proton pumps in a cell. Metagenomics studies have recently identified a new category of rhodopsin intermediates between type-1 rhodopsins and heliorhodopsins, named schizorhodopsins (SzRs). SzRs are light-driven inward proton pumps. Comprehensive resonance Raman measurements were conducted to characterize the structure of the retinal chromophore in the unphotolyzed state of four SzRs. The spectra of all four SzRs show that the retinal chromophore is in the all-trans and 15-anti configuration and that the Schiff base is protonated. The polyene chain is planar in the center of the retinal chromophore and is twisted in the vicinity of the protonated Schiff base. The protonated Schiff base in the SzRs forms a stronger hydrogen bond than that in outward proton-pumping rhodopsins. We determined that the hydrogen-bonding partner of the protonated Schiff base is not a water molecule but an amino acid residue, presumably an Asp residue in helix G. The present observations provide valuable insights into the inward proton-pumping mechanism of SzRs.
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Affiliation(s)
- Tomomi Shionoya
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, 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
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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17
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Das I, Pushkarev A, Sheves M. Light-Induced Conformational Alterations in Heliorhodopsin Triggered by the Retinal Excited State. J Phys Chem B 2021; 125:8797-8804. [PMID: 34342994 PMCID: PMC8389987 DOI: 10.1021/acs.jpcb.1c04551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Heliorhodopsins are a recently discovered
diverse retinal protein
family with an inverted topology of the opsin where the retinal protonated
Schiff base proton is facing the cell cytoplasmic side in contrast
to type 1 rhodopsins. To explore whether light-induced retinal double-bond
isomerization is a prerequisite for triggering protein conformational
alterations, we utilized the retinal oxime formation reaction and
thermal denaturation of a native heliorhodopsin of Thermoplasmatales archaeon SG8-52-1 (TaHeR) as well
as a trans-locked retinal analogue (TaHeRL) in which the critical C13=C14 double-bond
isomerization is prevented. We found that both reactions are light-accelerated
not only in the native but also in the “locked” pigment
despite lacking any isomerization. It is suggested that light-induced
charge redistribution in the retinal excited state polarizes the protein
and triggers protein conformational perturbations that thermally decay
in microseconds. The extracted activation energy and the frequency
factor for both the reactions reveal that the light enhancement of
TaHeR differs distinctly from the earlier studied type 1 microbial
rhodopsins.
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Affiliation(s)
- Ishita Das
- Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alina Pushkarev
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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18
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Abstract
Microbial rhodopsins are diverse photoreceptive proteins containing a retinal chromophore and are found in all domains of cellular life and are even encoded in genomes of viruses. These rhodopsins make up two families: type 1 rhodopsins and the recently discovered heliorhodopsins. These families have seven transmembrane helices with similar structures but opposing membrane orientation. Microbial rhodopsins participate in a portfolio of light-driven energy and sensory transduction processes. In this review we present data collected over the last two decades about these rhodopsins and describe their diversity, functions, and biological and ecological roles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; ,
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581, Japan;
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan;
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; ,
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19
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Tomida S, Kitagawa S, Kandori H, Furutani Y. Inverse Hydrogen-Bonding Change Between the Protonated Retinal Schiff Base and Water Molecules upon Photoisomerization in Heliorhodopsin 48C12. J Phys Chem B 2021; 125:8331-8341. [PMID: 34292728 DOI: 10.1021/acs.jpcb.1c01907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heliorhodopsin (HeR) is a new class of the rhodopsin family discovered in 2018 through functional metagenomic analysis (named 48C12). Similar to typical microbial rhodopsins, HeR possesses seven transmembrane (TM) α-helices and an all-trans-retinal covalently bonded to the lysine residue on TM7 via a protonated Schiff base. Remarkably, the HeR membrane topology is inverted compared with that of typical microbial rhodopsins. The X-ray crystal structure of HeR 48C12 was elucidated after the first report on a HeR variant from Thermoplasmatales archaeon SG8-52-1, which revealed the water-mediated hydrogen-bonding network connected to the Schiff base region in the cytoplasmic side. Herein, low-temperature light-induced FTIR spectroscopic analyses of HeR 48C12 and 15N isotopically labeled proteins were used to elucidate the structural changes during retinal photoisomerization. N-D stretching vibrations of the protonated retinal Schiff base (PRSB) at 2286 and 2302 cm-1 in the dark state, and 2239 and 2252 cm-1 in the K intermediate were observed. The frequency changes indicated that the hydrogen bond of PRSB strengthens upon photoisomerization in HeR. Moreover, O-D stretching vibration frequencies of the internal water molecules indicate that the hydrogen-bonding strength decreases concomitantly. Therefore, the PRSB hydrogen bond responds to photoisomerization in an opposite way to the hydrogen-bonding network involving water molecules. No frequency changes of the indole N-H or N-D stretching vibrations of tryptophan residues were observed upon photoisomerization, suggesting that all tryptophan residues in the HeR 48C12 maintained the hydrogen-bonding strengths in the K intermediate. These results provide insights into the molecular mechanism of the energy storage and propagation upon retinal photoisomerization in HeR.
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Affiliation(s)
- Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shinya Kitagawa
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, 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
| | - 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
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20
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Urui T, Mizuno M, Otomo A, Kandori H, Mizutani Y. Resonance Raman Determination of Chromophore Structures of Heliorhodopsin Photointermediates. J Phys Chem B 2021; 125:7155-7162. [PMID: 34167296 DOI: 10.1021/acs.jpcb.1c04010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Light is utilized as energy or information by rhodopsins (membrane proteins that contain a retinal chromophore). Heliorhodopsins (HeRs) are a new class of rhodopsins with low sequence identity (<15%) to microbial and animal rhodopsins. Their physiological roles remain unknown, although the involvement of a long-lived intermediate in the photocycle suggests a light-sensor function. Characterization of the molecular structures of the intermediates is essential to an understanding of the roles and mechanisms of HeRs. We determined the chromophore structures of the intermediates in HeR 48C12 by time-resolved resonance Raman spectroscopy and observed that the hydrogen bond of the protonated Schiff base strengthened prior to deprotonation. The chromophore is photoisomerized from the all-trans to the 13-cis form and is reisomerized in the transition from the O intermediate to the unphotolyzed state. Our results demonstrate that the chromophore structure evolves similarly to microbial rhodopsins, despite the dissimilarity in amino acid residues surrounding the chromophore.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akihiro Otomo
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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21
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Nakamizo Y, Fujisawa T, Kikukawa T, Okamura A, Baba H, Unno M. Low-temperature Raman spectroscopy of sodium-pump rhodopsin from Indibacter alkaliphilus: insight of Na + binding for active Na + transport. Phys Chem Chem Phys 2021; 23:2072-2079. [PMID: 33433533 DOI: 10.1039/d0cp05652a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We carried out the low-temperature Raman measurement of a sodium pump rhodopsin from Indibacter alkaliphilus (IaNaR) and examined the primary structural change for the light-driven Na+ pump. We observed that photoexcitation of IaNaR produced the distorted 13-cis retinal chromophore in the presence of Na+, while the structural distortion was significantly relaxed in the absence of Na+. This structural difference of the chromophore with/without Na+ was attributed to the Na+ binding to the protein, which alters the active site. Using the spectral sensitivity to the ion binding, we found that IaNaR had a second Na+ binding site in addition to the one already specified on the extracellular surface. To date, the Na+ binding has not been considered as a prerequisite for Na+ transport. However, this study provides insight that the protein structural change induced by the ion binding involved the formation of an R108-D250 salt bridge, which has critical importance in the active transport of Na+.
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Affiliation(s)
- Yushi Nakamizo
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan.
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22
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Abstract
Schizorhodopsins (SzRs), a new rhodopsin family identified in Asgard archaea, are phylogenetically located at an intermediate position between type-1 microbial rhodopsins and heliorhodopsins. SzRs work as light-driven inward H+ pumps as xenorhodopsins in bacteria. Although E81 plays an essential role in inward H+ release, the H+ is not metastably trapped in such a putative H+ acceptor, unlike the other H+ pumps. It remains elusive why SzR exhibits different kinetic behaviors in H+ release. Here, we report the crystal structure of SzR AM_5_00977 at 2.1 Å resolution. The SzR structure superimposes well on that of bacteriorhodopsin rather than heliorhodopsin, suggesting that SzRs are classified with type-1 rhodopsins. The structure-based mutagenesis study demonstrated that the residues N100 and V103 around the β-ionone ring are essential for color tuning in SzRs. The cytoplasmic parts of transmembrane helices 2, 6, and 7 are shorter than those in the other microbial rhodopsins, and thus E81 is located near the cytosol and easily exposed to the solvent by light-induced structural change. We propose a model of untrapped inward H+ release; H+ is released through the water-mediated transport network from the retinal Schiff base to the cytosol by the side of E81. Moreover, most residues on the H+ transport pathway are not conserved between SzRs and xenorhodopsins, suggesting that they have entirely different inward H+ release mechanisms.
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23
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Tanaka T, Singh M, Shihoya W, Yamashita K, Kandori H, Nureki O. Structural basis for unique color tuning mechanism in heliorhodopsin. Biochem Biophys Res Commun 2020; 533:262-267. [PMID: 32951839 DOI: 10.1016/j.bbrc.2020.06.124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
Microbial rhodopsins comprise an opsin protein with seven transmembrane helices and a retinal as the chromophore. An all-trans retinal is covalently bonded to a lysine residue through the retinal Schiff base (RSB) and stabilized by a negatively charged counterion. The distance between the RSB and counterion is closely related to the light energy absorption. However, in heliorhodopsin-48C12 (HeR-48C12), while E107 acts as the counterion, E107D mutation exhibits an identical absorption spectrum to the wild-type, suggesting that the distance does not affect its absorption spectra. Here we present the 2.6 Å resolution crystal structure of the Thermoplasmatales archaeon HeR E108D mutant, which also has an identical absorption spectrum to the wild-type. The structure revealed that D108 does not form a hydrogen bond with the RSB, and its counterion interaction becomes weaker. Alternatively, the serine cluster, S78, S112, and S238 form a distinct interaction network around the RSB. The absorption spectra of the E to D and S to A double mutants suggested that S112 influences the spectral shift by compensating for the weaker counterion interaction. Our structural and spectral studies have revealed the unique spectral shift mechanism of HeR and clarified the physicochemical properties of HeRs.
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Affiliation(s)
- Tatsuki Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
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24
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Ikuta T, Shihoya W, Sugiura M, Yoshida K, Watari M, Tokano T, Yamashita K, Katayama K, Tsunoda SP, Uchihashi T, Kandori H, Nureki O. Structural insights into the mechanism of rhodopsin phosphodiesterase. Nat Commun 2020; 11:5605. [PMID: 33154353 PMCID: PMC7644710 DOI: 10.1038/s41467-020-19376-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase and photosensitive adenylyl cyclase. Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The crystal structure of the rhodopsin domain at 2.6 Å resolution revealed a new topology of rhodopsins, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the rhodopsin domain (3.5 Å) and PDE domain (2.1 Å) with their connecting linkers, which showed a rough sketch of the full-length Rh-PDE. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.
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Affiliation(s)
- Tatsuya Ikuta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Kazuho Yoshida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Masahito Watari
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Takaya Tokano
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, 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
| | - Satoshi P Tsunoda
- 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
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, 444-8787, 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.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
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25
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Kandori H. Retinal Proteins: Photochemistry and Optogenetics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190292] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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26
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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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27
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Otomo A, Mizuno M, Inoue K, Kandori H, Mizutani Y. Allosteric Communication with the Retinal Chromophore upon Ion Binding in a Light-Driven Sodium Ion-Pumping Rhodopsin. Biochemistry 2020; 59:520-529. [PMID: 31887021 DOI: 10.1021/acs.biochem.9b01062] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Krokinobacter rhodopsin 2 (KR2) serves as a light-driven sodium ion pump in the presence of sodium ion and works as a proton pump in the presence of larger monovalent cations such as potassium ion, rubidium ion, and cesium ion. Recent crystallographic studies revealed that KR2 forms a pentamer and possesses an ion binding site at the subunit interface. It is assumed that sodium ion bound at this binding site is not transported but contributes to the thermal stability. Because KR2 can convert its function in response to coexisting cation species, this ion binding site is likely to be involved in ion transport selectively. However, how sodium ion binding affects the structure of the retinal chromophore, which plays a crucial role in ion transport, remains poorly understood. Here, we observed the structure of the retinal chromophore under a wide range of cation concentrations using visible absorption and resonance Raman spectroscopy. We discovered that the hydrogen bond formed between the Schiff base of the retinal chromophore and its counterion, Asp116, is weakened upon binding of sodium ion. This allosteric communication between the Schiff base and the ion binding site at the subunit interface likely increases the apparent efficiency of sodium ion transport. In addition, this study demonstrates the significance of sodium ion binding: even though sodium ion is not transported, binding regulates the structure around the Schiff base and stabilizes the oligomeric structure.
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Affiliation(s)
- Akihiro Otomo
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo , Kashiwa 277-8581 , Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan.,OptoBio Technology Research Center , Nagoya Institute of Technology , Showa-Ku, Nagoya 466-8555 , Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
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28
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Fujisawa T, Kiyota H, Kikukawa T, Unno M. Low-Temperature Raman Spectroscopy of Halorhodopsin from Natronomonas pharaonis: Structural Discrimination of Blue-Shifted and Red-Shifted Photoproducts. Biochemistry 2019; 58:4159-4167. [PMID: 31538771 DOI: 10.1021/acs.biochem.9b00643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
From the low-temperature absorption and Raman measurements of halorhodopsin from Natronomonas pharaonis (pHR), we observed that the two photoproducts were generated after exciting pHR at 80 K by green light. One photoproduct was the red-shifted K intermediate (pHRK) as the primary photointermediate for Cl- pumping, and the other was the blue-shifted one (pHRhypso), which was not involved in the Cl- pumping and thermally relaxed to the original unphotolyzed state by increasing temperature. The formation of these two kinds of photoproducts was previously reported for halorhodopsin from Halobacterium sarinarum [ Zimanyi et al. Biochemistry 1989 , 28 , 1656 ]. We found that the same took place in pHR, and we revealed the chromophore structures of the two photointermediates from their Raman spectra for the first time. pHRhypso had the distorted all-trans chromophore, while pHRK contained the distorted 13-cis form. The present results revealed that the structural analyses of pHRK carried out so far at ∼80 K potentially included a significant contribution from pHRhypso. pHRhypso was efficiently formed via the photoexcitation of pHRK, indicating that pHRhypso was likely a side product after photoexcitation of pHRK. The formation of pHRhypso suggested that the active site became tight in pHRK due to the slight movement of Cl-, and the back photoisomerization then produced the distorted all-trans chromophore in pHRhypso.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Hayato Kiyota
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science , Hokkaido University , Sapporo 060-0810 , Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education , Hokkaido University , Sapporo 060-0810 , Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
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29
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Shihoya W, Inoue K, Singh M, Konno M, Hososhima S, Yamashita K, Ikeda K, Higuchi A, Izume T, Okazaki S, Hashimoto M, Mizutori R, Tomida S, Yamauchi Y, Abe-Yoshizumi R, Katayama K, Tsunoda SP, Shibata M, Furutani Y, Pushkarev A, Béjà O, Uchihashi T, Kandori H, Nureki O. Crystal structure of heliorhodopsin. Nature 2019; 574:132-136. [DOI: 10.1038/s41586-019-1604-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 08/20/2019] [Indexed: 11/10/2022]
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30
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Shibukawa A, Kojima K, Nakajima Y, Nishimura Y, Yoshizawa S, Sudo Y. Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with Heliorhodopsin-48C12. Biochemistry 2019; 58:2934-2943. [DOI: 10.1021/acs.biochem.9b00257] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Atsushi Shibukawa
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Yu Nakajima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Yosuke Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8563, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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31
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Pedraza-González L, De Vico L, del Carmen Marín M, Fanelli F, Olivucci M. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement. J Chem Theory Comput 2019; 15:3134-3152. [PMID: 30916955 PMCID: PMC7141608 DOI: 10.1021/acs.jctc.9b00061] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild type and mutant rhodopsins. However, in its present version, input preparation requires a few hours long user's manipulation of the template protein structure, which also impairs the reproducibility of the generated models. This limitation, which makes model building semiautomatic rather than fully automatic, comprises four tasks: definition of the retinal chromophore cavity, assignment of protonation states of the ionizable residues, neutralization of the protein with external counterions, and finally congruous generation of single or multiple mutations. In this work, we show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input preparation time of minutes. The new protocol, called a-ARM, delivers fully reproducible (i.e., user independent) rhodopsin QM/MM models as well as an improved model quality. More specifically, we show that the trend in vertical excitation energies observed for a set of 25 wild type and 14 mutant rhodopsins is predicted by the new protocol better than when using the original. Such an agreement is reflected by an estimated (relative to the probed set) trend deviation of 0.7 ± 0.5 kcal mol-1 (0.03 ± 0.02 eV) and mean absolute error of 1.0 kcal mol-1 (0.04 eV).
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Affiliation(s)
- Laura Pedraza-González
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - María del Carmen Marín
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, I-41125 Modena, Italy
| | - Massimo Olivucci
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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32
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Tahara S, Singh M, Kuramochi H, Shihoya W, Inoue K, Nureki O, Béjà O, Mizutani Y, Kandori H, Tahara T. Ultrafast Dynamics of Heliorhodopsins. J Phys Chem B 2019; 123:2507-2512. [DOI: 10.1021/acs.jpcb.9b00887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shinya Tahara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Oded Béjà
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, 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
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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33
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Singh M, Katayama K, Béjà O, Kandori H. Anion binding to mutants of the Schiff base counterion in heliorhodopsin 48C12. Phys Chem Chem Phys 2019; 21:23663-23671. [DOI: 10.1039/c9cp04102h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The anion binds as the direct H-bonding acceptor of the Schiff base in E107A, while E107Q indirectly accommodates an anion.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
| | - Oded Béjà
- Faculty of Biology
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
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