1
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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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2
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Lim Y, Seo JH, Giovannoni SJ, Kang I, Cho JC. Cultivation of marine bacteria of the SAR202 clade. Nat Commun 2023; 14:5098. [PMID: 37607927 PMCID: PMC10444878 DOI: 10.1038/s41467-023-40726-8] [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: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023] Open
Abstract
Bacteria of the SAR202 clade, within the phylum Chloroflexota, are ubiquitously distributed in the ocean but have not yet been cultivated in the lab. It has been proposed that ancient expansions of catabolic enzyme paralogs broadened the spectrum of organic compounds that SAR202 bacteria could oxidize, leading to transformations of the Earth's carbon cycle. Here, we report the successful cultivation of SAR202 bacteria from surface seawater using dilution-to-extinction culturing. The growth of these strains is very slow (0.18-0.24 day-1) and is inhibited by exposure to light. The genomes, of ca. 3.08 Mbp, encode archaella (archaeal motility structures) and multiple sets of enzyme paralogs, including 80 genes coding for enolase superfamily enzymes and 44 genes encoding NAD(P)-dependent dehydrogenases. We propose that these enzyme paralogs participate in multiple parallel pathways for non-phosphorylative catabolism of sugars and sugar acids. Indeed, we demonstrate that SAR202 strains can utilize several substrates that are metabolized through the predicted pathways, such as sugars ʟ-fucose and ʟ-rhamnose, as well as their lactone and acid forms.
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Affiliation(s)
- Yeonjung Lim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
- Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea
| | - Ji-Hui Seo
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | | | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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3
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Chiba Y, Tsujimura M, Saito K, Ishikita H. pH-Dependent Binding and Releasing Mechanism of Acetate in the Inner Water Cavity of Heliorhodopsin. Biochemistry 2023; 62:2363-2370. [PMID: 37471424 PMCID: PMC10434121 DOI: 10.1021/acs.biochem.3c00193] [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: 04/14/2023] [Revised: 06/28/2023] [Indexed: 07/22/2023]
Abstract
The high-resolution structure of heliorhodopsin crystallized at low pH reveals the presence of a planar triangle molecule, acetate, in the inner water cavity. Here, we investigate how the acetate molecule is stabilized at the counterion Glu107 moiety, using molecular dynamics (MD) simulations and a quantum mechanical/molecular mechanical (QM/MM) approach. QM/MM calculations indicate that the density is best described as acetate among triangle acids, including nitric acid and bicarbonate. The calculated protonation state indicates that protonated acetate donates an H-bond to deprotonated Glu107 in the low-pH crystal structure. The observed red-shift of ∼30 nm in the absorption wavelength with pKa ≈ 4 is likely due to the His23/His80 protonation, rather than the Glu107 protonation. MD simulations also show that acetate can exist at the Glu107 moiety only when it is protonated. When ionized, acetate is released from the Glu107 moiety via Asn101 at the channel bottleneck and Arg91 on the intracellular protein surface. These observations could explain how acetate binds at low pH and releases at high pH.
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Affiliation(s)
- Yoshihiro Chiba
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Masaki Tsujimura
- Department
of Advanced Interdisciplinary Studies, The
University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keisuke Saito
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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4
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Ganapathy S, Meng X, Mossel D, Jagt M, Brinks D. Expanding the family of genetically encoded voltage indicators with a candidate Heliorhodopsin exhibiting near-infrared fluorescence. J Biol Chem 2023; 299:104771. [PMID: 37127067 DOI: 10.1016/j.jbc.2023.104771] [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: 11/17/2022] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/03/2023] Open
Abstract
Genetically encoded voltage indicators (GEVIs), particularly those based on microbial rhodopsins, are gaining traction in neuroscience as fluorescent sensors for imaging voltage dynamics with high-spatiotemporal precision. Here we establish a novel GEVI candidate based on the recently discovered subfamily of the microbial rhodopsin clade, termed heliorhodopsins. We discovered that upon excitation at 530-560nm, wild type heliorhodopsin exhibits near infra-red fluorescence which is sensitive to membrane voltage. We characterized the fluorescence brightness, photostability, voltage sensitivity and kinetics of wild type heliorhodopsin in HEK293T cells and further examined the impact of mutating key residues near the retinal chromophore. The S237A mutation significantly improved the fluorescence response of heliorhodopsin by 76% providing a highly promising starting point for further protein evolution.
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Affiliation(s)
- Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands; Department of Pediatrics & Cellular and Molecular Medicine, UCSD School of Medicine, San Diego, USA
| | - Xin Meng
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Delizzia Mossel
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Mels Jagt
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Daan Brinks
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands; Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
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5
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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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6
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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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7
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Tsujimura M, Chiba Y, Saito K, Ishikita H. Proton transfer and conformational changes along the hydrogen bond network in heliorhodopsin. Commun Biol 2022; 5:1336. [PMID: 36474019 PMCID: PMC9726877 DOI: 10.1038/s42003-022-04311-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Heliorhodopsin releases a proton from the Schiff base during the L-state to M-state transition but not toward the protein bulk surface. Here we investigate proton transfer and induced structural changes along the H-bond network in heliorhodopsin using a quantum mechanical/molecular mechanical approach and molecular dynamics simulations. Light-induced proton transfer could occur from the Schiff base toward Glu107, reorienting Ser76, followed by subsequent proton transfer toward His80. His80 protonation induces the reorientation of Trp246 on the extracellular surface, originating from the electrostatic interaction that propagates along the transmembrane H-bond network [His80…His23…H2O[H23/Q26]…Gln26…Trp246] over a distance of 15 Å. Furthermore, it induces structural fluctuation on the intracellular side in the H-bond network [His80…Asn16…Tyr92…Glu230…Arg104…Glu149], opening the inner cavity at the Tyr92 moiety. These may be a basis of how light-induced proton transfer causes conformational changes during the M-state to O-state transition.
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Affiliation(s)
- Masaki Tsujimura
- grid.26999.3d0000 0001 2151 536XDepartment of Advanced Interdisciplinary Studies, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan
| | - Yoshihiro Chiba
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan
| | - Keisuke Saito
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan ,grid.26999.3d0000 0001 2151 536XResearch Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan
| | - Hiroshi Ishikita
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan ,grid.26999.3d0000 0001 2151 536XResearch Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan
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8
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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] [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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9
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Yu CH, Wu HY, Lin HS, Yang CS. A conserved Trp residue in HwBR contributes to its unique tolerance toward acidic environments. Biophys J 2022; 121:3136-3145. [PMID: 35808832 PMCID: PMC9463644 DOI: 10.1016/j.bpj.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/10/2022] [Accepted: 07/06/2022] [Indexed: 11/20/2022] Open
Abstract
Bacteriorhodopsin (BR) is a light-driven outward proton pump found mainly in halophilic archaea. A BR from an archaeon Haloquadratum walsbyi (HwBR) was found to pump protons under more acidic conditions compared with most known BR proteins. The atomic structural study on HwBR unveiled that a pair of hydrogen bonds between the BC and FG loop in its periplasmic region may be a factor in such improved pumping capability. Here, we further investigated the retinal-binding pocket of HwBR and found that Trp94 contributes to the higher acid tolerance. Through single mutations in a BR from Halobacterium salinarum and HwBR, we examined the conserved tryptophan residues in the retinal-binding pocket. Among these residues of HwBR, mutagenesis at Trp94 facing the periplasmic region caused the most significant disruption to optical stability and proton-pumping capability under acidic conditions. The other tryptophan residues of HwBR exerted little impact on both maximum absorption wavelength and pH-dependent proton pumping. Our findings suggest that the residues from Trp94 to the hydrogen bonds at the BC loop confer both optical stability and functionality on the overall protein in low-pH environments.
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Affiliation(s)
- Cheng-Han Yu
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Hsiang-Yu Wu
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Hong-Syuan Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chii-Shen Yang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan.
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10
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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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11
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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12
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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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13
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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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14
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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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15
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Abstract
Microbial rhodopsins are distributed through many microorganisms. Heliorhodopsins are newly discovered but have an unclear function. They have seven transmembrane helices similar to type-I and type-II rhodopsins, but they are different in that the N-terminal region of heliorhodopsin is cytoplasmic. We chose 13 representative heliorhodopsins from various microorganisms, expressed and purified with an N-terminal His tag, and measured the absorption spectra. The 13 natural variants had an absorption maximum (λmax) in the range 530–556 nm similar to proteorhodopsin (λmax = 490–525 nm). We selected several candidate residues that influence rhodopsin color-tuning based on sequence alignment and constructed mutants via site-directed mutagenesis to confirm the spectral changes. We found two important residues located near retinal chromophore that influence λmax. We also predict the 3D structure via homology-modeling of Thermoplasmatales heliorhodopsin. The results indicate that the color-tuning mechanism of type-I rhodopsin can be applied to understand the color-tuning of heliorhodopsin.
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16
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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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17
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Abstract
Heliorhodopsin (HeR), a recently discovered new rhodopsin family, has an inverted membrane topology compared to animal and microbial rhodopsins, and no ion-transport activity. The slow photocycle of HeRs suggests a light-sensor function, although the function remains unknown. HeRs exhibit no specific binding of monovalent cations or anions. Despite this, ATR-FTIR spectroscopy in the present study demonstrates binding of Zn2+ to HeR from Thermoplasmatales archaeon (TaHeR). The biding of Zn2+ to 0.2 mM Kd is accompanied by helical structural perturbations without altering its color. Even though ion-specific FTIR spectra were observed for many divalent cations, only helical structural perturbations were observed for Zn2+-binding. Similar results were obtained for HeR 48C12. These findings suggest a possible modification of HeR function by Zn2+.
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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
| | - 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
| | - 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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18
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Sugiura M, Tsunoda SP, Hibi M, Kandori H. Molecular Properties of New Enzyme Rhodopsins with Phosphodiesterase Activity. ACS OMEGA 2020; 5:10602-10609. [PMID: 32426619 PMCID: PMC7227045 DOI: 10.1021/acsomega.0c01113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/02/2020] [Indexed: 05/08/2023]
Abstract
The choanoflagellate Salpingoeca rosetta contains a chimeric rhodopsin protein composed of an N-terminal rhodopsin (Rh) domain and a C-terminal cyclic nucleotide phosphodiesterase (PDE) domain. The Rh-PDE enzyme (SrRh-PDE), which decreases the concentrations of cyclic nucleotides such as cGMP and cAMP in light, is a useful tool in optogenetics. Recently, eight additional Rh-PDE enzymes were found in choanoflagellate species, four from Choanoeca flexa and the other four from other species. In this paper, we studied the molecular properties of these new Rh-PDEs, which were compared with SrRh-PDE. Upon expression in HEK293 cells, four Rh-PDE proteins, including CfRh-PDE2 and CfRh-PDE3, exhibited no PDE activity when assessed by in-cell measurements and in vitro HPLC analysis. On the other hand, CfRh-PDE1 showed light-dependent PDE activity toward cGMP, which absorbed maximally at 491 nm. Therefore, CfRh-PDE1 is presumably responsible for colony inversion in C. flexa by absorbing blue-green light. The molecular properties of MrRh-PDE were similar to those of SrRh-PDE, although the λmax of MrRh-PDE (516 nm) was considerably red-shifted from that of SrRh-PDE (492 nm). One Rh-PDE, AsRh-PDE, did not contain the retinal-binding Lys at TM7 and showed cAMP-specific PDE activity both in the dark and light. These results provide mechanistic insight into rhodopsin-mediated, light-dependent regulation of second-messenger levels in eukaryotic microbes.
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Affiliation(s)
- Masahiro Sugiura
- Department
of Life Science and Applied Chemistry, 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
- PRESTO, Japan
Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masahiko Hibi
- Division
of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, 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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19
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Kovalev K, Volkov D, Astashkin R, Alekseev A, Gushchin I, Haro-Moreno JM, Chizhov I, Siletsky S, Mamedov M, Rogachev A, Balandin T, Borshchevskiy V, Popov A, Bourenkov G, Bamberg E, Rodriguez-Valera F, Büldt G, Gordeliy V. High-resolution structural insights into the heliorhodopsin family. Proc Natl Acad Sci U S A 2020; 117:4131-4141. [PMID: 32034096 PMCID: PMC7049168 DOI: 10.1073/pnas.1915888117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Rhodopsins are the most abundant light-harvesting proteins. A new family of rhodopsins, heliorhodopsins (HeRs), has recently been discovered. Unlike in the known rhodopsins, in HeRs the N termini face the cytoplasm. The function of HeRs remains unknown. We present the structures of the bacterial HeR-48C12 in two states at the resolution of 1.5 Å, which highlight its remarkable difference from all known rhodopsins. The interior of HeR's extracellular part is completely hydrophobic, while the cytoplasmic part comprises a cavity (Schiff base cavity [SBC]) surrounded by charged amino acids and containing a cluster of water molecules, presumably being a primary proton acceptor from the Schiff base. At acidic pH, a planar triangular molecule (acetate) is present in the SBC. Structure-based bioinformatic analysis identified 10 subfamilies of HeRs, suggesting their diverse biological functions. The structures and available data suggest an enzymatic activity of HeR-48C12 subfamily and their possible involvement in fundamental redox biological processes.
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Affiliation(s)
- K Kovalev
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Institute of Crystallography, University of Aachen (Rheinisch-Westfälische Technische Hochschule Aachen [RWTH]), 52062 Aachen, Germany
| | - D Volkov
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - R Astashkin
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - A Alekseev
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Institute of Crystallography, University of Aachen (Rheinisch-Westfälische Technische Hochschule Aachen [RWTH]), 52062 Aachen, Germany
| | - I Gushchin
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - J M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, 03202 San Juan de Alicante, Spain
| | - I Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - S Siletsky
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M Mamedov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - A Rogachev
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - T Balandin
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - V Borshchevskiy
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - A Popov
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - G Bourenkov
- Hamburg Unit care of Deutsches Elektronen-Synchrotron (DESY), European Molecular Biology Laboratory, 22607 Hamburg, Germany
| | - E Bamberg
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Biophysical Chemistry, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - F Rodriguez-Valera
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, 03202 San Juan de Alicante, Spain
| | - G Büldt
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - V Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France;
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
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20
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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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21
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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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22
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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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23
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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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24
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Watari M, Ikuta T, Yamada D, Shihoya W, Yoshida K, Tsunoda SP, Nureki O, Kandori H. Spectroscopic study of the transmembrane domain of a rhodopsin-phosphodiesterase fusion protein from a unicellular eukaryote. J Biol Chem 2019; 294:3432-3443. [PMID: 30622140 DOI: 10.1074/jbc.ra118.006277] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/31/2018] [Indexed: 02/02/2023] Open
Abstract
The choanoflagellate Salpingoeca rosetta contains a chimeric rhodopsin protein composed of an N-terminal rhodopsin (Rh) domain and a C-terminal cyclic nucleotide phosphodiesterase (PDE) domain. The Rh-PDE enzyme light-dependently decreases the concentrations of cyclic nucleotides such as cGMP and cAMP. Photoexcitation of purified full-length Rh-PDE yields an "M" intermediate with a deprotonated Schiff base, and its recovery is much faster than that of the enzyme domain. To gain structural and mechanistic insights into the Rh domain, here we expressed and purified the transmembrane domain of Rh-PDE, Rh-PDE(TMD), and analyzed it with transient absorption, light-induced difference UV-visible, and FTIR spectroscopy methods. These analyses revealed that the "K" intermediate forms within 0.005 ms and converts into the M intermediate with a time constant of 4 ms, with the latter returning to the original state within 4 s. FTIR spectroscopy revealed that all-trans to 13-cis photoisomerization occurs as the primary event during which chromophore distortion is located at the middle of the polyene chain, allowing the Schiff base to form a stronger hydrogen bond. We also noted that the peptide backbone of the α-helix becomes deformed upon M intermediate formation. Results from site-directed mutagenesis suggested that Glu-164 is protonated and that Asp-292 acts as the only Schiff base counterion in Rh-PDE. A strong reduction of enzymatic activity in a D292N variant, but not in an E164Q variant, indicated an important catalytic role of the negative charge at Asp-292. Our findings provide further mechanistic insights into rhodopsin-mediated, light-dependent regulation of second-messenger levels in eukaryotic microbes.
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Affiliation(s)
- Masahito Watari
- From the Department of Life Science and Applied Chemistry and
| | - Tatsuya Ikuta
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Daichi Yamada
- From the Department of Life Science and Applied Chemistry and
| | - Wataru Shihoya
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Kazuho Yoshida
- From the Department of Life Science and Applied Chemistry and
| | - Satoshi P Tsunoda
- From the Department of Life Science and Applied Chemistry and.,the 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
| | - Osamu Nureki
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Hideki Kandori
- From the Department of Life Science and Applied Chemistry and .,the OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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25
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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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26
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Otomo A, Mizuno M, Singh M, Shihoya W, Inoue K, Nureki O, Béjà O, Kandori H, Mizutani Y. Resonance Raman Investigation of the Chromophore Structure of Heliorhodopsins. J Phys Chem Lett 2018; 9:6431-6436. [PMID: 30351947 DOI: 10.1021/acs.jpclett.8b02741] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Heliorhodopsins (HeRs) are a new category of retinal-bound proteins recently discovered through functional metagenomics analysis that exhibit obvious differences from type-1 microbial rhodopsins. We conducted the first detailed structural characterization of the retinal chromophore in HeRs using resonance Raman spectroscopy. The observed spectra clearly show that the Schiff base of the chromophore is protonated and forms a strong hydrogen bond to a species other than a water molecule, highly likely a counterion residue. The vibrational mode of the Schiff base of HeRs exhibits similarities with that of photosensory microbial rhodopsins, that is consistent with the previous proposal that HeRs function as photosensors. We also revealed unusual spectral features of the in-plane chain vibrations of the chromophore, suggesting an unprecedented geometry of the Schiff base caused by a difference in the retinal pocket structure of HeRs. These data demonstrate structural characteristics of the photoreceptive site in this novel type of rhodopsin family.
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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
| | - Manish Singh
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , 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
- 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
- The Institute for Solid State Physics , The University of Tokyo , Kashiwa 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
| | - 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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