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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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Chen Q, Yamada T, Miyagawa K, Murata A, Shoji M, Nakatani K. A new small molecule DoNA binding to CAG repeat RNA. Bioorg Med Chem 2024; 98:117580. [PMID: 38194737 DOI: 10.1016/j.bmc.2023.117580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/23/2023] [Accepted: 12/24/2023] [Indexed: 01/11/2024]
Abstract
We here report a new molecule DoNA binding to a CAG repeat RNA. DoNA is a dimer of the NA molecule that we previously reported. NA binds with high affinity to a CAG repeat DNA but not significantly to a CAG repeat RNA. Binding analyses using SPR and CSI-TOF MS indicated a significant increase in the affinity of DoNA to a single stranded CAG repeat RNA compared to NA. Systematic investigation of the RNA motifs bound by DoNA using hairpin RNA models revealed that DoNA binds to the CAG units at overhang and terminal positions, and notably, it binds to the structurally flexible internal and hairpin loop region.
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Affiliation(s)
- Qingwen Chen
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeshi Yamada
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; Current address: Nucleotide and Peptide Drug Discovery Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Asako Murata
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; Current address: Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Kazuhiko Nakatani
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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Sato A, Shoji M, Watanabe N, Boero M, Shigeta Y, Umemura M. Origin of Homochirality in Amino Acids Induced by Lyman-α Irradiation in the Early Stage of the Milky Way. ASTROBIOLOGY 2023; 23:1019-1026. [PMID: 37737584 DOI: 10.1089/ast.2022.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
The enantiomeric excess (ee) of l-form amino acids found in the Murchison meteorite poses some issues about the cosmic origin of their chirality. Circular dichroism (CD) spectra of amino acids in the far-ultraviolet (FUV) at around 6.8 eV (182 nm) indicate that the circularly polarized light can induce ee through photochemical reactions. Here, we resort to ab initio calculations to extract the CD spectra up to the vacuum-ultraviolet (VUV) region (∼11 eV), and we propose a novel equation to compute the ee applicable to a wider range of light frequency than what is available to date. This allows us to show that the strength of the induced ee (|ee|) in the 10 eV VUV region is comparable to the one in the 6.8 eV FUV region. This feature is common for some key amino acids (alanine, 2-aminobutyric acid, and valine). In space, intense Lyman-α (Lyα) light of 10.2 eV is emitted from star forming regions. This study provides a theoretical basis that Lyα emitter from an early starburst in the Milky Way plays a crucial role in initiating the ee of amino acids.
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Affiliation(s)
- Akimasa Sato
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
- JST-PRESTO, Kawaguchi, Japan
| | - Natsuki Watanabe
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mauro Boero
- Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504, University of Strasbourg, Strasbourg, France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masayuki Umemura
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Watanabe N, Hori Y, Shoji M, Boero M, Shigeta Y. Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theory. Chirality 2023. [PMID: 37122074 DOI: 10.1002/chir.23573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/30/2023] [Accepted: 04/14/2023] [Indexed: 05/02/2023]
Abstract
Aldehydes and carboxylic acids are widely used as catalysts for efficient racemization process of amino acids. However, the detailed reaction mechanism remains unclear. This work aims to clarify the racemization mechanism of aspartic acid (Asp) catalyzed by salicylaldehyde and acetic acid by using computational approaches. Density functional theory was used to obtain the structures and relative energies of 10 intermediates and five transition states, thus characterizing the main stages of the reaction. The calculated energy diagram shows that the dehydration step has the highest energy barrier, followed by the reaction step to change the chirality of Asp, which is a crucial process for racemization. In the dehydration reaction, water molecules can induce a remarkable decrease in the required energy.
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Affiliation(s)
- Natsuki Watanabe
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuta Hori
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
- JST-PRESTO, Kawaguchi, Japan
| | - Mauro Boero
- Institut de Physique et Chimie des Matériaux de Strasbourg, University of Strasbourg, CNRS, UMR 7504, 23 Rue du Loess, France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Shoji M, Kitazawa Y, Sato A, Watanabe N, Boero M, Shigeta Y, Umemura M. Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids. J Phys Chem Lett 2023; 14:3243-3248. [PMID: 36975120 PMCID: PMC10084466 DOI: 10.1021/acs.jpclett.2c03862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
High enantiomeric excesses (ee's) of l-amino acids, including non-proteinogenic amino acid isovaline (Iva), were discovered in the Murchison meteorite, but the detailed molecular mechanism responsible for the observed ee of amino acids remains elusive and inconsistent, because Iva has an inverted circular dichroism (CD) spectrum with respect to α-H amino acids, e.g., alanine. To address this issue, we resort to accurate ab initio calculations for amino acids and their precursors in the Strecker synthesis. We evaluated their photolysis-induced ee in the range 5-11 eV including the Lyman alpha emission line (Lyα), the typical intensive 10.2 eV radiation ascribed to the early phase of galactic evolution. We show that only the aminonitrile precursors are characterized by positive ee in the Lyα region, explaining why right-handed circularly polarized Lyα (R-CP-Lyα) induces homologous l-amino acids. This study shows that the homochirality of amino acids is produced at the aminonitrile precursors stage.
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Affiliation(s)
- Mitsuo Shoji
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- JST-PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuya Kitazawa
- Graduate
School of Pure and Applied Sciences, University
of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Akimasa Sato
- Graduate
School of Pure and Applied Sciences, University
of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Natsuki Watanabe
- Graduate
School of Pure and Applied Sciences, University
of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Mauro Boero
- University
of Strasbourg, Institut de Physique
et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504, 23 rue du Loess, Strasbourg F-67034, France
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Masayuki Umemura
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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