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Maity B, Shoji M, Luo F, Nakane T, Abe S, Owada S, Kang J, Tono K, Tanaka R, Pham TT, Kojima M, Hishikawa Y, Tanaka J, Tian J, Nagama M, Suzuki T, Noya H, Nakasuji Y, Asanuma A, Yao X, Iwata S, Shigeta Y, Nango E, Ueno T. Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography. Nat Commun 2024; 15:5518. [PMID: 38951539 PMCID: PMC11217357 DOI: 10.1038/s41467-024-49814-9] [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: 11/06/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
Determining short-lived intermediate structures in chemical reactions is challenging. Although ultrafast spectroscopic methods can detect the formation of transient intermediates, real-space structures cannot be determined directly from such studies. Time-resolved serial femtosecond crystallography (TR-SFX) has recently proven to be a powerful method for capturing molecular changes in proteins on femtosecond timescales. However, the methodology has been mostly applied to natural proteins/enzymes and limited to reactions promoted by synthetic molecules due to structure determination challenges. This work demonstrates the applicability of TR-SFX for investigations of chemical reaction mechanisms of synthetic metal complexes. We fix a light-induced CO-releasing Mn(CO)3 reaction center in porous hen egg white lysozyme (HEWL) microcrystals. By controlling light exposure and time, we capture the real-time formation of Mn-carbonyl intermediates during the CO release reaction. The asymmetric protein environment is found to influence the order of CO release. The experimentally-observed reaction path agrees with quantum mechanical calculations. Therefore, our demonstration offers a new approach to visualize atomic-level reactions of small molecules using TR-SFX with real-space structure determination. This advance holds the potential to facilitate design of artificial metalloenzymes with precise mechanisms, empowering design, control and development of innovative reactions.
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Affiliation(s)
- Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan.
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Fangjia Luo
- JASRI, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Takanori Nakane
- Institute of Protein Research, Osaka University, Osaka, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Shigeki Owada
- JASRI, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | | | - Kensuke Tono
- JASRI, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thuc Toan Pham
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Yuki Hishikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Junko Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Jiaxin Tian
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Misaki Nagama
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Taiga Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Hiroki Noya
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Yuto Nakasuji
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Asuka Asanuma
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Xinchen Yao
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.
- Tohoku University. Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan.
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 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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4
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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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5
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Hori Y, Nakamura H, Sakawa T, Watanabe N, Kayanuma M, Shoji M, Umemura M, Shigeta Y. Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in Space. ASTROBIOLOGY 2022; 22:1330-1336. [PMID: 36067332 PMCID: PMC9618371 DOI: 10.1089/ast.2022.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
The preferential synthesis or destruction of a single enantiomer by ultraviolet circularly polarized light (UV-CPL) has been proposed as a possible triggering mechanism for the extraterrestrial origin of homochirality. Herein, we investigate the photoabsorption property of propylene oxide (c-C3H6O) for UV-CPL in the Lyman-α region. Our calculations show that c-C3H6O was produced by CH3+ and CH3CH(OH)CH3 or C3H7• and O (triplet). The computed electronic circular dichroism spectra show that c-C3H6O and the intermediate (CH3CH(OH)CH2+) could absorb the UV-CPL originating from the Lyman-α emitter spectrum, suggesting that the photolysis of c-C3H6O or CH3CH(OH)CH2+ upon irradiation could induce chiral symmetry breakage.
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Affiliation(s)
- Yuta Hori
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Honami Nakamura
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Takahide Sakawa
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Natsuki Watanabe
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Megumi Kayanuma
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Masayuki Umemura
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
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8
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Shoji M, Murakawa T, Nakanishi S, Boero M, Shigeta Y, Hayashi H, Okajima T. Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase. Chem Sci 2022; 13:10923-10938. [PMID: 36320691 PMCID: PMC9491219 DOI: 10.1039/d2sc01356h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/16/2022] [Indexed: 11/21/2022] Open
Abstract
Copper amine oxidase from Arthrobacter globiformis (AGAO) catalyses the oxidative deamination of primary amines via a large conformational change of a topaquinone (TPQ) cofactor during the semiquinone formation step. This conformational change of TPQ occurs in the presence of strong hydrogen bonds and neighboring bulky amino acids, especially the conserved Asn381, which restricts TPQ conformational changes over the catalytic cycle. Whether such a semiquinone intermediate is catalytically active or inert has been a matter of debate in copper amine oxidases. Here, we show that the reaction rate of the Asn381Ala mutant decreases 160-fold, and the X-ray crystal structures of the mutant reveals a TPQ-flipped conformation in both the oxidized and reduced states, preceding semiquinone formation. Our hybrid quantum mechanics/molecular mechanics (QM/MM) simulations show that the TPQ conformational change is realized through the sequential steps of the TPQ ring-rotation and slide. We determine that the bulky side chain of Asn381 hinders the undesired TPQ ring-rotation in the oxidized form, favoring the TPQ ring-rotation in reduced TPQ by a further stabilization leading to the TPQ semiquinone form. The acquired conformational flexibility of TPQ semiquinone promotes a high reactivity of Cu(i) to O2, suggesting that the semiquinone form is catalytically active for the subsequent oxidative half-reaction in AGAO. The ingenious molecular mechanism exerted by TPQ to achieve the “state-specific” reaction sheds new light on a drastic environmental transformation around the catalytic center. The large conformational change of topaquinone in bacterial copper amine oxidase occurs through the TPQ ring rotation and slide, which are essential to stabilize the semiquinone form.![]()
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Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba 305-8577 Ibaraki Japan
- JST-PRESTO 4-1-8 Honcho Kawaguchi 332-0012 Saitama Japan
| | - Takeshi Murakawa
- Department of Biochemistry, Osaka Medical and Pharmaceutical University 2-7 Daigakumachi Takatsuki 569-8686 Osaka Japan
| | - Shota Nakanishi
- Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Osaka Japan
| | - Mauro Boero
- University of Strasbourg, Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504 23 rue du Loess F-67034 France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba 305-8577 Ibaraki Japan
| | - Hideyuki Hayashi
- Department of Chemistry, Osaka Medical and Pharmaceutical University 2-7 Daigakumachi Takatsuki 569-8686 Osaka Japan
| | - Toshihide Okajima
- Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Osaka Japan
- Department of Chemistry, Osaka Medical and Pharmaceutical University 2-7 Daigakumachi Takatsuki 569-8686 Osaka Japan
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