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Development of D amino acid derivative synthetic method by ancestral L-amino acid oxidases

Research Project

Project/Area Number 21K05395
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 38030:Applied biochemistry-related
Research InstitutionUniversity of Shizuoka

Principal Investigator

Nakano Shogo  静岡県立大学, 食品栄養科学部, 准教授 (80748541)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2023: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2022: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2021: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords祖先型再構成法 / L-アミノ酸酸化酵素 / X線結晶構造解析 / 光学分割 / 物質生産 / 祖先型設計 / D-アミノ酸 / D-アミノ酸合成
Outline of Research at the Start

本研究では、広基質選択性を有するL-アミノ酸酸化酵素 (AncLAAO) を研究対象とし、本酵素を用いたD-アミノ酸誘導体の微生物生産系の構築に取り組む。AncLAAOの高機能化 (耐熱性と耐久性の向上)、構造機能解析による本酵素の基質認識機構の解明と合理的変異導入による基質選択性改変を実現、L-アミノ酸誘導体をD体へと変換可能な本酵素を軸とする微生物生産系の構築を行う。本研究が完遂されることで、様々なD-アミノ酸誘導体を高純度かつ大量に合成することが可能となり、ペプチド医薬品を含むファインケミカル合成への貢献が期待される。

Outline of Final Research Achievements

Through the integration of an innovative enzyme classification method and ancestral sequence reconstruction, we engineered hyperthermostable ancestral L-amino acid oxidases (HTAncLAAO2). Structural analysis, including crystallography, delineated the substrate entrance pathway and elucidated the mechanism of substrate recognition for HTAncLAAO2. The HTAncLAAO2(W220A) variant demonstrated heightened activity towards L-Trp, making it a promising candidate for the deracemization of D,L-amino acids to D-forms. Consequently, this enabled the establishment of a chemo-enzymatic system for the production of D-Trp derivatives from racemic mixtures, utilizing the HTAncLAAO2(W220A) variant as a biocatalyst.

Academic Significance and Societal Importance of the Research Achievements

データベースに登録されている配列の多くは、その機能が同定されておらず未利用資源として存在している。本研究を通してL-アミノ酸酸化酵素を題材としつつ、未利用資源の中から産業応用のポテンシャルを秘めた新規酵素の探索を可能にする技術開発を実現できた。今後ますます増大するであろう配列データの有効利用を実現可能にするための基盤となる研究成果であり、学術的にも社会的にも意義が高いものであると信じている。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • Research Products

    (26 results)

All 2024 2023 2022 2021

All Journal Article (15 results) (of which Peer Reviewed: 15 results,  Open Access: 7 results) Presentation (11 results) (of which Int'l Joint Research: 3 results,  Invited: 9 results)

  • [Journal Article] Development of evolutionary algorithm-based protein redesign method2024

    • Author(s)
      Ozawa Hiroki、Unno Ibuki、Sekine Ryohei、Chisuga Taichi、Ito Sohei、Nakano Shogo
    • Journal Title

      Cell Reports Physical Science

      Volume: 5 Issue: 1 Pages: 101758-101758

    • DOI

      10.1016/j.xcrp.2023.101758

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive Epitope Analysis of Monoclonal Antibodies Binding to Hen Egg Ovalbumin Using a Peptide Array2024

    • Author(s)
      Terada Yuko、Akimoto Masanobu、Sakoda Hirofumi、Yamamoto Shunsuke、Kubota Mayuka、Motoyama Tomoharu、Imanaka Yo、Nakano Shogo、Ito Sohei、Kato Shigeki、Ito Keisuke
    • Journal Title

      Foods

      Volume: 13 Issue: 3 Pages: 407-407

    • DOI

      10.3390/foods13030407

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of an Enzyme Cascade System for the Synthesis of Enantiomerically Pure D‐Amino Acids Utilizing Ancestral L‐Amino Acid Oxidase2024

    • Author(s)
      Araseki Hayato、Sugishima Narumi、Chisuga Taichi、Nakano Shogo
    • Journal Title

      ChemBioChem

      Volume: - Issue: 8

    • DOI

      10.1002/cbic.202400036

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Design of Ancestral Sortase E that is Applicable in Protein Biomaterial Synthesis2024

    • Author(s)
      Miyata Azusa、Chisuga Taichi、Kambe Akira、Miyata Ryo、Kawamura Yui、Takeda Hiroyuki、Ito Sohei、Nakano Shogo
    • Journal Title

      ACS Catalysis

      Volume: 14 Issue: 5 Pages: 3514-3523

    • DOI

      10.1021/acscatal.4c00487

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Definition of an Index Parameter To Screen Highly Functional Enzymes Derived from a Biochemical and Thermodynamic Analysis of Ancestral meso‐Diaminopimelate Dehydrogenases2023

    • Author(s)
      Araseki Hayato、Kawasaki Mayu、Kambe Akira、Kozuka Kohei、Ito Sohei、Nakano Shogo
    • Journal Title

      ChemBioChem

      Volume: 24 Issue: 13

    • DOI

      10.1002/cbic.202200727

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Time-Series Sensory Analysis Provided Important TI Parameters for Masking the Beany Flavor of Soymilk2023

    • Author(s)
      Masuda Miyu、Terada Yuko、Tsuji Ryoki、Nakano Shogo、Ito Keisuke
    • Journal Title

      Foods

      Volume: 12 Issue: 14 Pages: 2752-2752

    • DOI

      10.3390/foods12142752

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural and functional analysis of hyper-thermostable ancestral L-amino acid oxidase that can convert Trp derivatives to D-forms by chemoenzymatic reaction2023

    • Author(s)
      Kawamura Yui、Ishida Chiharu、Miyata Ryo、Miyata Azusa、Hayashi Seiichiro、Fujinami Daisuke、Ito Sohei、Nakano Shogo
    • Journal Title

      Communications Chemistry

      Volume: 6 Issue: 1 Pages: 200-200

    • DOI

      10.1038/s42004-023-01005-1

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Direct evaluation of polarity of the ligand binding pocket in retinoid X receptor using a fluorescent solvatochromic agonist2023

    • Author(s)
      Miura Kizuku、Fujihara Michiko、Watanabe Masaki、Takamura Yuta、Kawasaki Mayu、Nakano Shogo、Kakuta Hiroki
    • Journal Title

      Bioorganic & Medicinal Chemistry Letters

      Volume: 96 Pages: 129536-129536

    • DOI

      10.1016/j.bmcl.2023.129536

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ligand Screening System for the RXRα Heterodimer Using the Fluorescence RXR Agonist CU-6PMN2023

    • Author(s)
      Kawasaki Mayu、Motoyama Tomoharu、Yamada Shoya、Watanabe Masaki、Fujihara Michiko、Kambe Akira、Nakano Shogo、Kakuta Hiroki、Ito Sohei
    • Journal Title

      ACS Medicinal Chemistry Letters

      Volume: 14 Issue: 3 Pages: 291-296

    • DOI

      10.1021/acsmedchemlett.2c00509

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Dynamical Interaction Analysis of Proteins by a Random Forest-Fragment Molecular Orbital (RF-FMO) Method and Application to Src Tyrosine Kinase2023

    • Author(s)
      Yamamoto Yuta、Nakano Shogo、Shigeta Yasuteru
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 96 Issue: 1 Pages: 42-47

    • DOI

      10.1246/bcsj.20220304

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Reaction Mechanism of Ancestral <scp>l</scp>-Lys α-Oxidase from <i>Caulobacter</i> Species Studied by Biochemical, Structural, and Computational Analysis2022

    • Author(s)
      Motoyama Tomoharu、Yamamoto Yuta、Ishida Chiharu、Hasebe Fumihito、Kawamura Yui、Shigeta Yasuteru、Ito Sohei、Nakano Shogo
    • Journal Title

      ACS Omega

      Volume: 7 Issue: 48 Pages: 44407-44419

    • DOI

      10.1021/acsomega.2c06334

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Enzymatic Conjugation of Modified RNA Fragments by Ancestral RNA Ligase AncT4_22022

    • Author(s)
      Kajimoto Shohei、Ohashi Miwa、Hagiwara Yusuke、Takahashi Daisuke、Mihara Yasuhiro、Motoyama Tomoharu、Ito Sohei、Nakano Shogo
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 88 Issue: 23

    • DOI

      10.1128/aem.01679-22

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Reconstruction of Hyper‐Thermostable Ancestral L‐Amino Acid Oxidase to Perform Deracemization to D‐Amino Acids2021

    • Author(s)
      Ishida Chiharu、Miyata Ryo、Hasebe Fumihito、Miyata Azusa、Kumazawa Shigenori、Ito Sohei、Nakano Shogo
    • Journal Title

      ChemCatChem

      Volume: 13 Issue: 24 Pages: 5228-5235

    • DOI

      10.1002/cctc.202101296

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining2021

    • Author(s)
      Sugiura Sayaka、Nakano Shogo、Niwa Masazumi、Hasebe Fumihito、Matsui Daisuke、Ito Sohei
    • Journal Title

      Journal of Biological Chemistry

      Volume: 297 Issue: 3 Pages: 101043-101043

    • DOI

      10.1016/j.jbc.2021.101043

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Design of a Full‐Consensus Glutamate Decarboxylase and Its Application to GABA Biosynthesis2021

    • Author(s)
      Takagi Hiroshi、Kozuka Kohei、Mimura Kenta、Nakano Shogo、Ito Sohei
    • Journal Title

      ChemBioChem

      Volume: - Issue: 8

    • DOI

      10.1002/cbic.202100447

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Presentation] タンパク質インシリコ分子進化法の開発と実験的検証2024

    • Author(s)
      中野 祥吾
    • Organizer
      予知生合成 第三回公開シンポジウム
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] ファインケミカル合成に応用可能な祖先型酵素群の開発2024

    • Author(s)
      中野 祥吾
    • Organizer
      日本薬学会第144回年会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] ネットワーク理論に基づく酵素ホモログ配列分類法の開発と応用2023

    • Author(s)
      中野 祥吾
    • Organizer
      「高速分子動画」若手シンポジウム
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 進化的計算法による高機能化タンパク質のデザイン2023

    • Author(s)
      中野 祥吾
    • Organizer
      第23回蛋白質科学会年会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Design of Ancestral Sortase E that can apply to synthesize protein materials2023

    • Author(s)
      Shogo Nakano
    • Organizer
      The 67th annual meeting of Australian Society for Biochemistry & Molecular Biology (ASBMB2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 配列データベースから取得した祖先型Sortase Eの機能解析と応用2023

    • Author(s)
      中野 祥吾
    • Organizer
      第46回日本分子生物学会大会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] アミノ酸配列に刻まれた進化情報を利用した高機能化タンパク質の創出2023

    • Author(s)
      中野 祥吾
    • Organizer
      新資源生物変換研究会 第3回公開勉強会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 遺伝的アルゴリズムと立体構造を用いた高機能化酵素デザイン2022

    • Author(s)
      中野祥吾
    • Organizer
      物性研短期研究会「理論タンパク質物性科学の最前線:理論と実験との密な協働」
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] Development of genetic algorithm-based consensus protein design method to generate highly functional enzymes2022

    • Author(s)
      Shogo Nakano
    • Organizer
      Active Enzyme Molecule 2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] インシリコでの人工酵素配列設計と酵素探索2022

    • Author(s)
      中野 祥吾
    • Organizer
      第61回 澱粉研究懇談会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] Design of artificial L-amino acid oxidases generated by ancestral sequence reconstruction which can apply to deracemize to aromatic D-amino acid derivatives2021

    • Author(s)
      Shogo Nakano
    • Organizer
      Pacifichem2021
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research

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Published: 2021-04-28   Modified: 2025-01-30  

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