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Study of protein performance modification based on canonical molecular orbital analysis

Research Project

Project/Area Number 21H02056
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 37010:Bio-related chemistry
Research InstitutionThe University of Tokyo

Principal Investigator

Sato Fumitoshi  東京大学, 生産技術研究所, 教授 (00235392)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000)
Fiscal Year 2023: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2022: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2021: ¥15,470,000 (Direct Cost: ¥11,900,000、Indirect Cost: ¥3,570,000)
Keywordsタンパク質 / 正準分子軌道計算 / 密度汎関数法 / 正準分子軌道 / タンパク質工学 / タンパク質性能改変
Outline of Research at the Start

本研究では、タンパク質の分子軌道を制御している機構を明らかにすることで、化学的根拠に基づいたタンパク質改変の基盤技術を構築する。
・本申請者らが開発した標準のハイブリッド密度汎関数法に基づく正準分子軌道法を用いて、タンパク質の分子軌道の形状を系統的に分析・解析する。タンパク質の全ての分子軌道を計算できるソフトは他にない。
・どのアミノ酸残基が活性中心に影響を及ぼしているかを明らかにする方法を提案・検証する。
・タンパク質工学に適したアミノ酸残基置換法で、量子化学的根拠を以ってタンパク質の性能改変を解析・予測する。

Outline of Final Research Achievements

To understand the canonical molecular orbitals of proteins and their properties, several methods were developed to analyze the results of large-scale protein canonical molecular orbital calculations. This has enabled a comprehensive and objective investigation of the spread and interactions of protein canonical molecular orbitals. These findings are expected to build the foundation technology for new protein design based on quantum effects, opening up new possibilities for protein design and its applications.

Academic Significance and Societal Importance of the Research Achievements

成果成果を公開するものとして論文・研究発表などのほか、開発した手法・アルゴリズムはインターネット上ですでに公開しているProteinDFやQCLObotに実装している。これらはGNU GPL v3ライセンスのもとオープンソースとして公開しており、自由に利用できる。
本研究の成果は、タンパク質に限らずさまざまな含金属・非金属物質および材料系に適用可能であり、大規模正準分子軌道計算の解析法の一つとして大いに利用されるものと考えている。

Report

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

    (24 results)

All 2024 2023 2022 2021

All Journal Article (10 results) (of which Peer Reviewed: 5 results,  Open Access: 3 results) Presentation (14 results) (of which Int'l Joint Research: 5 results,  Invited: 2 results)

  • [Journal Article] Study on Analysis Approach of Canonical Molecular Orbital Calculation in Large-scale Molecular System2024

    • Author(s)
      Toshiyuki Hirano, Fumitoshi Sato
    • Journal Title

      AIP Conference Proceedings

      Volume: 3030 Pages: 020008-020008

    • DOI

      10.1063/5.0192921

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of electronic structure of the complexes of peptides derived from transactivation domain of the tumor suppressor p53 and MDM2 protein2023

    • Author(s)
      小杉亨, 平野敏行, 田原才静, 佐藤文俊
    • Journal Title

      SEISAN KENKYU

      Volume: 75 Issue: 2 Pages: 123-129

    • DOI

      10.11188/seisankenkyu.75.123

    • ISSN
      0037-105X, 1881-2058
    • Year and Date
      2023-05-01
    • Related Report
      2023 Annual Research Report
  • [Journal Article] タンパク質の正準分子軌道計算シミュレーション2023

    • Author(s)
      佐藤文俊, 平野敏行
    • Journal Title

      シミュレーション

      Volume: 42 Pages: 115-121

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Study on the Role in the Catalytic Reaction Occurrence of the Active Site in PETase by Canonical Molecular Orbital Method2022

    • Author(s)
      王 天宇、平野 敏行、佐藤 文俊
    • Journal Title

      SEISAN KENKYU

      Volume: 74 Issue: 2 Pages: 161-167

    • DOI

      10.11188/seisankenkyu.74.161

    • ISSN
      0037-105X, 1881-2058
    • Year and Date
      2022-05-01
    • Related Report
      2022 Annual Research Report
    • Open Access
  • [Journal Article] Study on mechanism of electronic states of Interferon alpha22022

    • Author(s)
      中岡 亮太、平野 敏行、佐藤 文俊
    • Journal Title

      SEISAN KENKYU

      Volume: 74 Issue: 2 Pages: 153-159

    • DOI

      10.11188/seisankenkyu.74.153

    • ISSN
      0037-105X, 1881-2058
    • Year and Date
      2022-05-01
    • Related Report
      2022 Annual Research Report
    • Open Access
  • [Journal Article] Theoretical Study of the Receptor-Binding Domain of Spike Protein of SARS-CoV-2 by Canonical Molecular Orbital Calculation2022

    • Author(s)
      Hirano Toshiyuki Hirano, Sato Fumitoshi
    • Journal Title

      AIP Conference Proceedings

      Volume: 2611 Pages: 020005-020005

    • DOI

      10.1063/5.0119366

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 分子軌道法によるタンパク質のシミュレーション2022

    • Author(s)
      佐藤 文俊
    • Journal Title

      機械の研究

      Volume: 74 Pages: 247-251

    • Related Report
      2022 Annual Research Report
  • [Journal Article] Analysis of Electronic Structure of Photoactive Yellow Protein by Canonical Molecular Orbitals Calculation2021

    • Author(s)
      前田 大陸、平野 敏行、佐藤 文俊
    • Journal Title

      SEISAN KENKYU

      Volume: 73 Issue: 3 Pages: 157-163

    • DOI

      10.11188/seisankenkyu.73.157

    • NAID

      130008049208

    • ISSN
      0037-105X, 1881-2058
    • Year and Date
      2021-05-01
    • Related Report
      2021 Annual Research Report
    • Open Access
  • [Journal Article] Multiple mutations in RNA polymerase β-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory2021

    • Author(s)
      Ogawa Saori、Shimidzu Hitomi、Fukuda Koji、Tsunekawa Naoki、Hirano Toshiyuki、Sato Fumitoshi、Yura Kei、Hasunuma Tomohisa、Ochi Kozo、Yamamoto Michio、Sakamoto Wataru、Hashimoto Kentaro、Ogata Hiroyuki、Kanao Tadayoshi、Nemoto Michiko、Inagaki Kenji、Tamura Takashi
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 85 Issue: 5 Pages: 1275-1282

    • DOI

      10.1093/bbb/zbab011

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Interaction energy analysis based on canonical Kohn-Sham molecular orbitals calculation of protein2021

    • Author(s)
      Hirano Toshiyuki、Sato Fumitoshi
    • Journal Title

      AIP Conference Proceedings

      Volume: 2343 Pages: 020007-020007

    • DOI

      10.1063/5.0047812

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Presentation] 化学反応シミュレータの研究開発と将来展望2024

    • Author(s)
      高橋 英男,戸丸 辰也,平野 敏行,田原 才静,佐藤 文俊
    • Organizer
      ワークショップ: 力学の未来(量子化学分野:量子コンピューティング)
    • Related Report
      2023 Annual Research Report
  • [Presentation] アミロイド線維コアおよび細胞内天然型プリオンの電子構造研究2023

    • Author(s)
      植弘 雄斗,平野 敏行,田原 才静,佐藤 文俊
    • Organizer
      第17回分子科学討論会2023
    • Related Report
      2023 Annual Research Report
  • [Presentation] 軌道重なり法を用いたタンパク質正準分子軌道計算解析法の研究2023

    • Author(s)
      平野敏行, Zheng Haojie, 佐藤文俊
    • Organizer
      第17回分子科学討論会2023
    • Related Report
      2023 Annual Research Report
  • [Presentation] Principal Component Analysis of Energies Derived from Canonical Molecular Orbital Calculations of Proteins2023

    • Author(s)
      Toshiyuki Hirano, Fumitoshi Sato
    • Organizer
      ICNAAM2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Insight into electronic structure of insulin analogues bound to IGF-1 receptor by quantum-chemistry calculation2023

    • Author(s)
      Zheng Haojie, Hirano Toshiyuki, Tahara Saisei, Sato Fumitoshi
    • Organizer
      Bio UT 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Electronic structure of insulin and its analogues bound to IGF-1 receptor by canonical molecular orbital calculations2023

    • Author(s)
      Zheng Haojie, 平野敏行, 田原才静, 佐藤文俊
    • Organizer
      第25回理論化学討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Study on Analysis Approach of Canonical Kohn-Sham Molecular Orbital Calculation in Large-scale Molecular System2022

    • Author(s)
      Hirano Toshiyuki Hirano, Sato Fumitoshi
    • Organizer
      17th International Conference of Computational Methods in Sciences and Engineering (ICCMSE2022)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 大規模正準分子軌道計算の実情と今後2022

    • Author(s)
      平野敏行, 佐藤文俊
    • Organizer
      令和4年電気学会基礎・材料・共通部門大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ACE2におけるスパイクタンパク質結合部位の電子状態2022

    • Author(s)
      平野敏行, 佐藤文俊
    • Organizer
      第16回分子科学討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Theoretical study of the receptor-binding domain of spike protein of SARS-CoV-2 by canonical molecular orbital calculation2021

    • Author(s)
      Hirano Toshiyuki, Sato Fumitoshi
    • Organizer
      16th International Conference of Computational Methods in Sciences and Engineering (ICCMSE2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Orchestration software for canonical Kohn-Sham molecular orbital calculation of proteins: QCLObot2021

    • Author(s)
      Hirano Toshiyuki, Sato Fumitoshi
    • Organizer
      Pacifichem 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 新型コロナウイルスRNA結合ドメインの電子状態2021

    • Author(s)
      平野敏行, 坂口優羽, 佐藤文俊
    • Organizer
      第15回分子科学討論会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 正準分子軌道法によるPETase活性中心の電子状態についての研究2021

    • Author(s)
      王天宇, 平野敏行, 佐藤文俊
    • Organizer
      第15回分子科学討論会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 正準分子軌道計算によるインターフェロンα2の電子状態解析2021

    • Author(s)
      中岡亮太, 平野敏行, 佐藤文俊
    • Organizer
      第15回分子科学討論会
    • Related Report
      2021 Annual Research Report

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

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