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多元素が関わる酵素反応機構の計算化学的解明

Publicly Offered Research

Project AreaStimuli-responsive Chemical Species for the Creation of Functional Molecules
Project/Area Number 15H00913
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionIbaraki University

Principal Investigator

森 聖治  茨城大学, 理学部, 教授 (50332549)

Project Period (FY) 2015-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2016: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2015: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords酵素反応機構 / 量子化学計算 / QM/MM法 / 金属触媒 / アロステリック効果 / 分子動力学計算
Outline of Annual Research Achievements

(1)ヘム分解産物のビリベルジンIXα(BV)が、フェレドキシン依存的な酵素phycocyanobilin:ferredoxin oxidoreductase(PCyA)によって還元され、生成する機構を昨年度に続いて行った。本年度はONIOM計算を行い、中性子結晶構造解析だけでも断定できない水素の位置(とくにBVの4つのピロール環、His74, His88やAsp105の近く)について、多くの候補から絞ることができた。基質の水素化状態について、占有率で示される実験結果を説明することができた。またAsp105と基質との相互作用の仕方によるプロトン移動についても検討した。次年度以降、学術誌論文につながる結果を得た。
(2) 有機合成化学上重要なRh(I)-BINAP触媒によるアリルアミンの水素異性化の反応経路を人工力誘起反応(AFIR)法により探索すると、複雑な反応経路ネットワークが見つかった。さらにこの複雑な反応経路ネットワークから有力な反応経路に絞る際に、グラフ理論に基づいたPrimアルゴリズムが有効であることを示した。この論文は学術誌論文Chemical Scienceへの掲載を許可された。本研究は同じ新学術領域の公募班員との共同研究の成果である。
(3) リポカリン型プロスタグランジン(PG)合成酵素によるPGH2の異性化によるPGD2の生合成反応機構の検討を検討した。システイン残基が基質と反応する経路において、基質のペルオキシド酸素への求核攻撃の反応経路がエネルギー的に有利であることがわかり、酵素の効果が重要であることが示された。

Research Progress Status

28年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

28年度が最終年度であるため、記入しない。

Report

(2 results)
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (20 results)

All 2017 2016 2015 Other

All Int'l Joint Research (4 results) Journal Article (3 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 3 results,  Open Access: 1 results,  Acknowledgement Compliant: 2 results) Presentation (10 results) (of which Int'l Joint Research: 10 results,  Invited: 9 results) Remarks (2 results) Funded Workshop (1 results)

  • [Int'l Joint Research] University of Houston(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Kasetsart University/Mahidol University(Thailand)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] ハノイ科学大学(ベトナム)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] カセサート大学(タイ)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Exploring Full Catalytic Cycle of Rhodium(I)-BINAP Catalyzed Isomerisation of Allylic Amines: A Graph Theoretical Approach for Path Optimisation2017

    • Author(s)
      Takayoshi Yoshimura, Satoshi Maeda, Tetsuya Taketsugu, Masaya Sawamura, Keiji Morokuma, Seiji Mori
    • Journal Title

      Chemical Science

      Volume: 印刷中

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Investigation of substitution effect on fluorescence properties of Zn 2+-selective ratiometric fluorescent compounds: 2-(2′-Hydroxyphenyl) benzimidazole derivatives2016

    • Author(s)
      Kazuhiro Akutsu, Seiji Mori, Kenichi Shinmei, Hiroki Iwase, Yoshiharu Nakano, Yuki Fujii
    • Journal Title

      Talanta

      Volume: 146 Pages: 575-584

    • DOI

      10.1016/j.talanta.2015.09.001

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The molecular mechanism of palladium-catalysed cyanoesterification of methyl cyanoformate onto norbornene2016

    • Author(s)
      Takuya Ishitsuka, Yasuhiro Okuda, Robert K. Szilagyi, Seiji Mori, and Yasushi Nishihara
    • Journal Title

      Dalton Transactions

      Volume: 45 Issue: 18 Pages: 7786-7793

    • DOI

      10.1039/c6dt00341a

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Theoretical Investigations of PGH2 to PGD2 Isomerization Reaction by Lipocalin-Type Prostaglandin D Synthase using Quantum Mechanics/Molecular Mechanics Method2017

    • Author(s)
      SATO, Takehiro; SHIMAMOTO, Shigeru; ARITAKE, Kosuke; URADE, Yoshihiro; MORI, Seiji
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      横浜
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Mechanistic Insights into Molecular Activation Reactions Based on Computational Chemistry2017

    • Author(s)
      Seiji Mori
    • Organizer
      10th International Conference on Computational Physics
    • Place of Presentation
      Macau, China
    • Year and Date
      2017-02-18
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical Studies of Molecular Activation Reactions -Mechanistic Insights and Rational Design of Catalysis-2017

    • Author(s)
      Seiji Mori
    • Organizer
      Fifth Modeling of Chemical and Biological (Re)activity
    • Place of Presentation
      Chennai, India
    • Year and Date
      2017-02-18
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The Wonder of Enzymes with Ingenious Mechanisms2016

    • Author(s)
      Seiji Mori
    • Organizer
      The 4th International Symposium for Young Chemists on Stimuli-Responsive Chemical Species for the Creation of Functional Molecules
    • Place of Presentation
      大阪
    • Year and Date
      2016-12-12
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Introduction of Quantum Beam Science and Applications to Chemistry and Related Sciences2016

    • Author(s)
      Seiji Mori
    • Organizer
      8th International Kasetsart University Science and Technology Annual Research Symposium
    • Place of Presentation
      Bangkok, Thailand
    • Year and Date
      2016-06-02
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical Studies of Molecular Activation Reactions-Mechanistic Insights and Rational Design of Catalysis-2016

    • Author(s)
      Seiji Mori
    • Organizer
      APCTCC-7
    • Place of Presentation
      台湾、高雄
    • Year and Date
      2016-01-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Exploring Full Catalytic Cycle of Rh(I)-BINAP Catalyzed Isomerization of Allylic Amines2016

    • Author(s)
      Takayoshi Yoshimura, Satoshi Maeda, Masaya Sawamura, Tetsuya Taketsugu, Keiji Morokuma, and Seiji Mori
    • Organizer
      APCTCC-7
    • Place of Presentation
      台湾、高雄
    • Year and Date
      2016-01-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Thai-Japan Symposium in Chemistry2016

    • Author(s)
      Seiji Mori
    • Organizer
      Theoretical Insights into Molecular Activation Reactions
    • Place of Presentation
      Chiang Mai, Thailand
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical Studies of Molecular Activation Reactions-Mechanistic Insights and Rational Design of Catalysis-,2015

    • Author(s)
      Seiji Mori
    • Organizer
      Molecular Designs for Advanced Materials: Workshop and Conference
    • Place of Presentation
      Chiang Mai, Thailand
    • Year and Date
      2015-11-24
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Computational Studies on Mechanistic Insights Into Prostaglandin Synthases2015

    • Author(s)
      Seiji Mori
    • Organizer
      ICoBio 2015
    • Place of Presentation
      Bogor, Indonesia
    • Year and Date
      2015-08-05
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Remarks] 森研究室ホームページ

    • URL

      http://smori.sci.ibaraki.ac.jp/

    • Related Report
      2016 Annual Research Report
  • [Remarks] 森研究室ホームページ

    • URL

      http://smori.sci.ibaraki.ac.jp

    • Related Report
      2015 Annual Research Report
  • [Funded Workshop] 2016 Japan-Thai-Vietnam Joint Workshop for Theoretical and Computational Chemistry2016

    • Place of Presentation
      Mito, Ibaraki
    • Year and Date
      2016-01-18
    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2022-01-28  

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