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Elucidation of functional mechanism based on the dynamic properties for the ongene products Ras

Research Project

Project/Area Number 17K15106
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionKyoto University (2021)
Institute of Physical and Chemical Research (2018-2020)
Kobe University (2017)

Principal Investigator

Matsumoto Shigeyuki  京都大学, 医学研究科, 特定准教授 (00753906)

Project Period (FY) 2017-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
KeywordsRas / がん変異体 / X線結晶構造解析 / 分子動力学計算 / 動的平衡 / state transition / 分子動力学シミュレーション / 立体構造 / State遷移 / ダイナミクス / NMR
Outline of Final Research Achievements

GTP-bound forms of Ras proteins adopt two interconverting conformations, “inactive” state 1 and “active” state 2. The crystal structure of wild-type H-Ras in state 1 showed that Gln61, on which an oncogenic mutation frequently occurs, plays a central role in its conformational stabilization. Here, aiming at investigating the relationships between the representative mutations, Q61L and Q61H, and their activation mechanism, we determine their crystal structures in state 1, and carry out the molecular dynamics simulations to obtain the dynamics properties. The results show that these mutations induce rearrangements of the interaction manners in the neighboring regions, and further, Q61L mutation results in acquirement of “active” state 2-like structural features.

Academic Significance and Societal Importance of the Research Achievements

低分子量GTPaseであるがん遺伝子産物Rasは、ヒトのがん全体の20-30%において突然変異による恒常的活性化が見られることから、学術的側面のみならずがん治療薬開発の標的として社会的に重要な生体高分子である。これまで変異によるRasの恒常的活性化メカニズムはGTP加水分解活性の低下の側面から主に議論されてきた。本研究の成果はがん変異により引き起こされる構造的特徴の変調を介した別の活性化メカニズムの存在を示唆しており、新たな作用機序を持つ分子標的薬開発のための手掛かりを与えるかもしれない。

Report

(6 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (9 results)

All 2021 2020 2017

All Journal Article (5 results) (of which Peer Reviewed: 5 results,  Open Access: 1 results) Presentation (4 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results)

  • [Journal Article] Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein2021

    • Author(s)
      Matsumoto Shigeyuki、Taniguchi-Tamura Haruka、Araki Mitsugu、Kawamura Takashi、Miyamoto Ryo、Tsuda Chiemi、Shima Fumi、Kumasaka Takashi、Okuno Yasushi、Kataoka Tohru
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 565 Pages: 85-90

    • DOI

      10.1016/j.bbrc.2021.05.084

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Extraction of protein dynamics information from cryo-EM maps using deep learning2021

    • Author(s)
      Matsumoto Shigeyuki、Ishida Shoichi、Araki Mitsugu、Kato Takayuki、Terayama Kei、Okuno Yasushi
    • Journal Title

      Nature Machine Intelligence

      Volume: 3 Issue: 2 Pages: 153-160

    • DOI

      10.1038/s42256-020-00290-y

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] E487K-induced disorder in functionally relevant dynamics of mitochondrial aldehyde dehydrogenase 22020

    • Author(s)
      Matsumoto S, Araki M, Isaka Y, Ono F, Hirohashi K, Ohashi S, Muto M, Okuno Y
    • Journal Title

      Biophysical Journal

      Volume: 119 Issue: 3 Pages: 628-637

    • DOI

      10.1016/j.bpj.2020.07.002

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural basis for intramolecular interaction of post-translationally modified H-Ras?GTP prepared by protein ligation2017

    • Author(s)
      Ke Haoliang、Matsumoto Shigeyuki、Murashima Yosuke、Taniguchi-Tamura Haruka、Miyamoto Ryo、Yoshikawa Yoko、Tsuda Chiemi、Kumasaka Takashi、Mizohata Eiichi、Edamatsu Hironori、Kataoka Tohru
    • Journal Title

      FEBS Letters

      Volume: 591 Issue: 16 Pages: 2470-2481

    • DOI

      10.1002/1873-3468.12759

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy2017

    • Author(s)
      Matsunaga Shota、Hano Yuta、Saito Yuta、Fujimoto Kazuhiro J.、Kumasaka Takashi、Matsumoto Shigeyuki、Kataoka Tohru、Shima Fumi、Tanaka Shigenori
    • Journal Title

      Journal of Molecular Graphics and Modelling

      Volume: 77 Pages: 51-63

    • DOI

      10.1016/j.jmgm.2017.07.028

    • NAID

      120006406708

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] 深層学習技術による cryo-EM密度マップデータに隠された動的情報の抽出2020

    • Author(s)
      松本篤幸
    • Organizer
      第一回クライオ電子顕微鏡画像からの高度情報処理研究会
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] Novel insights into the structural perturbation induced by the oncogenic mutations, Q61L and Q61H, in Ras state 12020

    • Author(s)
      Shigeyuki Matsumoto
    • Organizer
      64th Annual Meeting of the Biophysical Society
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 翻訳後修飾型H-Ras・GTPにおける分子内相互作用によるc-Raf-1認識のための立体構造の形成2017

    • Author(s)
      松本 篤幸 柯 浩亮 村嶋 陽亮 谷口-田村 はるか 宮本 涼生、吉川 陽子 津田 智恵美 熊坂 崇 溝端 栄一 枝松 裕紀 片岡 徹
    • Organizer
      consortium of biological sciences 2017
    • Related Report
      2017 Research-status Report
  • [Presentation] がん遺伝子産物H-RasQ61L 変異体の構造解析2017

    • Author(s)
      谷口-田村 はるか 松本 篤幸 宮本 涼生  河村 高志 熊坂 崇 片岡 徹
    • Organizer
      平成29年度 日本結晶学会年会
    • Related Report
      2017 Research-status Report

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Published: 2017-04-28   Modified: 2023-01-30  

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