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Theoretical study of clock proteins focusing on cooperation of spatio-temporal dynamics

Research Project

Project/Area Number 18K14185
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 32010:Fundamental physical chemistry-related
Research InstitutionInstitute for Molecular Science

Principal Investigator

Koda Shin-ichi  分子科学研究所, 理論・計算分子科学研究領域, 助教 (10790404)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2020: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2019: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2018: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords体内時計 / シアノバクテリア / 時計タンパク質 / 数理モデル / 概日リズム / 反応モデル / ATP加水分解 / 階層性 / シミュレーション
Outline of Final Research Achievements

In this project, we conducted theoretical research on the clock proteins, KaiA, KaiB, and, KaiC, which constitute the core oscillator of the cyanobacterial biological clock. In particular, we focused on the KaiB-KaiC complex formation and theoretically proposed its detailed process. In this study, we theoretically and numerically established important overlooked mechanisms through a detailed review of previously published experimental data. For example, in 2020, we showed that the origin of the slowness of the KaiB-KaiC complex formation is on the KaiC side, contrary to the previous account. In the final year, we proposed a new mechanism of the cooperation between KaiB-KaiC complex formation and KaiC ATP hydrolysis from a theoretical viewpoint.

Academic Significance and Societal Importance of the Research Achievements

体内時計は多くの生物が備える機能であり、その原理の解明は重要である。特にシアノバクテリアの体内時計はわずか3種のタンパク質から構成されており、時計の原理を分子レベルで理解するために格好のモデルである。本研究は振動子の発振において中枢的な役割を担うKaiB-KaiC複合体形成の機構を素過程レベルで明らかにした。これは振動子の分子レベルの動作原理の更なる理解につながるものと考えられる。

Report

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

    (3 results)

All 2022 2020 2018

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 2 results) Presentation (1 results)

  • [Journal Article] Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition2022

    • Author(s)
      Shin-ichi Koda, Shinji Saito
    • Journal Title

      PLOS Computational Biology

      Volume: 18 Issue: 3 Pages: e1009243-e1009243

    • DOI

      10.1371/journal.pcbi.1009243

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins2020

    • Author(s)
      Koda Shin-ichi、Saito Shinji
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 10439-10439

    • DOI

      10.1038/s41598-020-67298-7

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 時計タンパク質KaiCの一方向的アロステリに関する反応モデル構築に基づく考察2018

    • Author(s)
      甲田信一、斉藤真司
    • Organizer
      第21回理論化学討論会
    • Related Report
      2018 Research-status Report

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Published: 2018-04-23   Modified: 2023-01-30  

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