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Molecular mechanisms of a Condensin molecular motor explored by DNA curtain assays and coarse-grained molecular dynamics simulations

Research Project

Project/Area Number 19H03194
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43040:Biophysics-related
Research InstitutionKyoto University

Principal Investigator

Terakawa Tsuyoshi  京都大学, 理学研究科, 助教 (20809652)

Project Period (FY) 2019-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2021: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2020: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2019: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Keywords1分子蛍光イメージング / DNAカーテン / 粗視化分子動力学シミュレーション / コンデンシン / 蛍光顕微鏡観察 / 一分子実験 / 分子モーター
Outline of Research at the Start

クロマチンの構造とその変化は、DNAの転写・修復・複製に重要な役割を果たし、真核生物の根幹を支える現象である。クロマチンは、細胞分裂期にコンパクトな棒状の構造に変化する。申請者は近年、この構造変化を引き起こすコンデンシンというタンパク質が分子モーターであることを明らかにした。本研究では、粗視化分子動力学シミュレーションと1分子蛍光イメージングを併用することで、コンデンシン分子モーターの作動機構を解明する。

Outline of Final Research Achievements

Condensin is a molecular motor protein that induces chromatin condensation by forming DNA loops in mitosis. Molecular mechanisms of the DNA loop formation remains unknown. In this study, single molecule fluorescence imaging (DNA curtain assays) and coarse-grained molecular dynamics simulations revealed that (i) the conformational change of the Condensin hinge region enables DNA binding, that (ii) Condensin with distinct nucleotide states has different conformations, respectively, and that (iii) Condensin translocations have two modes, one of which can bypass obstacles on DNA.

Academic Significance and Societal Importance of the Research Achievements

染色体凝縮は、複製されたゲノムDNAの娘細胞への正確な分配を保証する、生命の根幹をなす重要な現象である。本研究では、染色体凝集を引き起こすコンデンシンが、染色体ループを形成する分子機構を明らかにすることができた。これは、複製されたゲノムDNAが娘細胞に正確に分配されるしくみを明らかにするために重要な成果である。また、コンデンシンのように染色体の構造形成に関わるタンパク質の不全はCornelia de Lange症候群のような遺伝疾患を引き起こす。それらの深刻な疾患の分子機序の理解に重要な成果である。

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (10 results)

All 2021 2020

All Journal Article (3 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 3 results,  Open Access: 2 results) Presentation (7 results) (of which Int'l Joint Research: 1 results,  Invited: 2 results)

  • [Journal Article] Single-molecule junction spontaneously restored by DNA zipper2021

    • Author(s)
      Harashima Takanori、Fujii Shintaro、Jono Yuki、Terakawa Tsuyoshi、Kurita Noriyuki、Kaneko Satoshi、Kiguchi Manabu、Nishino Tomoaki
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 5762-5762

    • DOI

      10.1038/s41467-021-25943-3

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The lane-switch mechanism for nucleosome repositioning by DNA translocase2021

    • Author(s)
      Nagae Fritz、Brandani Giovanni B、Takada Shoji、Terakawa Tsuyoshi
    • Journal Title

      Nucleic Acids Research

      Volume: 49 Issue: 16 Pages: 9066-9076

    • DOI

      10.1093/nar/gkab664

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy2021

    • Author(s)
      Koide Hiroki、Kodera Noriyuki、Bisht Shveta、Takada Shoji、Terakawa Tsuyoshi
    • Journal Title

      PLOS Computational Biology

      Volume: 17 Issue: 7 Pages: e1009265-e1009265

    • DOI

      10.1371/journal.pcbi.1009265

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Evaluation of DNA binding of yeast replisome toward single-molecule observation of DNA replication2021

    • Author(s)
      Mayu S. Terakawa、Tsuyoshi Terakawa
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Molecular mechanism of MutS sliding on DNA explored by coarse-grained molecular dynamics simulations2021

    • Author(s)
      Keisuke Inoue、Shoji Takada、Tsuyoshi Terakawa
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] The lane switch mechanism: Nucleosome repositioning induced by a DNA translocase2021

    • Author(s)
      Fritz Nagae、Giovanni B. Brandani、Shoji Takada、Tsuyoshi Terakawa
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Molecular dynamics simulations of the yeast condensin holo complex towards elucidation of the mechanism of DNA loop extrusion2021

    • Author(s)
      Hiiroki Koide、Shoji Takada、Tsuyoshi Terakawa
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Nucleosome repositioning dynamics upon collision with a translocase2021

    • Author(s)
      Tsuyoshi Terakawa
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] DNA translocase repositions a nucleosome by the lane-switch mechanism2021

    • Author(s)
      Fritz Nagae、Giovanni B. Brandani、Shoji Takada、Tsuyoshi Terakawa
    • Organizer
      20th IUPAB Congress
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Reconstitution of protein functions on chromatin curtain2020

    • Author(s)
      寺川剛
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Invited

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Published: 2019-04-18   Modified: 2023-01-30  

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