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Analysis of conformational change of nucleosome by molecular dynamics simulation

Research Project

Project/Area Number 18K06173
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 43040:Biophysics-related
Research InstitutionNational Institutes for Quantum and Radiological Science and Technology

Principal Investigator

Ishida Hisashi  国立研究開発法人量子科学技術研究開発機構, 量子生命科学領域, 上席研究員(定常) (60360418)

Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2020: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2019: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2018: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Keywordsヌクレオソーム / DNA / 構造変化 / 遺伝子発現 / ねじれ / 分子動力学シミュレーション / 自由エネルギー計算 / DNA解離 / ヒストン / 自由エネルギー
Outline of Final Research Achievements

The free energy calculations using molecular dynamics simulations showed that DNA dissociation of CENP-A nucleosomes in the chromosomal centromere region is more likely to occur than that of canonical nucleosomes. Furthermore, a molecular dynamics simulation was performed in which a force imitating the twisting force generated by RNA polymerase was applied to both ends of the canonical nucleosome DNA. The results indicated that when a left-handed twisting force was applied, the DNA was easily dissociated from the histone, and conversely, when a right-handed twisting force was applied, the DNA was difficult to be dissociated from the histone. These were found to be caused by the geometrical property of the DNA double helix structure and the physical characteristics of DNA such as flexibiity and bendability.

Academic Significance and Societal Importance of the Research Achievements

ヌクレオソームのDNAに作用するねじれの力が、ヌクレオソームの大規模な構造変化を引き起こすことがわかった。その分子論的原因は、DNAが右巻きのらせんの形をしている幾何学的特性とDNA固有の物性的特性(柔らかさ、曲がりやすさ)に起因することがわかった。このことはヌクレオソーム構造変化を伴う複雑な遺伝子発現メカニズムが「DNAのらせん構造」と「ねじれの力の向き」といった単純な仕組みによっても調節されている可能性を示している。本研究は、分子動力学シミュレーション法を最大限に活用したヌクレオソームの機能発現メカニズムの解析であり、将来的に遺伝子発現機構の全容解明につながる。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report

Research Products

(12 results)

All 2021 2020 2019

All Journal Article (3 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 3 results,  Open Access: 2 results) Presentation (9 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results)

  • [Journal Article] Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA2021

    • Author(s)
      Ishida Hisashi、Kono Hidetoshi
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 118

    • DOI

      10.1073/pnas.2020452118

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nucleosome unwrapping and unstacking2020

    • Author(s)
      Kono Hidetoshi、Ishida Hisashi
    • Journal Title

      Current Opinion in Structural Biology

      Volume: 64 Pages: 119-125

    • DOI

      10.1016/j.sbi.2020.06.020

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome2019

    • Author(s)
      Kono Hidetoshi、Sakuraba Shun、Ishida Hisashi
    • Journal Title

      BIOPHYSICS

      Volume: 16 Issue: 0 Pages: 337-343

    • DOI

      10.2142/biophysico.16.0_337

    • NAID

      130007752747

    • ISSN
      2189-4779
    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 分子シミュレーションによるヌクレオソーム構造変化の網羅的探索2020

    • Author(s)
      石田恒
    • Organizer
      第7回「京」を中核とするHPCIシステム利用研究課題 成果報告会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 全原子分子動力学シミュレーションを用いた、ヌクレオソーム安定性に対するねじれストレス影響の解析2020

    • Author(s)
      石田恒
    • Organizer
      量子生命科学会第2回大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Positive torsional stress on DNA enhances unwrapping of nucleosomal DNA2020

    • Author(s)
      Hisashi Ishida, Hidetoshi Kono
    • Organizer
      Biophysical Society Annual Meeting 2020
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Sequence dependence of nucleosomal DNA unwrapping2019

    • Author(s)
      角南 智子, ルオ ディ, 石田 恒, 河野 秀俊
    • Organizer
      第3回DSB研究成果報告会
    • Related Report
      2019 Research-status Report
  • [Presentation] 分子シミュレーションによるヌクレオソーム構造変化の網羅的探索 ヌクレオソームのH2A/H2B脱離メカニズム解析2019

    • Author(s)
      石田 恒
    • Organizer
      第6回「京」を中核とする HPCI システム利用研究課題 成果報告会
    • Related Report
      2019 Research-status Report
  • [Presentation] Free energy profile of eviction of H2A/H2B dimer from nucleosome2019

    • Author(s)
      Hisashi Ishida, Hidetoshi Kono
    • Organizer
      3rd QST International Symposium
    • Related Report
      2019 Research-status Report
  • [Presentation] Integrated approach of experimental data and computer modeling and simulation for understanding chromatin structure and dynamics2019

    • Author(s)
      Hidetoshi Kono, Atsushi Matsumoto, Shun Sakuraba, Hisashi Ishida
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] ヌクレオソームの崩壊と転写2019

    • Author(s)
      河野 秀俊, ルオ ディ, 石田 恒
    • Organizer
      第19回日本蛋白質科学会年会・第71回日本細胞生物学会大会 合同年次大会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] FREE ENERGY PROFILES FOR UNWRAPPING THE OUTER SUPERHELICAL2019

    • Author(s)
      石田恒、河野秀俊
    • Organizer
      Multiscale Modeling of Chromatin:Bridging Experiment with Theory
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research

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Published: 2018-04-23   Modified: 2022-01-27  

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