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Force fields for the molecular dynamics of modified nucleic acids

Research Project

Project/Area Number 16K17778
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionNational Institutes for Quantum and Radiological Science and Technology (2018-2019)
The University of Tokyo (2016-2017)

Principal Investigator

Sakuraba Shun  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, 主任研究員(任常) (90647380)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2016: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Keywords分子動力学法 / 力場 / RNA / RNA修飾 / 修飾核酸塩基 / 自由エネルギー計算 / 力場パラメータ / イノシン / N6-メチルアデニン / 修飾核酸 / 分子動力学シミュレーション / 二次構造予測 / 零多重極子和法 / 古典分子動力学シミュレーション / リボ核酸 / 化学物理 / 分子シミュレーション / 分子動力学
Outline of Final Research Achievements

We constructed a pipeline to generate a classical molecular dynamics force field for modified RNAs. We further constructerd the free-energy calculation pipeline to evaluate the generated force field. By using the force field from the same protocol we proved that RNA's stability can be predicted from simulations.
Additionally, based on the free-energy calculation pipeline we created in this project, we constructed a pipeline that can predict the stability change upon introducing a single mutation to the protein. We showed that the thermal stability change of the protein can be predicted with this pipeline.

Academic Significance and Societal Importance of the Research Achievements

生体内には様々な修飾塩基が存在し近年その役割が注目されている。修飾塩基のシミュレーションはこれまで高い精度で実施することが困難であったが、本研究によりその原子単位の振る舞いを予測することが可能になった。さらに、高精度の力場により自由エネルギー変化が予測可能であることを示したことで、コストなどの面で実験が困難な修飾塩基に対し、計算を用いることでその様態を予測することを可能にした。また、本研究計画で作成した力場作成パイプラインはSARS-CoV-2での修飾mRNA研究を迅速に立ち上げるために活用された。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (12 results)

All 2020 2019 2018 2017 2016

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Open Access: 1 results) Presentation (8 results) (of which Int'l Joint Research: 3 results)

  • [Journal Article] Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities2018

    • Author(s)
      Hagio Taichi、Sakuraba Shun、Iwakiri Junichi、Mori Ryota、Asai Kiyoshi
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: Suppl 1 Pages: 38-38

    • DOI

      10.1186/s12859-018-2018-4

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation2018

    • Author(s)
      Kasahara Kota、Sakuraba Shun、Fukuda Ikuo
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 122 Issue: 9 Pages: 2495-2503

    • DOI

      10.1021/acs.jpcb.7b10830

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Performance Evaluation of the Zero-Multipole Summation Method in Modern Molecular Dynamics Software2018

    • Author(s)
      Shun Sakuraba, Ikuo Fukuda
    • Journal Title

      Journal of Computational Chemistry

      Volume: 印刷中 Issue: 20 Pages: 1551-1560

    • DOI

      10.1002/jcc.25228

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data2018

    • Author(s)
      Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 印刷中

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] Shun Sakuraba2020

    • Author(s)
      A COMPUTATIONAL STUDY OF FREE-ENERGY CHANGES UPON PROTEIN MUTATIONS
    • Organizer
      2020 Biophysical Society Annual Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] FEP/RESTによるタンパク質の変異安定性予測2019

    • Author(s)
      櫻庭 俊
    • Organizer
      計算タンパク質科学研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] FEP/REST法によるタンパク質変異体の自由エネルギー計算2019

    • Author(s)
      櫻庭 俊
    • Organizer
      第33回分子シミュレーション討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Stable Interdomain Interfaces of Heterochromatin Protein 1: Modeling all-atom Dinucleosome HP1 complex2019

    • Author(s)
      Amarjeet Kumar, Shun Sakuraba, Atsushi Matsumoto, Hidetoshi Kono
    • Organizer
      3rd QST International Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RNA nearest-neighbor parameters for inosine-cytosine pairs derived from a combined experiment-simulation approach2019

    • Author(s)
      Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai
    • Organizer
      Annual Meeting of the Biophysical Society
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 修飾核酸の分子動力学シミュレーション2018

    • Author(s)
      桜庭 俊
    • Organizer
      第20回日本RNA学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 修飾核酸の分子動力学シミュレーション2017

    • Author(s)
      桜庭俊、浅井潔
    • Organizer
      日本RNA学会
    • Related Report
      2017 Research-status Report
  • [Presentation] RNA-RNA の相対結合自由エネルギー計算2016

    • Author(s)
      桜庭 俊, 浅井 潔, 亀田 倫史
    • Organizer
      理論化学討論会年会
    • Place of Presentation
      早稲田大学 西早稲田キャンパス(東京都新宿区)
    • Year and Date
      2016-05-23
    • Related Report
      2016 Research-status Report

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Published: 2016-04-21   Modified: 2021-02-19  

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