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Breakthrough on the high pressure biomolecule reaction with computational chemistry of the volume change

Research Project

Project/Area Number 25410025
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Yu Isseki  国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 研究員 (90402544)

Research Collaborator Sugita Yuji  国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 主任研究員
Wang Po-hung  国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 特別研究員
Project Period (FY) 2013-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2013: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Keywords高圧 / 細胞環境 / 分子混雑 / 分子動力学 / 蛋白質 / 水和 / 部分モル体積 / 深海 / 分子動力学シミュレーション
Outline of Final Research Achievements

This project investigates the influence of the high hydrostatic pressure on the structure and dynamics of proteins by calculating the protein volume in solution with all-atom molecular dynamics simulations. On the other hand, the cytoplasm, which is exposed to high pressure, is highly crowded with various kinds of proteins and nucleic acids. This project investigates also physicochemical characteristics of such a cellular environment and its response to high pressure. Throughout this project, the hydration volume of proteins and excluded volume effect of macromolecules in cell are understood at the molecular level. In addition, the computer programs to analyze the geometric properties of molecule are developed and parallelized in order to perform the project-related calculations on the super computer systems. These programs will be released near future.

Report

(5 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (17 results)

All 2017 2016 2015 2014 2013

All Journal Article (3 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 2 results,  Acknowledgement Compliant: 2 results,  Open Access: 1 results) Presentation (14 results) (of which Int'l Joint Research: 1 results,  Invited: 6 results)

  • [Journal Article] Influence of Protein Crowder Size on Hydration Structure and Dynamics in Macromolecular Crowding2017

    • Author(s)
      Po-hung Wang, Isseki Yu, Michael Feig, Yuji Sugita
    • Journal Title

      Chemical Physics Letters

      Volume: 671 Pages: 63-70

    • DOI

      10.1016/j.cplett.2017.01.012

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] バクテリア細胞質中の代謝物-蛋白質間相互作用:全原子細胞質モデルと大規模分子動力学計算による理論的研究2017

    • Author(s)
      優乙石, 杉田有治
    • Journal Title

      分子シミュレーション研究会誌「アンサンブル」

      Volume: Vol. 19, No. 2 Pages: 75-80

    • NAID

      130006729057

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm2016

    • Author(s)
      Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M
    • Journal Title

      eLife

      Volume: 5

    • DOI

      10.7554/elife.19274

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] 全原子細胞質モデルと大規模分子動力学計算による細胞内生体分子ダイナミクスの理論的解明2017

    • Author(s)
      優乙石
    • Organizer
      物性研究所スパコン共同利用・CCMS合同研究会「計算物質科学の今と未来」
    • Place of Presentation
      東京大学 千葉県柏市
    • Year and Date
      2017-04-04
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Theoretical Study of the Influence of Cellular Crowding on the Dynamics and Interactions of proteins2016

    • Author(s)
      優乙石、森貴治、安藤格士、Jaewoon Jung、原田隆平、Michael Feig、杉田有治
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜 神奈川県横浜市
    • Year and Date
      2016-12-01
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Influence of Macromolecular Crowding on the Dynamics and Interactions of proteins: All-atom Molecular Dynamics Study2016

    • Author(s)
      Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Michael Feig, Yuji Sugita
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      エポカルつくば 茨城県つくば市
    • Year and Date
      2016-11-26
    • Related Report
      2016 Annual Research Report
  • [Presentation] バクテリア細胞質中の混み合い環境下における蛋白質と代謝物の全原子分子動力学シミュレーション2015

    • Author(s)
      Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
    • Organizer
      38回日本分子生物学会年会、88回 日本生化学大会 合同大会
    • Place of Presentation
      兵庫県・神戸市
    • Year and Date
      2015-12-01
    • Related Report
      2015 Research-status Report
  • [Presentation] 細胞内環境での蛋白質の分子運動と機能2015

    • Author(s)
      Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
    • Organizer
      生命医薬情報学連合大会2015大会スポンサーセッション生命科学におけるインフォマティクスと物理化学の融合
    • Place of Presentation
      京都・京都大学・宇治キャンパス
    • Year and Date
      2015-10-30
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Dynamics, Stability, and Interactions of Proteins and Metabolites in Bacterial Cytoplasm: All-atom Molecular Dynamics Study2015

    • Author(s)
      Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      石川県・金沢大学
    • Year and Date
      2015-09-15
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Atomistic Molecular Dynamics Simulation of a Complete Model of Bacterial Cytoplasm2015

    • Author(s)
      Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
    • Organizer
      International Conference on Computational Methods (ICCM) 2015
    • Place of Presentation
      ニュージーランド・オークランド
    • Year and Date
      2015-07-15
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] All-atom Molecular Dynamics Simulation of the Complete Model of Bacterial Cytoplasm”2014

    • Author(s)
      Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
    • Organizer
      第5回AICS国際シンポジウム
    • Place of Presentation
      計算科学研究機構/神戸市/兵庫県
    • Year and Date
      2014-12-08 – 2014-12-09
    • Related Report
      2014 Research-status Report
  • [Presentation] Po-hung Wang, Isseki Yu, Michael Feig, and Yuji Sugita2014

    • Author(s)
      The solvent-accessible surface area of proteins affects water structure and dynamics
    • Organizer
      第5回AICS国際シンポジウム
    • Place of Presentation
      計算科学研究機構/神戸市/兵庫県
    • Year and Date
      2014-12-08 – 2014-12-09
    • Related Report
      2014 Research-status Report
  • [Presentation] Dynamics and Interactions of Macromolecules in the Bacterial Cytoplasm: All-atom Molecular Dynamics Study2014

    • Author(s)
      Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌コンベンションセンター/札幌/北海道
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] The solvent-accessible surface area of proteins affects water structure and dynamics2014

    • Author(s)
      Po-hung Wang, Isseki Yu, Michael Feig, and Yuji Sugita
    • Organizer
      日本生物物理学会第52回年会
    • Place of Presentation
      札幌コンベンションセンター/札幌/北海道
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] Dynamics and Interactions of Macromolecules in the Cytoplasm of Mycoplasma Genitalium: All-atom Molecular Dynamics Study2014

    • Author(s)
      Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
    • Organizer
      Workshop on Computer Modeling and Simulation of Biomolecular Systems
    • Place of Presentation
      理化学研究所/和光市/埼玉県
    • Year and Date
      2014-09-22
    • Related Report
      2014 Research-status Report
  • [Presentation] Space-Time Characteristics of the Protein Thermodynamic Quantities under the Molecular Crowding Condition of Cytoplasm in Extremophiles: Kirkwood-Buff Approach Combined with Molecular Dynamics Simulation2014

    • Author(s)
      Isseki Yu
    • Organizer
      Biophysical Society 58th Annual Meeting
    • Place of Presentation
      サンフランシスコ
    • Related Report
      2013 Research-status Report
  • [Presentation] Kirkwood-Buff積分法による蛋白質移相自由エネルギーの三次元可視化: 細胞内分子混雑効果の微視的理解に向けて2013

    • Author(s)
      優 乙石
    • Organizer
      計算統計物理学第4回研究会
    • Place of Presentation
      山口大学
    • Related Report
      2013 Research-status Report
    • Invited

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Published: 2014-07-25   Modified: 2019-07-29  

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