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Molecular Informatical Breakthrough on the Water Molecule Network Controlled by Biomacromolecules and Cosolvents

Research Project

Project/Area Number 19750004
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Physical chemistry
Research InstitutionAoyama Gakuin University (2008-2009)
Nagoya University (2007)

Principal Investigator

YU Isseki  Aoyama Gakuin University, 理工学部, 助教 (90402544)

Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥3,730,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥330,000)
Fiscal Year 2009: ¥260,000 (Direct Cost: ¥200,000、Indirect Cost: ¥60,000)
Fiscal Year 2008: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2007: ¥2,300,000 (Direct Cost: ¥2,300,000)
Keywords分子動力学 / タンパク質 / エクトイン / 溶媒効果 / 選択的水和 / Kirkwood-Buff理論 / 計算化学 / 理論化学 / 生物物理
Research Abstract

In the cells of organisms living in the extreme environments, organic cosolvents, such as amino acids or sugars, are accumulated in high concentrations. This study aims to understand the influence of cosolvent additions on the property of water molecules and on the function of biomacromolecules. Using the molecular dynamic simulation combined with the statistical mechanical theory of liquid, some of the microscopic mechanisms of cosolvent protecting the protein structure against the high temperature were elucidated.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (32 results)

All 2009 2008 2007

All Journal Article (9 results) (of which Peer Reviewed: 7 results) Presentation (21 results) Book (2 results)

  • [Journal Article] Intrinsic Alterations in the Partial Molar Volume on the Protein Denaturation: Surficial Kirkwood-Buff Approach2009

    • Author(s)
      Isseki Yu, Masayoshi Takayanagi, Masataka Nagaoka
    • Journal Title

      Journal of Physical Chemistry B 113

      Pages: 3543-3547

    • Related Report
      2009 Final Research Report
  • [Journal Article] Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations: Time-Resolved Vibrational Analysis and Surficial Kirkwood-Buff Theory2009

    • Author(s)
      Masataka Nagaoka, Isseki Yu, Masayoshi Takayanagi
    • Journal Title

      Proteins: Energy, Heat and Signal Flow (D.M. Leitner and I.E. Straub, Eds. )

      Pages: 169-196

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations : Time-Resolved Vibrational Analysis and Surficial Kirkwood-Buff Theory2009

    • Author(s)
      Masataka Nagaoka, Isseki Yu, Masayoshi Takayanagi
    • Journal Title

      Proteins : Energy, Heat and Signal Flow

      Pages: 169-196

    • Related Report
      2009 Annual Research Report
  • [Journal Article] IntrinSiC Alterations in the Partial Molar Volume on the Protein Denaturation : Surficial Kirkwood-Buff Approach2009

    • Author(s)
      Isseki Yu, Masayoshi Takayanagi and Masataka Nagaoka
    • Journal Title

      Journal of PhySiCal Chemistry B 113

      Pages: 3543-3547

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Carrier Method for the General Evaluation and Control of Pose, Molecular Conformation, Tracking, and the Like2009

    • Author(s)
      Eckhard Hitzer, Kanta Tachibana, Sven Buchholz and Isseki Yu
    • Journal Title

      Advances in Applied Clifford Algebras (印刷中)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Surficial Kirkwood-Buff Approach on the Preferential Interaction of Urea and Ectoine with Protein2008

    • Author(s)
      Isseki Yu, Masataka Nagaoka
    • Journal Title

      Proceedings of International Symposium on Frontiers of Computational Science

      Pages: 9-14

    • Related Report
      2009 Final Research Report 2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Carrier Method for the General Evaluation and Control of Pose, Molecular Conformation, Tracking, etc.2008

    • Author(s)
      Eckhard Hitzer, Kanta Tachibana, Sven Buchholz, Isseki Yu
    • Journal Title

      Advances in Applied Clifford Algebras 19

      Pages: 339-364

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration2007

    • Author(s)
      Isseki Yu, Masataka Nagaoka
    • Journal Title

      Journal of Physical Chemistry B 111

      Pages: 10231-10238

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration.2007

    • Author(s)
      優 乙石, 長岡 正隆
    • Journal Title

      Journal of Physical Chemistry B 111

      Pages: 10231-10238

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] Molecular Picture of Protein Volume Paradox: A Study by Surficial Kirkwood-Buff Integral Method2009

    • Author(s)
      Isseki YU, Masataka Nagaoka
    • Organizer
      The fourth Asian Pacific Conference on Theoretical & Computational Chemistry
    • Place of Presentation
      クアラルンプール
    • Year and Date
      2009-12-22
    • Related Report
      2009 Final Research Report
  • [Presentation] Molecular Picture of Protein Volume Paradox : A Studv by Surficial Kirkwood-Buff Integral Method2009

    • Author(s)
      優乙石, 長岡正隆
    • Organizer
      The fourth Asian Pacific Conference on Theoretical & Computational Chemistry
    • Place of Presentation
      ポートディクソンマレーシア
    • Year and Date
      2009-12-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Protein Volume Paradox and its Molecular Picture: A Study by Surficial Kirkwood-Buff Integral Method2009

    • Author(s)
      優乙石長岡正隆
    • Organizer
      第47回生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      2009-11-01
    • Related Report
      2009 Final Research Report
  • [Presentation] Protein Volume Paradox and its Molecular Picture : A Study by Surficial Kirkwood-Buff Integral Method2009

    • Author(s)
      優乙石, 長岡正隆
    • Organizer
      第47回生物物理学会
    • Place of Presentation
      徳島
    • Year and Date
      2009-10-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] 部分モル体積の空間分布から見たタンパク質変性:カークウツド-パフ積分法による考察2009

    • Author(s)
      優乙石、長岡正隆
    • Organizer
      第3回分子科学討論会
    • Place of Presentation
      名古屋
    • Year and Date
      2009-09-22
    • Related Report
      2009 Final Research Report
  • [Presentation] 表面カークウツド. パフ積分法によるタンパク質部分モル体積不変性の微視的理解2009

    • Author(s)
      優乙石、長岡正隆
    • Organizer
      理論化学討論会
    • Place of Presentation
      東京
    • Year and Date
      2009-05-30
    • Related Report
      2009 Final Research Report
  • [Presentation] 表面カークウッド-バフ積分法によるタンパク質部分モル体積不変性の微視的理解2009

    • Author(s)
      優乙石, 長岡正隆
    • Organizer
      第12回理論化学討論会
    • Place of Presentation
      東京
    • Year and Date
      2009-05-28
    • Related Report
      2009 Annual Research Report
  • [Presentation] 部分モル体積の空間分布から見たタンパク質変性:カークウッド-パフ積分法による考察2009

    • Author(s)
      優乙石, 長岡正隆
    • Organizer
      第3回分子科学討論会
    • Place of Presentation
      名古屋
    • Year and Date
      2009-05-28
    • Related Report
      2009 Annual Research Report
  • [Presentation] Solvent Effect on the Protein Structure : Surficial Kirkwood?Buff Approach2009

    • Author(s)
      Isseki Yu, Masataka Nagaoka
    • Organizer
      International Symposium on Frontiers of Computational Science
    • Place of Presentation
      Nagoya, Japan
    • Year and Date
      2009-03-16
    • Related Report
      2008 Annual Research Report
  • [Presentation] Surficial Kirkwood-Buff Approach on the Preferential Interaction of Urea and Ectoine with Protein2008

    • Author(s)
      Isseki YU, Masataka Nagaoka
    • Organizer
      Intemational Symposium on Frontiers of Computational Science
    • Place of Presentation
      名古屋
    • Year and Date
      2008-11-29
    • Related Report
      2009 Final Research Report
  • [Presentation] Surficial Kirkwood?Buff Approach Combined with All-Atom Molecular Dynamics Simulation : Analysis of Solvent Structure around Biomolecules2008

    • Author(s)
      Isseki Yu, Masataka Nagaoka
    • Organizer
      International Symposium on Frontiers of Computational Science
    • Place of Presentation
      Nagoya, Japan
    • Year and Date
      2008-11-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] 表面Kirkwood-Buff法による補償溶質エクトイン選択的排除の分子論的理解2008

    • Author(s)
      優乙石、長岡正隆
    • Organizer
      日本化学会第88回春季会
    • Place of Presentation
      東京
    • Year and Date
      2008-03-28
    • Related Report
      2009 Final Research Report
  • [Presentation] 表面Kirkwood-Buff法による補償溶質エクトイン選択的排除の分子論的理解2008

    • Author(s)
      優 乙石, 長岡 正隆
    • Organizer
      日本化学会第88春季年会
    • Place of Presentation
      東京
    • Year and Date
      2008-03-28
    • Related Report
      2007 Annual Research Report
  • [Presentation] Molecular Mechanism of the Preferential Exclusion of Compatible Solute Ectoine on the Protein Surface2007

    • Author(s)
      優乙石、長岡正隆
    • Organizer
      第45回生物物理学会年会
    • Place of Presentation
      東京
    • Year and Date
      2007-12-23
    • Related Report
      2009 Final Research Report
  • [Presentation] Molecular Mechanism of the Preferential Exclusion of Compatible Solute Ectoine on the Protein Surface2007

    • Author(s)
      優 乙石, 長岡 正隆
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Surficial Kirkwood-Buff Approach2007

    • Author(s)
      Isseki YU, Masataka Nagaoka
    • Organizer
      The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry
    • Place of Presentation
      北京
    • Year and Date
      2007-09-23
    • Related Report
      2009 Final Research Report
  • [Presentation] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Surficial Kirkwood-Buff Approach2007

    • Author(s)
      優 乙石, 長岡 正隆
    • Organizer
      The 3rd Asian Pacific Conference of Theoretical and Computational Chemistry (APCTCIII)
    • Place of Presentation
      北京
    • Year and Date
      2007-09-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] エクトイン水溶液中のタンパク質および小ペプチド表面における選択的水和の微視的描像2007

    • Author(s)
      優 乙石, 長岡 正隆
    • Organizer
      第1回分子科学討論会
    • Place of Presentation
      仙台
    • Year and Date
      2007-09-20
    • Related Report
      2007 Annual Research Report
  • [Presentation] エクトイン水溶液中のタンパク質および小ペプチド表面における選択的水和2007

    • Author(s)
      優乙石、長岡正隆
    • Organizer
      第1回分子科学討論会
    • Place of Presentation
      仙台
    • Year and Date
      2007-09-19
    • Related Report
      2009 Final Research Report
  • [Presentation] エクトイン水溶液中のタンパク質表面における選択的水和発現機構の分子論的考察2007

    • Author(s)
      優乙石、長岡正隆
    • Organizer
      第10回理論化学討論会
    • Place of Presentation
      名古屋
    • Year and Date
      2007-05-15
    • Related Report
      2009 Final Research Report
  • [Presentation] エクトイン水溶液中のタンパク質表面における選択的水和発現機構の分子論的考察2007

    • Author(s)
      優 乙石, 長岡 正隆
    • Organizer
      第10同理論化学討論会
    • Place of Presentation
      名古屋
    • Year and Date
      2007-05-14
    • Related Report
      2007 Annual Research Report
  • [Book] すぐできる分子シミュレーションビギナーズマニュアル2008

    • Author(s)
      長岡正隆編・著優乙石, 他7名著
    • Publisher
      講談社
    • Related Report
      2009 Final Research Report
  • [Book] すぐできる分子シミュレーションビギナーズマニュアル2008

    • Author(s)
      長岡正隆(編・著)優乙石, 他(著)
    • Total Pages
      291
    • Publisher
      講談社サイエンティフィク
    • Related Report
      2008 Annual Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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