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2013 Fiscal Year Final Research Report

Development and validation of a new force field depending on protein structures for molecular dynamics simulations

Research Project

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Project/Area Number 23657103
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionOsaka University

Principal Investigator

NAKAMURA Haruki  大阪大学, たんぱく質研究所, 教授 (80134485)

Co-Investigator(Kenkyū-buntansha) TAKANO Yu  大阪大学, たんぱく質研究所, 助教 (30403017)
Project Period (FY) 2011 – 2012
Keywords蛋白質 / 生物物理 / 分子シミュレーション / 構造エネルギー / 構造予測
Research Abstract

In order to develop a new force field depending on the tertiary structures of proteins, which can be used in classical molecular dynamics simulations, we performed highly accurate quantum chemical computations for typical and stable secondary structures, alpha-helices and beta-sheets (both parallel and anti-parallel conformations). Then, the conformation energies of a variety of the peptide structures were compared with those calculated with AMBER99-SB classical force field. Consequently, for parallel and anti-parallel beta-sheets, the energies given by the classical force field almost agreed with those by quantum chemical calculations. On the contrary, the former energies were much lower than the latter energies for alpha-helices, and alpha-helices were more stabilized as the peptide becomes longer with the classical force field. These deviations in the conformation energies calculated with the classical force field were well compensated depending on the tertiary structures.

  • Research Products

    (10 results)

All 2014 2013 2012 Other

All Journal Article (2 results) (of which Peer Reviewed: 2 results) Presentation (7 results) (of which Invited: 2 results) Remarks (1 results)

  • [Journal Article] Density functional study of the phosphodiester hydrolysis of RNA in RNA/DNA hybrid by RNase H2014

    • Author(s)
      Kita M, Nakamura H, Takano Y
    • Journal Title

      Mol. Phys

      Volume: 112 Pages: 355-364

    • DOI

      10.1080/00268976.2013.820854

    • Peer Reviewed
  • [Journal Article] Electron density based interaction energy estimation of the special pair in the photosynthetic reaction center2012

    • Author(s)
      Yamasaki H, Nakamura H
    • Journal Title

      Chem. Phys. Lett

      Volume: 536 Pages: 129-135

    • DOI

      10.1016/j.cplett.2012.03.087

    • Peer Reviewed
  • [Presentation] Density functional study of molecular interactions in secondary structures of proteins2014

    • Author(s)
      Takano Y, Nakamura H
    • Organizer
      The 4th Asia Pacific Protein Association (APPA) Conference
    • Place of Presentation
      ICC Jeju, Korea
    • Year and Date
      20140517-20
  • [Presentation] Density functional study of local and nonlocal molecular interactions in secondary structure2014

    • Author(s)
      Takano Y, Nakamura H
    • Organizer
      54th Sanibel Symposium
    • Place of Presentation
      The King and Prince Golf & Beach Resort, Georgia, USA
    • Year and Date
      2014-02-18
  • [Presentation] 二次構造形成に関する局所および非局所相互作用に関する計算化学的研究2014

    • Author(s)
      鷹野 優, 中村 春木
    • Organizer
      スーパーコンピュータ・ワークショップ2013
    • Place of Presentation
      自然科学研究機構・岡崎コンファレンスセンター(岡崎市)
    • Year and Date
      2014-01-21
  • [Presentation] Theoretical study of local- and nonlocal- molecular interactions in secondary structures2013

    • Author(s)
      Takano Y, Nakamura H
    • Organizer
      5th JCS (Japan, Czech, Slovakia) International Symposium on Theoretical Chemistry
    • Place of Presentation
      東大寺総合文化センター(奈良市)
    • Year and Date
      20131203-04
    • Invited
  • [Presentation] Towards quantitative analysis and prediction of protein-protein interactions2013

    • Author(s)
      Nakamura H
    • Organizer
      5th JCS (Japan, Czech, Slovakia) International Symposium on Theoretical Chemistry
    • Place of Presentation
      東大寺総合文化センター(奈良市)
    • Year and Date
      2013-12-03
    • Invited
  • [Presentation] Quantum chemical study of intra- and inter- molecular interactions in secondary structures2013

    • Author(s)
      鷹野 優, 中村 春木
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      京都国際会議場(京都市)
    • Year and Date
      2013-10-28
  • [Presentation] Atoms in molecules 法によるタンパク質α へリックス, β シートの水素結合相互作用の理論解析2012

    • Author(s)
      山崎 秀樹, 中村 春木
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス(名古屋市)
    • Year and Date
      20120922-24
  • [Remarks]

    • URL

      http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_pi.html

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Published: 2015-06-25  

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