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Development of a complex structure prediction method between proteins using binding free-energy as a scoring function

Research Project

Project/Area Number 25440070
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biophysics
Research InstitutionInstitute of Physical and Chemical Research (2015)
Osaka University (2013-2014)

Principal Investigator

Kamiya Narutoshi  国立研究開発法人理化学研究所, 計算科学研究機構, 研究員 (80420462)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2014: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2013: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Keywords自由エネルギー / 分子動力学シミュレーション / 抗原抗体 / 立体構造予測
Outline of Final Research Achievements

A computational method that can predict both the complex structure and the affinity between proteins such as antigen-antibody with high speed and accuracy has been developed. This method is composed of decoy generation by rough docking, followed by ranking of the decoys using the free-energy obtained from molecular dynamics simulation as a scoring function. We applied this method to PPARγ, which revealed that as the ligand dissociates, it passes near R288. Decoy sets of hemagglutinin-antibody and adenosine receptor-antibody were ranked by GB/SA scoring, where the near-native decoy was ranked within top 2. The binding free-energy calculation of hemagglutinin-antibody reproduced the experimental value better in comparison with the GB/SA method.

Report

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

    (24 results)

All 2016 2015 2014 2013 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 3 results,  Acknowledgement Compliant: 1 results) Presentation (16 results) (of which Int'l Joint Research: 3 results) Book (1 results) Remarks (1 results)

  • [Journal Article] NMR Characterization of the Interaction of the Endonuclease Domain of MutL with Divalent Metal Ions and ATP2014

    • Author(s)
      Mizushima R, Kim JK, Suetake I, Tanaka H, Takai T, Kamiya N, Takano Y, Mishima Y, Tajima S, Goto Y, Fukui K, *Lee YH
    • Journal Title

      PLoS One

      Volume: 9 Issue: 6 Pages: e98554-e98554

    • DOI

      10.1371/journal.pone.0098554

    • NAID

      120006557621

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The Zero-multipole summation method for estimating electrostatic interactions in molecular dynamics : analysis of the accuracy and application to liquid systems2014

    • Author(s)
      Fukuda I, Kamiya N, Nakamura H
    • Journal Title

      J. Chem. Phys

      Volume: 140 Issue: 19 Pages: 194307-194307

    • DOI

      10.1063/1.4875693

    • NAID

      120005596268

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure of the entire stalk region of the dynein motor domain2014

    • Author(s)
      Yosuke Nishikawa, Takuji Oyama, Narutoshi Kamiya, Takahide Kon, Yoko Y. Toyoshima, Haruki Nakamura, Genji Kurisu
    • Journal Title

      Journal of Molecular Biology

      Volume: 426 Issue: 19 Pages: 3232-3245

    • DOI

      10.1016/j.jmb.2014.06.023

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Specific non-local interactions are not necessary for recovering native protein dynamics2014

    • Author(s)
      Dasgupta B, Kasahara K, Kamiya N, Nakamura H, Kinjo AR
    • Journal Title

      PLoS ONE

      Volume: 9 Issue: 3 Pages: e91347-e91347

    • DOI

      10.1371/journal.pone.0091347

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics simulations of a double-stranded DNA in an explicit solvent model with zero-dipole summation method2013

    • Author(s)
      Arakawa T, Kamiya N, Nakamura H, Fukuda I
    • Journal Title

      PLoS ONE

      Volume: 8 Issue: 10 Pages: e76606-e76606

    • DOI

      10.1371/journal.pone.0076606

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions2013

    • Author(s)
      Mashimo T, Fukunishi Y, Kamiya N, Takano Y, Fukuda I, Nakamura H
    • Journal Title

      J. Chem. Theory Comput

      Volume: 9 Issue: 12 Pages: 5599-5609

    • DOI

      10.1021/ct400342e

    • NAID

      120005604144

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] Ligand binding studies of the nuclear receptor PPARgamma using FRET and MD2016

    • Author(s)
      N. Kamiya, T. Shiraki
    • Organizer
      The 60th annual meeting of Biophysical Society
    • Place of Presentation
      Los Angeles convention center, Los Angeles, USA
    • Year and Date
      2016-02-28
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Accurate ensemble modeling of CDR-H3 loop in antibody2015

    • Author(s)
      H. Nishigami, G.-J. Bekker, N. Kamiya, J. Higo, H. Nakamura
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学 角間キャンパス, 金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] A novel method to determine the optimal unbinding path between receptor and ligand using advanced molecular dynamics simulations2015

    • Author(s)
      G.-J. Bekker, N. Kamiya, H. Nakamura
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学 角間キャンパス, 金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] In-vitro and in-silico studies of ligand binding to the nuclear receptor PPARgamma using FRET and MD2015

    • Author(s)
      N. Kamiya, G.-J. Bekker, T. Shiraki, H. Nakamura
    • Organizer
      The 29th annual symposium of the Protein Society
    • Place of Presentation
      Fira de Barcelona, Barcelona, Spain
    • Year and Date
      2015-07-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development and application of novel non-Ewald methods for calculating electrostatic interactions in molecular simulations2015

    • Author(s)
      I. Fukuda, N. Kamiya, H. Wang, K. Kasahara, H. Nakamura
    • Organizer
      The 29th annual symposium of the Protein Society
    • Place of Presentation
      Fira de Barcelona, Barcelona, Spain
    • Year and Date
      2015-07-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] FRET法とRAMD法を用いた核内受容体PPARγのリガンド結合に関する実験・理論的研究2015

    • Author(s)
      神谷 成敏、ベッカー ガージャン、白木 琢磨、中村 春木
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール, 徳島
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] Elastic property of dynein motor domain obtained from all-atom molecular dynamics simulations in explicit water2015

    • Author(s)
      N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
    • Organizer
      Biophysical society 59th annual meeting
    • Place of Presentation
      Baltimore convention center, Baltimore, USA
    • Year and Date
      2015-02-07 – 2015-02-11
    • Related Report
      2014 Research-status Report
  • [Presentation] 溶媒を陽に考慮した全原子分子動力学シミュレーションから得られたダイニンの弾性2014

    • Author(s)
      N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
    • Organizer
      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
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] Model building of antibody-antigen complex structures using GB/SA scores2014

    • Author(s)
      N. Kamiya, N. Shimba, H. Nakamura
    • Organizer
      The 28th annual meeting of the protein society
    • Place of Presentation
      The Manchester grand Hyatt San Diego, San Diego, USA
    • Year and Date
      2014-07-27 – 2014-07-30
    • Related Report
      2014 Research-status Report
  • [Presentation] 抗原抗体ドッキングのデコイセット評価法2014

    • Author(s)
      榛葉 教子、神谷 成敏、中村 春木
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      ワークピア横浜、横浜
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Research-status Report
  • [Presentation] Molecular dynamics study on evaluation of a decoy set generated by docking between antibody and antigen2014

    • Author(s)
      N. Kamiya, N. Shimba, H. Nakamura
    • Organizer
      The 4th Asia pacific protein association conference
    • Place of Presentation
      International convention center, Jeju, Korea
    • Year and Date
      2014-05-17 – 2014-05-20
    • Related Report
      2014 Research-status Report
  • [Presentation] A comparison of 3D conformations of endothelin-1 analogs to find the pharmacophore model required for endothelin ligand2014

    • Author(s)
      B. Ma, T. Kawabata, N. Kamiya, H. Nakamura
    • Organizer
      Biophysical society 58th annual meeting
    • Place of Presentation
      Moscone center, San Francisco, USA
    • Related Report
      2013 Research-status Report
  • [Presentation] Molecular dynamics simulations of dynein motor domain in explicit water2014

    • Author(s)
      N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
    • Organizer
      Biophysical society 58th annual meeting
    • Place of Presentation
      Moscone center, San Francisco, USA
    • Related Report
      2013 Research-status Report
  • [Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water2013

    • Author(s)
      N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
    • Organizer
      The 27th annual symposium of the protein society
    • Place of Presentation
      Boston marriott copley place, Boston, USA
    • Related Report
      2013 Research-status Report
  • [Presentation] Crystal structure of endo-1,3-beta-glucanase and its binding to laminarioligosaccharide2013

    • Author(s)
      M. Oda, Y. Tanabe, N. Komichi, N. Kamiya, H. Nakamura, B. Mikami
    • Organizer
      The 27th annual symposium of the protein society
    • Place of Presentation
      Boston marriott copley place, Boston, USA
    • Related Report
      2013 Research-status Report
  • [Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water2013

    • Author(s)
      N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura
    • Organizer
      Dynein 2013 international workshop
    • Place of Presentation
      Orbis Hall, Kobe, Japan
    • Related Report
      2013 Research-status Report
  • [Book] 見てわかる構造生命科学2014

    • Author(s)
      中村 春木 編
    • Total Pages
      326
    • Publisher
      化学同人
    • Related Report
      2014 Research-status Report
  • [Remarks] 大阪大学 蛋白質研究所 附属蛋白質解析先端研究センター 蛋白質情報科学研究室

    • URL

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

    • Related Report
      2014 Research-status Report

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

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