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Analysis on the structural polymorphism of IDPs by computer simulation

Planned

Project AreaTarget recognition and expression mechanism of intrinsically disordered protein
Project/Area Number 21113006
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionOsaka University

Principal Investigator

HIGO Junichi  大阪大学, たんぱく質研究所, 特任研究員 (80265719)

Co-Investigator(Kenkyū-buntansha) TAKANO Mitsunori  早稲田大学, 理工学術院, 教授 (40313168)
KIKUCHI Macoto  大阪大学, サイバーメディアセンター, 教授 (50195210)
Project Period (FY) 2009-07-23 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥102,180,000 (Direct Cost: ¥78,600,000、Indirect Cost: ¥23,580,000)
Fiscal Year 2013: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2012: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2011: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2010: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2009: ¥22,100,000 (Direct Cost: ¥17,000,000、Indirect Cost: ¥5,100,000)
Keywordsフォールディング / ドッキング / 自由エネルギー地形 / 計算機シミュレーション / 全原子モデル / 粗視化モデル
Research Abstract

Computer simulations were performed to physico-chemically understand the coupled folding and binding of intrinsically disordered proteins (IDPs). We expressed the system (IDP, its partner molecule, and solvent molecules) by an all-atom model, and an effective conformational sampling method, multicanonical molecular dynamics, was applied to the system. We visualized the fine structure of a free-energy landscape of the coupled folding and binding of the system. The free-energy landscape consisted of the native-like complex cluster and small non-native complex clusters, where free-energy barriers separated the clusters. Then, to understand the precise free-energy landscape from a more physical point of view, we used a coarse-grained model. The inter-cluster conformational transitions were explained by cooperative and competitive interactions in IDPs.

Report

(6 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • 2009 Annual Research Report

Research Products

(51 results)

All 2014 2013 2012 2011 2010 2009 Other

All Journal Article (32 results) (of which Peer Reviewed: 30 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (6 results) Book (7 results) Remarks (6 results)

  • [Journal Article] Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin2014

    • Author(s)
      Nie, QM., Togashi, A., Sasaki, TN., Takano, M., Sasai, M., Terada, TP
    • Journal Title

      PLoS Comp. Biol.

      Volume: 10

    • DOI

      10.1371/journal.pcbi.1003552

    • NAID

      120005476003

    • Related Report
      2013 Final Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin2014

    • Author(s)
      Q-M Nie, A. Togashi, T. N. Sasaki, M. Takano, M. Sasai, T. P. Terada
    • Journal Title

      PLoS Comput. Biol.

      Volume: 10

    • NAID

      120005476003

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Local representation of N-body Coulomb energy with path integrals2014

    • Author(s)
      T. Sugihara, J. Higo, H. Nakamura
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 未定

    • NAID

      40020091368

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations2014

    • Author(s)
      H. Shirai, K. Ikeda, K. Yamashita, Y. Tsuchiya, J. Sarmiento, S. Liang, T. Morokata, K. Mizuguchi, J. Higo, D. M. Standley, H. Nakamura
    • Journal Title

      Proteins

      Volume: 未定

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 全原子コンピュータシミュレーションで解き明かす、天然変成タンパク質の分子認識機構2014

    • Author(s)
      肥後順一、梅澤公二
    • Journal Title

      生物物理学会会誌「生物物理」

      Volume: 54 Pages: 96-99

    • Related Report
      2013 Annual Research Report
  • [Journal Article] A virtual-system coupled multicanonical molecular dynamics simulation : Principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent2013

    • Author(s)
      J. Higo, K. Umezawa, H. Nakamura
    • Journal Title

      J. Chem. Phys.

      Volume: 138 Pages: 184106-184106

    • DOI

      10.1063/1.4803468

    • Related Report
      2013 Final Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural flexibility of intrinsically disordered proteins induces stepwise target recognition2013

    • Author(s)
      Shirai, N.C., Kikuchi, M
    • Journal Title

      J. Chem. Phys

      Volume: 139 Pages: 225103-225103

    • DOI

      10.1063/1.4838476

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Frustration-induced protein intrinsic disorder2013

    • Author(s)
      Matsushita, K., Kikuchi, M
    • Journal Title

      J. Chem. Phys.

      Volume: 138 Pages: 105101-105101

    • DOI

      10.1063/1.4794781

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Short polypeptide with metastable structure2013

    • Author(s)
      K. Matsushita, M. Kikuchi
    • Journal Title

      Interdisciplinary Information Sciences

      Volume: 19 Pages: 29-34

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Frustration-induced protein intrinsic disorder2013

    • Author(s)
      K. Matsushita, M. Kikuchi
    • Journal Title

      J. Chem. Phys.

      Volume: 138 Pages: 105101-105101

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural flexibility of intrinsically disordered proteins induces stepwise target recognition2013

    • Author(s)
      N. C. Shirai, M. Kikuchi
    • Journal Title

      J. Chem. Phys.

      Volume: 139 Pages: 225103-225103

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multicanonical simulation of coupled folding and binding of intrinsically disordered protein using an Ising-like protein model2013

    • Author(s)
      K. Matsushita, M. Kikuchi
    • Journal Title

      J. Phys.: Conf. Ser.

      Volume: 454 Pages: 12034-12034

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A virtual-system coupled multicanonical molecular dynamics simulation: Principle and its application to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent2013

    • Author(s)
      J. Higo, K. Umezawa, H. Nakamura
    • Journal Title

      J. Chem. Phys.

      Volume: 138 Pages: 184106-184106

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A virtual-system coupled multicanonical molecular dynamics simulation: Principle and its application to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent2013

    • Author(s)
      Junichi Higo
    • Journal Title

      J. Chem. Phys.

      Volume: 未定

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Frustration-induced protein intrinsic disorder2013

    • Author(s)
      Katsuyoshi Matsushita
    • Journal Title

      J. Chem. Phys.

      Volume: 138 Pages: 105101-105101

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multicanonical Simulation of Coupled Folding and Binding of Intrinsically Disordered Protein using an Ising-Like Protein Model2013

    • Author(s)
      Katsuyoshi Matsushita
    • Journal Title

      Journal of Physics

      Volume: 未定

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Virtual states introduced for overcoming entropic barriers in conformational space2012

    • Author(s)
      Higo, J., Nakamura, H
    • Journal Title

      BIOPHYSICS

      Volume: 8 Issue: 0 Pages: 104-121

    • DOI

      10.2142/biophysics.8.139

    • NAID

      130002061588

    • ISSN
      1349-2942
    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes2012

    • Author(s)
      Higo, J., Ikebe, J., Kamiya, N., Nakamura, H
    • Journal Title

      Biophysical Reviews

      Volume: 4 Pages: 10448-10458

    • DOI

      10.1007/s12551-011-0063-6

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics2012

    • Author(s)
      Umezawa, K., Ikebe, J., Takano, M., Nakamura, H., Higo, J
    • Journal Title

      Biomolecules

      Volume: 2 Pages: 104-121

    • DOI

      10.3390/biom2010104

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Virtual states introduced for overcoming entropic barriers in conformational space2012

    • Author(s)
      Junichi Higo
    • Journal Title

      Biophysics

      Volume: 8 Pages: 104-121

    • NAID

      130002061588

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Temperature-enhanced association of proteins due to electrostatic interaction: A coarse-grained simulation of actin-myosin binding2012

    • Author(s)
      K. Okazaki
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 134 Pages: 8918-8925

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes2012

    • Author(s)
      J.Higo, J.Ikebe, N.Kamiya, H.Nakamura
    • Journal Title

      Biophysical Rev.

      Volume: 4 Pages: 27-44

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Free-energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-atom Computations2011

    • Author(s)
      Higo J, Nishimura Y, Nakamura H
    • Journal Title

      Journal of American Chemical Society

      Volume: 133 Pages: 10448-10458

    • DOI

      10.1021/ja110338e

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theory for Trivial Trajectory Parallelization of Multicanonical Molecular Dynamics and Application to a Polypeptide in Water2011

    • Author(s)
      Ikebe, J., Umezawa, K., Kamiya, N., Sugihara, T., Yonezawa, Y., Takano, Y., Nakamura, H., Higo, J
    • Journal Title

      J. Comput. Chem.

      Volume: 32 Pages: 1286-1297

    • DOI

      10.1002/jcc.21710

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A Free-energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-atom Computations2011

    • Author(s)
      J.Higo, Y.Nishimura, H.Nakamura
    • Journal Title

      J.Am.Chem.Soc.

      Volume: 133 Pages: 10448-10458

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster2011

    • Author(s)
      Ikebe, J., Standley, D.M., Nakamura, H., Higo J.
    • Journal Title

      Protein Science

      Volume: 20 Pages: 187-196

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theory for Trivial Trajectory Parallelization of Multicanonical Molecular Dynamics and Application to a Polypeptide in Water2011

    • Author(s)
      Ikebe, J., Umezawa, K., Kamiya, N., Sugihara, T., Yonezawa, Y., Takano, Y., Nakamura, H., Higo J.
    • Journal Title

      Journal of Computational Chemistry

      Volume: 32 Pages: 1286-1297

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor2010

    • Author(s)
      M. Takano, T. P. Terada, and M. Sasai
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: Vol.107, No.17 Pages: 7769-7774

    • DOI

      10.1073/pnas.0911830107

    • NAID

      120005475997

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor2010

    • Author(s)
      Takano, M., Terada, T.P., Sasai, M.
    • Journal Title

      Proc.Natl.Acad.Sci.USA

      Volume: 107 Pages: 7769-7774

    • NAID

      120005475997

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theory for Trivial Trajectory Parallelization of Multicanonical Molecular Dynamics and Application to a Polypeptide in Water2010

    • Author(s)
      Ikebe, J., Higo, J.
    • Journal Title

      Journal Computational Chemistry

      Volume: (in press 現在未定)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 単純軌跡和マルチカノニカル分子動力学法2010

    • Author(s)
      肥後順一
    • Journal Title

      アンサンブル(分子シミュレーション研究会会誌)

      Volume: 12 Pages: 8-10

    • NAID

      130004566659

    • Related Report
      2009 Annual Research Report
  • [Journal Article] Residue network in protein native structure belongs to the universality class of a three-dimensional critical percolation cluster2009

    • Author(s)
      Morita, H., Takano, M
    • Journal Title

      Phys. Rev

      Volume: E 79

    • DOI

      10.1103/physreve.79.020901

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Presentation] Effects of metastable structures on intrinsic disorder of protein2013

    • Author(s)
      Katsuyoshi Matsushita
    • Organizer
      The 2nd International Symposium on Intrinsically Disordered Proteins (ISIDP)
    • Place of Presentation
      理化学研究所横浜キャンパス ( 神奈川県 )
    • Year and Date
      2013-01-23
    • Related Report
      2012 Annual Research Report
  • [Presentation] Phosphorylation effect on the bound and free states of intrinsically disordered proteins investigated by coarse-grained model2013

    • Author(s)
      Koji Umezawa
    • Organizer
      The 2nd International Symposium on Intrinsically Disordered Proteins (ISIDP)
    • Place of Presentation
      理研横浜 ( 神奈川県 )
    • Year and Date
      2013-01-23
    • Related Report
      2012 Annual Research Report
  • [Presentation] Multicanonical Simulation of Coupled Folding and Binding of Intrinsically Disordered Protein on a Lattice Gas Protein2012

    • Author(s)
      Katsuyoshi Matsushita
    • Organizer
      CCP2012
    • Place of Presentation
      ニチイ学館 ・ 神戸ポートアイランドセンター ( 兵庫県 )
    • Year and Date
      2012-10-15
    • Related Report
      2012 Annual Research Report
  • [Presentation] 天然変性タンパク質の構造ゆらぎを生かした密度変化誘起型シグナル伝達過程2012

    • Author(s)
      白井伸宙
    • Organizer
      第12回蛋白質科学会
    • Place of Presentation
      名古屋国際会議場 ( 愛知県 )
    • Year and Date
      2012-06-21
    • Related Report
      2012 Annual Research Report
  • [Presentation] Free-energy landscape : the road map for protein conformational changes2011

    • Author(s)
      肥後順一
    • Organizer
      第34回に本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)(招待講演)
    • Year and Date
      2011-12-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] 天然変性タンパク質NRSFとパートナー蛋白質Sin3の結合/折れ畳みの自由エネルギー地名2010

    • Author(s)
      肥後順一
    • Organizer
      第10回蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(札幌)(招待講演)
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Book] Free-energy landscape of Intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics, Chapter 14 in "Protein Conformational Dynamics" (Han, K., Zhang, X., and Yang, M.eds.) Advances in Experimental Medicine and Biology 8052014

    • Author(s)
      Higo, J., Umezawa, K
    • Publisher
      Springer
    • Related Report
      2013 Final Research Report
  • [Book] Protein Conformational Dynamics, Advances in Experimental Medicine and Biology2014

    • Author(s)
      J. Higo, K. Umezawa
    • Total Pages
      21
    • Publisher
      Springer
    • Related Report
      2013 Annual Research Report
  • [Book] 生物物理学会会誌「生物物理」2013

    • Author(s)
      肥後順一
    • Total Pages
      5
    • Publisher
      全原子コンピュータシミュレーションで解き明かす、天然変成タンパク質の分子認識機構
    • Related Report
      2012 Annual Research Report
  • [Book] Protein Conformational Dynamics (Springer)2013

    • Author(s)
      Junichi Higo
    • Total Pages
      10
    • Publisher
      Free-energy landscape of Intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics
    • Related Report
      2012 Annual Research Report
  • [Book] 分子シミュレーション研究会会誌「アンサンブル」2012

    • Author(s)
      梅澤公二
    • Total Pages
      5
    • Publisher
      タンパク質表面近傍における水分子の集団的な動き(並進と配向)の解析
    • Related Report
      2012 Annual Research Report
  • [Book] 日本生物物理学会誌2012

    • Author(s)
      高野光則
    • Total Pages
      2
    • Publisher
      アクチン・ミオシン結合の計算機実験
    • Related Report
      2012 Annual Research Report
  • [Book] コンプレックス・ダイナミクスの挑戦第2章の"ダイナミックな蛋白質計算機シミュレーションの挑戦"(pp.39-76)の部分を担当2011

    • Author(s)
      高野光則
    • Total Pages
      38
    • Publisher
      共立出版
    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/IDP/

    • Related Report
      2013 Final Research Report
  • [Remarks] 天然変性タンパク質の分子認識機構と機能発現

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/IDP/

    • Related Report
      2013 Annual Research Report
  • [Remarks] 天然変性タンパク質の分子認識機構と機能発現

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/IDP/

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/IDP/index.html

    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/IDP/index.html

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/IDP/

    • Related Report
      2009 Annual Research Report

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Published: 2009-03-31   Modified: 2018-03-28  

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