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2013 Fiscal Year Final Research Report

Analysis on the structural polymorphism of IDPs by computer simulation

Planned Research

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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
Keywordsフォールディング / ドッキング / 自由エネルギー地形
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.

  • Research Products

    (13 results)

All 2014 2013 2012 2011 2010 2009 Other

All Journal Article (11 results) (of which Peer Reviewed: 10 results) Book (1 results) Remarks (1 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 Comput Biol

      Volume: 10 Pages: e1003552

    • DOI

      10.1371/journal.pcbi.1003552

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

      J. Chem. Phys

      Volume: 138 Pages: 184106

    • DOI

      10.1063/1.4803468

    • Peer Reviewed
  • [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

    • DOI

      10.1063/1.4838476

    • Peer Reviewed
  • [Journal Article] Frustration-induced protein intrinsic disorder2013

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

      J. Chem. Phys

      Volume: 138 Pages: 105101

    • DOI

      10.1063/1.4794781

    • 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 Pages: 139-144

    • DOI

      10.2142/biophysics.8.139

    • 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 Rev

      Volume: 4 Pages: 27-44

    • DOI

      10.1007/s12551-011-0063-6

  • [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

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

      J. Am. Chem. Soc

      Volume: 133 Pages: 10448-10458

    • DOI

      10.1021/ja110338e

    • 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

    • 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

    • DOI

      10.1073/pnas.0911830107

    • Peer Reviewed
  • [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 Pages: 020901®

    • DOI

      10.1103/PhysRevE.79.020901

    • Peer Reviewed
  • [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
    • Total Pages
      331-351
    • Publisher
      Springer
  • [Remarks]

    • URL

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

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Published: 2015-06-25  

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