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2010 Fiscal Year Final Research Report

Roles of hyper-anisotropic dynamics and frustration on protein function investigated in sub-msec order

Research Project

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Project/Area Number 19370062
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionThe University of Tokyo

Principal Investigator

KITAO Akio  The University of Tokyo, 分子細胞生物学研究所, 准教授 (30252422)

Project Period (FY) 2007 – 2010
Keywordsタンパク質 / 超異方性 / 動態 / 機能 / フラストレーション
Research Abstract

To elucidate the detailed protein functional principle in broad time and space ranges, we focused on the dynamics of nano to sub-milli sec order, observed function relevant protein dynamics by molecular simulation, and studied the hyper anisotropy and frustration of the systems. We also have developed the methods to calculate free energy landscape from massive parallel simulations and to extract correlated motions in high dimensional dynamics and used them to investigate the relation between protein dynamics and function.

  • Research Products

    (19 results)

All 2011 2010 2009 2008 2007 Other

All Journal Article (18 results) (of which Peer Reviewed: 17 results) Remarks (1 results)

  • [Journal Article] Multi-scale free energy landscape calculation method by combination of coarse-grained and all-atom models2011

    • Author(s)
      Ryuhei Harada, Akio Kitao
    • Journal Title

      Chemical Physics Letters 503(1-3)

      Pages: 145-152

    • Peer Reviewed
  • [Journal Article] Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding2011

    • Author(s)
      Mariko Higuchi, Jumpei Fujii, Yoshiteru, Yonetani, Akio Kitao, Nobuhiro Go
    • Journal Title

      Journal of Structural Biology 173

      Pages: 20-28

    • Peer Reviewed
  • [Journal Article] Detecting coupled collective motions in protein by independent subspace analysis2010

    • Author(s)
      Shun Sakuraba, Yasumasa Joti, Akio Kitao
    • Journal Title

      Journal of Chemical Physics 133(18)

      Pages: 185102(1-10)

    • Peer Reviewed
  • [Journal Article] The Effect of End Constraints on Protein Loop Kinematics2010

    • Author(s)
      Steven Hayward, Akio Kitao
    • Journal Title

      Biophys.J. 98(9)

      Pages: 1976-1985

    • Peer Reviewed
  • [Journal Article] Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export2010

    • Author(s)
      Yumiko Saijo-Hamamoto, Katsumi Imada, Tohru Minamino, May Kihara, Masafumi Shimada, Akio Kitao, Keiichi Namba
    • Journal Title

      Mol.Microbiol. 76(1)

      Pages: 260-268

    • Peer Reviewed
  • [Journal Article] Mechanical unfolding of bacterial flagellar filament protein by molecular dynamics simulation2010

    • Author(s)
      Choon-Peng Chng, Akio Kitao
    • Journal Title

      J.Mol.Graph.Model. 28

      Pages: 548-554

    • Peer Reviewed
  • [Journal Article] Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure2009

    • Author(s)
      Hannes H. Loeffler, Akio Kitao
    • Journal Title

      Biophys.J. Vol.97

      Pages: 2541-2549

    • Peer Reviewed
  • [Journal Article] Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations2009

    • Author(s)
      Shun Sakuraba, Akio Kitao
    • Journal Title

      J.Comp.Chem. 30

      Pages: 1850-1858

    • Peer Reviewed
  • [Journal Article] DTA: Dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins2009

    • Author(s)
      Wataru Nishima, Guoying Qi, Steven Hayward, Akio Kitao
    • Journal Title

      Bioinformatics 25(5)

      Pages: 628-635

    • Peer Reviewed
  • [Journal Article] Principal Component Analysis of Native Ensembles of Biomolecular Structures (PCA_NEST) : Insights into Functional Dynamics2009

    • Author(s)
      Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao
    • Journal Title

      Bioinformatics 25(5)

      Pages: 606-614

    • Peer Reviewed
  • [Journal Article] Hydration affects both harmonic and anharmonic nature of protein dynamics2008

    • Author(s)
      Hiroshi Nakagawa, Yasumasa Joti, Akio Kitao, Mikio Kataoka
    • Journal Title

      Biophys.J. 95

      Pages: 2916-2923

    • Peer Reviewed
  • [Journal Article] 【総説】細菌べん毛繊維は分子間相互作用とフラストレーションを利用して超らせん構造の変化を制御する2008

    • Author(s)
      北尾彰朗,今田勝巳,難波啓一
    • Journal Title

      生物物理 40(1)

      Pages: 11-17

  • [Journal Article] Hydration effects on low-frequency protein dynamics observed in simulated neutron scattering spectra2008

    • Author(s)
      Yasumasa Joti, Hiroshi Nakagawa, Mikio Kataoka, Akio Kitao
    • Journal Title

      Biophys.J. 94

      Pages: 4435-4443

    • Peer Reviewed
  • [Journal Article] Thermal Unfolding Simulations of Bacterial Flagellin : Insight into its Refolding before Assembly2008

    • Author(s)
      Choon-Peng Chng, Akio Kitao
    • Journal Title

      Biophys.J. 94

      Pages: 3858-3871

    • Peer Reviewed
  • [Journal Article] Hydration-Dependent Protein Dynamics Revealed by Molecular Dynamics Simulation of Crystalline Staphylococcal Nuclease2008

    • Author(s)
      Yasumasa Joti, Hiroshi Nakagawa, Mikio Kataoka, Akio Kitao
    • Journal Title

      J.Phys.Chem.B 112

      Pages: 3522-3528

    • Peer Reviewed
  • [Journal Article] Picosecond fluctuating protein energy landscape mapped by pressure-temperature molecular dynamics simulation Lars Meinhold. S2007

    • Author(s)
      Lars Meinhold, Jeremy C. Smith, Akio Kitao, Ahmed H.Zewail
    • Journal Title

      Proc.Natl.Acad.Sci.USA 104(44)

      Pages: 17261-17265

    • Peer Reviewed
  • [Journal Article] Effects of Water Model and Simulation Box Size on Protein Diffusional Motions2007

    • Author(s)
      Kazuhiro Takemura, Akio Kitao
    • Journal Title

      J.Phys.Chem.B 111

      Pages: 11870-11872

    • Peer Reviewed
  • [Journal Article] Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation2007

    • Author(s)
      Atsushi Tokuhisa, Yasumasa Joti, Hiroshi Nakagawa, Akio Kitao, Kaoru Shibata, Mikio Kataoka
    • Journal Title

      Phys.Rev.E 75

      Pages: 41912

    • Peer Reviewed
  • [Remarks] ホームページ

    • URL

      http://www.iam.u-tokyo.ac.jp/MolDes/

URL: 

Published: 2012-01-26   Modified: 2016-04-21  

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