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2009 Fiscal Year Final Research Report

Development of simulation methods for biological supramolecular structure and function analyses

Research Project

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Project/Area Number 16087202
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
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) 2004 – 2009
Keywordsシミュレーション / ナノバイオ / 分子機械 / 生体超分子 / 生物物理
Research Abstract

We have developed the methods and simulation systems in which functional process of biological supramolecules is observed in silico in high resolution by using molecular simulations. We have also developed the methods to construct the structure and refine it to be energetically more stable one. In addition, we have designed the simulation methods to investigate functional mechanism more efficiently.

  • Research Products

    (31 results)

All 2010 2009 2008 2007 2006 2005 2004 Other

All Journal Article (29 results) (of which Peer Reviewed: 25 results) Book (1 results) Remarks (1 results)

  • [Journal Article] The Effect of End Constraints on Protein Loop Conformations2010

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

      Biophys. J. 98

      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

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

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

      Biophys. J 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

  • [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

    • Peer Reviewed
  • [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-temperaturer 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
  • [Journal Article] Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint2007

    • Author(s)
      Tadaomi Furuta, Hideyuki Matsunami, Katsumi Imada, Keiichi Namba, Akio Kitao
    • Journal Title

      Fadel A. Samatey, J. Struct. Biol 157

      Pages: 481-491

    • Peer Reviewed
  • [Journal Article] 蛋白質の効率的機能を支えるメカニズム2006

    • Author(s)
      城地保昌, 北尾彰朗
    • Journal Title

      蛋白質核酸酵素 51(8)

      Pages: 972-978

    • Peer Reviewed
  • [Journal Article] 分子シミュレーションと中性子散乱による蛋白質ダイナミクスの研究2006

    • Author(s)
      城地保昌, 北尾彰朗
    • Journal Title

      分子シミュレーション研究会会誌「アンサンブル」 8

      Pages: 44-47

  • [Journal Article] Molecular Dynamics Simulations of NAD+-induced Domain Closure in Horse Liver Alcohol Dehydrogenase2006

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

      Biophysical Journal 91

      Pages: 1823-1831

    • Peer Reviewed
  • [Journal Article] Hydration-coupled protein boson peak measured by incoherent neutron scattering2006

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

      Physica B 385-6

      Pages: 871-873

    • Peer Reviewed
  • [Journal Article] Dynamical heterogeneity of protein dynamics studied by elastic incoherent neutron scattering and molecular simulations2006

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

      Material Science and Engineering A 442

      Pages: 356-360

    • Peer Reviewed
  • [Journal Article] Switch interactions control energy frustration and multiple flagellar filament structures2006

    • Author(s)
      Akio Kitao, Koji Yonekura, Saori Maki-Yonekura, Fadel A. Samatey, Katsumi Imada, Keiichi Namba, Nobuhiro Go
    • Journal Title

      Proc. Natl. Acad. Sci 103

      Pages: 4894-4899

    • Peer Reviewed
  • [Journal Article] Amplitudes and directions of internal protein motions from a JAM analysis of 15N relaxation data2006

    • Author(s)
      Akio Kitao, Gerhard Wagner
    • Journal Title

      Magn. Reson. Chem 44

      Pages: S130-S142

    • Peer Reviewed
  • [Journal Article] べん毛による細菌の泳ぎ方と方向転換の分子機構2005

    • Author(s)
      今田勝巳, Fadel A. Samatey, 松波秀行, 長島重広, 北尾彰朗, 米倉功治, 眞木さおり, 難波啓一
    • Journal Title

      蛋白質核酸酵素 50(10)

      Pages: 1328-1334

    • Peer Reviewed
  • [Journal Article] 生体超分子のユニバーサルジョイント-in silicoで探る細菌べん毛フックのメカニズム2005

    • Author(s)
      北尾彰朗, Fadel A. Samatey, 松波秀行, 今田勝巳, 難波啓一
    • Journal Title

      蛋白質核酸酵素 50(10)

      Pages: 1335-1340

    • Peer Reviewed
  • [Journal Article] Protein Boson Peak Originated from Hydration-Related Multiple Minima Energy Landscape2005

    • Author(s)
      asumasa Joti, Akio Kitao, Nobuhiro Go
    • Journal Title

      J. Am. Chem. Soc 127

      Pages: 8705-8709

    • Peer Reviewed
  • [Journal Article] Slow Protein Dynamics to be detected in Inelastic Neutron Scattering Spectra Studied by Molecular Simulations", Proceedings of 3rd International Symposium on Slow Dynamics in Complex Systems2004

    • Author(s)
      Yasumasa Joti, Akio Kitao, Nobuhiro Go
    • Journal Title

      edited by M. Tokuyama & I. Oppenheim

      Pages: 358-359

    • Peer Reviewed
  • [Journal Article] Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism2004

    • Author(s)
      Fadel A. Samatey, Hideyuki Matsunami, Katsumi Imada, Shigehiro Nagashima, Tanvir R. Shaikh, Dennis R. Thomas, James Z. Chen, David J. De Rosier, Akio Kitao, Keiichi Namba
    • Journal Title

      Nature 431

      Pages: 1062-1068

    • Peer Reviewed
  • [Journal Article] Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering2004

    • Author(s)
      Yasumasa Joti, Akio Kitao, Nobuhiro Go
    • Journal Title

      Physica B 350

      Pages: e627-e630

  • [Book] Extension of the Normal Mode Concept: Principal Component Analysis, Jumping-Among-Minima Model and their Applicaions to Experimental Data Analysis(edited by Qiang Cui & lvet Bahar, in Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, Chapter 12)2006

    • Author(s)
      Akio Kitao
    • Total Pages
      233-251
  • [Remarks]

    • URL

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

URL: 

Published: 2011-06-18   Modified: 2016-04-21  

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