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Underlying mechanism of bio-nano-machine investigated by massive molecular dynamics method

Research Project

Project/Area Number 15300103
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionThe University of Tokyo

Principal Investigator

KITAO Akio  The University of Tokyo, Institute of Molecular and Cellular Biosciences, Associate Professor, 分子細胞生物学研究所, 助教授 (30252422)

Co-Investigator(Kenkyū-buntansha) JOTI Yasumasa  The University of Tokyo, Institute of Molecular and Cellular Biosciences, Research Associate, 分子細胞生物学研究所, 助手 (30360415)
石田 恒  日本原子力研究所, 中性子利用研究センター, 研究員
Project Period (FY) 2003 – 2006
Project Status Completed (Fiscal Year 2006)
Budget Amount *help
¥15,900,000 (Direct Cost: ¥15,900,000)
Fiscal Year 2006: ¥3,000,000 (Direct Cost: ¥3,000,000)
Fiscal Year 2005: ¥3,700,000 (Direct Cost: ¥3,700,000)
Fiscal Year 2004: ¥3,900,000 (Direct Cost: ¥3,900,000)
Fiscal Year 2003: ¥5,300,000 (Direct Cost: ¥5,300,000)
KeywordsMassive molecular dynamics / Bio-nano-machine / bacterial flagella / Salmonella / Flagellar filament / Supercoil / Conformational transition / Torque / サヌモネラ菌
Research Abstract

Bacterial flagellar filament is a macromolecular assembly consisting of single protein, flagellin. Bacterial swimming is controlled by the conformational transitions of this filament between left- and right-handed supercoils induced by the flagellar motor torque. We present that a massive molecular dynamics simulation was successful in constructing the atomic-level supercoil structures consistent to various experimental data and further in elucidating the detailed underlying molecular mechanisms of the polymorphic supercoiling. We have found that the following three types of interactions are keys to understanding the supercoiling mechanism. "Permanent" interactions are always maintained between subunits in the various supercoil structures. "Sliding" interactions are formed between variable hydrophilic or hydrophobic residue pairs, allowing intersubunit shear without large change in energy. The formation and breakage of "switch" interactions stabilize inter- and intrasubunit interactions, respectively. We conclude that polymorphic supercoiling is due to the energy frustration between them. The transition between supercoils is achieved by a "transform and relax" mechanism : the filament structure is geometrically transformed rapidly and then slowly relaxes to energetically meta-stable states by rearranging interactions.

Report

(5 results)
  • 2006 Annual Research Report   Final Research Report Summary
  • 2005 Annual Research Report
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • Research Products

    (28 results)

All 2007 2006 2005 2004 Other

All Journal Article (24 results) Book (2 results) Publications (2 results)

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

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

      Journal of Structural Biology 157

      Pages: 481-490

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint.2007

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

      Journal of Structural Biology 157

      Pages: 481-499

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [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

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [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

      Magnetic Resonance in Chemistry 44

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [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 (13)

      Pages: 4894-4899

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Molecular Dynamics Simulations of NAD+-induced Domain Closure in Horse Liver Alcohol Dehydrogenase_2006

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

      Biophysical Journa1 91

      Pages: 1823-1831

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [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(13)

      Pages: 4893-4899

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [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

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Hydration-coupled protein boson peak measured by incoherent neutron scattering2006

    • Author(s)
      H.Nakagawa, M.Kataoka, Y.Joti, A.Kitao, K.Shibata, A.Tokuhisa, I.Tsukushi, N.Go
    • Journal Title

      Physica B 385-385

      Pages: 871-873

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Amplitudes and directions of intemal protein motions from a JAM analysis of 15N relaxation data2006

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

      Magnetic Resonance in Chemistry 44

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Amplitudes and directions of internal protein motions from a JAM analysis of ^<15>N relaxation data2006

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

      Magnetic Resonance in Chemistry (In press)

    • Related Report
      2005 Annual Research Report
  • [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(13)

      Pages: 4894-4899

    • Related Report
      2005 Annual Research Report
  • [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

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Universal joint mechanism of Biological Supramolecule2005

    • Author(s)
      Akio Kitao, Fadel A.Samatey, Hideyuki Matsunami, Katsumi Imada, Keiichi Namba
    • Journal Title

      Protein, Nucreic Acid and Enzyme 50(10)

      Pages: 1335-1340

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] 蛋白質の効率的機能を支えるメカニズム2005

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

      蛋白質核酸酵素 51(8)

      Pages: 972-978

    • Related Report
      2006 Annual Research Report
  • [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

    • Related Report
      2005 Annual Research Report
  • [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

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Protein Boson Peak Originated from Hydration-RelatedMultiple Minima Energy Landscape2005

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

      J.Am.Chem.Soc 127

      Pages: 8705-8709

    • Related Report
      2005 Annual Research Report
  • [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

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [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

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering2004

    • Author(s)
      Yasumasa Joti
    • Journal Title

      Physica B 350

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism2004

    • Author(s)
      FA.Samatey
    • Journal Title

      Nature 431

      Pages: 1062-1068

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Slow Protein Dynamics to be detected in Inelastic Neutron Scattering Spectra Studied by Molecular Simulations2004

    • Author(s)
      Yasumasa Joti
    • Journal Title

      Proceedings of 3^<rd> International Symposium on Slow Dynamics in Complex Systems

      Pages: 358-359

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 蛋白質の立体構造ダイナミクスと中性子散乱2004

    • Author(s)
      城地 保昌
    • Journal Title

      日本中性子科学会誌「波紋」 14

      Pages: 39-40

    • NAID

      130001998650

    • Related Report
      2004 Annual Research Report
  • [Book] Normal Mode Analysis : Theory and Applications to Biological and Chemical Systems, Chapter 122006

    • Author(s)
      Akio Kitao
    • Total Pages
      406
    • Publisher
      Chapman & Hall/CRC
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] Normal Mode Analysis : Theory and Applications to Biological and Chemical Systems, Chapter 122006

    • Author(s)
      Akio Kitao
    • Total Pages
      406
    • Publisher
      Chapman & Hall/CRC
    • Related Report
      2005 Annual Research Report
  • [Publications] Jun Funahashi, Yuji Sugita, Akio Kitao, Katsuhide Yutani: "How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme"Protein Science. 16. 665-671 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yasumasa Joti, Akio Kitao, Nobuhiro Go: "Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering"Physica B. (in press).

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2016-04-21  

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