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Simulation study of biomolecular motors: Structural analysis of regulation mechanisms of chemical reaction by motor movements

Research Project

Project/Area Number 22370057
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionKyoto University

Principal Investigator

TAKADA Shoji  京都大学, 大学院・理学研究科, 教授 (60304086)

Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥18,980,000 (Direct Cost: ¥14,600,000、Indirect Cost: ¥4,380,000)
Fiscal Year 2012: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2011: ¥7,670,000 (Direct Cost: ¥5,900,000、Indirect Cost: ¥1,770,000)
Fiscal Year 2010: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Keywordsキネシン / ATP加水分解 / 分子動力学 / 粗視化モデル / APT加水分解
Research Abstract

As a working principle of biomolecular motors, it is important to understand the regulation of chemical reactions by motor movements and conformational changes in enzymes. Here, we studied theoretically how a double-headed kinesin, one of the best characterized molecular motors, can regulate motions of two heads and addressed what is the structural basis for this cooperation. We found that the nucleotide-dependent tensions between the two heads are the fundamentals, and by that, unidirectional and chemically tight coupling between two heads are realized.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (86 results)

All 2013 2012 2011 2010 Other

All Journal Article (22 results) (of which Peer Reviewed: 22 results) Presentation (58 results) (of which Invited: 4 results) Book (6 results)

  • [Journal Article] ATP hydrolysis mechanism in kinesin studied by combined quantum-mechanical molecular-mechanical metadynamics2013

    • Author(s)
      M. J. McGrath、I-F. W. Kuo, S.Hayashi, S. Takada
    • Journal Title

      J. Amer. Chem. Soc.

      Volume: (in press) Issue: 24 Pages: 8908-891

    • DOI

      10.1021/ja401540g

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Protein-Specific Force Field Derived from the Fragment Molecular Orbital Method can Improve Protein-Ligand Binding Interactions2013

    • Author(s)
      L. Chang, T. Ishikawa, K. Kuwata, and S. Takada
    • Journal Title

      J. Comp. Chem

      Volume: vol. 34 Issue: 14 Pages: 1251-1257

    • DOI

      10.1002/jcc.23250

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin2013

    • Author(s)
      R. Kanada, T. Kuwata, H. Kenzaki, S.Takada
    • Journal Title

      PLOS Comp.Biol.

      Volume: 9(2) Issue: 2 Pages: e1002907-e1002907

    • DOI

      10.1371/journal.pcbi.1002907

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] p53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domains2012

    • Author(s)
      T. Terakawa, H. Kenzaki, S. Takada
    • Journal Title

      J. Amer.Chem. Soc.

      Volume: 134 Issue: 35 Pages: 14555-14562

    • DOI

      10.1021/ja305369u

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching2012

    • Author(s)
      N. Hori and S. Takada
    • Journal Title

      J. Chem. Theory and Comp.

      Volume: 8 Pages: 3384-3394

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot2012

    • Author(s)
      W. Li, T. Terakawa, W. Wang, S.Takada
    • Journal Title

      Proc. Nat. Acad. Sci. USA

      Volume: 44 Issue: 44 Pages: 17789-17794

    • DOI

      10.1073/pnas.1201807109

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Coarse-grained molecular simulations of large biomolecules2012

    • Author(s)
      S. Takada
    • Journal Title

      Curr. Opinion Struct. Biol.

      Volume: Vol.22 Issue: 2 Pages: 130-137

    • DOI

      10.1016/j.sbi.2012.01.010

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rigor of cell fate decision by variable p53 pulses and roles of cooperative gene expression by p532012

    • Author(s)
      Y. Murakami and S. Takada
    • Journal Title

      BIOPHYSICS

      Volume: 8 Pages: 41-50

    • DOI

      10.2142/biophysics.8.41

    • NAID

      130002061596

    • ISSN
      1349-2942
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Coarse-grained structure-based model for RNA - protein complexes developed by fluctuation matching2012

    • Author(s)
      Naoto Hori, Shoji Takada
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 8 Issue: 9 Pages: 3384-3394

    • DOI

      10.1021/ct300361j

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain2011

    • Author(s)
      T. Terakawa, S. Takada
    • Journal Title

      Biophys. J

      Volume: vol.101 Issue: 6 Pages: 1450-1458

    • DOI

      10.1016/j.bpj.2011.08.003

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CafeMol : A coarse-grained biomolecular simulator for simulating proteins at work2011

    • Author(s)
      Hiroo Kenzaki, Nobuyasu Koga, Naoto Hori, Ryo Kanada, Wenfei Li, Kei-ichi Okazaki, Xin-Qiu Yao, Shoji Takada
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 7 Issue: 6 Pages: 1979-1989

    • DOI

      10.1021/ct2001045

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural comparison of F1-ATPase: Interplay among enzyme structures, catalysis,and rotations2011

    • Author(s)
      K. Okazaki S. Takada
    • Journal Title

      Structure

      Volume: vol.19 Issue: 4 Pages: 588-598

    • DOI

      10.1016/j.str.2011.01.013

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins2011

    • Author(s)
      W. Li, P. G. Wolynes, S. Takada
    • Journal Title

      Proc. Nat. Acad. Sci.USA

      Volume: vol.108, No.9 Issue: 9 Pages: 3504-3509

    • DOI

      10.1073/pnas.1018983108

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] On easy implementation of a variant of the replica exchange with solute tempering in GROMACS2011

    • Author(s)
      T. Terakawa, T. Kameda, S. Takada
    • Journal Title

      J. Comp.Chem

      Volume: vol.32, No.7 Issue: 7 Pages: 1228-1234

    • DOI

      10.1002/jcc.21703

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins2011

    • Author(s)
      Wenfei Li, Peter G.Wolynes, Shoji Takada
    • Journal Title

      Proceedings of the National Academy of Sciences USA

      Volume: vol.108, No.9 Pages: 3504-3509

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations2010

    • Author(s)
      X-Q. Yao, H. Kenzaki, S. Murakami, S.Takada
    • Journal Title

      Nature communications

      Volume: vol.1.1 Issue: 1 Pages: 117-117

    • DOI

      10.1038/ncomms1116

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Characterizing protein energy landscape by the self-learning multiscale simulations: Application to a designed β-hairpin2010

    • Author(s)
      W. Li, S. Takada
    • Journal Title

      Biophys. J.

      Volume: vol.99, No.9 Issue: 9 Pages: 3029-3037

    • DOI

      10.1016/j.bpj.2010.08.041

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Multiscale methods for protein folding simulations2010

    • Author(s)
      W. Li, H. Yoshii, N. Hori, T. Kameda, S. Takada
    • Journal Title

      Methods

      Volume: vol.52, No.1 Issue: 1 Pages: 106-114

    • DOI

      10.1016/j.ymeth.2010.04.014

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Multiscale methods for protein folding simulations2010

    • Author(s)
      Wenfei Li, Hiroaki Yoshii, Naoto Hori, Tomoshi Kameda, Shoji Takada
    • Journal Title

      ELSEVIER

      Volume: vol.52, No.1 Pages: 106-114

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterizing protein energy landscape by the self-learning multiscale simulations : Application to a designed β-hairpin2010

    • Author(s)
      Wenfei Li, Shoji Takada
    • Journal Title

      Biophysical Journal

      Volume: vol.99, No.9 Pages: 3029-3037

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] On easy implementation of a variant of the replica exchange with solute tempering in GROMACS2010

    • Author(s)
      Tsuyoshi Terakawa, Tomoshi Kameda, Shoji Takada
    • Journal Title

      Journal of Computational Chemistry

      Volume: vol.32, No.7 Pages: 1228-1234

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations2010

    • Author(s)
      Xin-Qiu Yao, Hiroo Kenzaki, Satoshi Murakami, Shoji Takada
    • Journal Title

      Nature communications

      Volume: vol.1.1

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Coarse-grained molecular simulations of large biomolecules:From theory to applications2012

    • Author(s)
      S. Takada
    • Organizer
      The 9th Fukui Inst Fundamental Chemistry Seminar(招待講演)
    • Place of Presentation
      Fukui Inst. Fundamental Chem.(Kyoto)
    • Year and Date
      2012-03-06
    • Related Report
      2012 Final Research Report
  • [Presentation] Kinetic parameter analysis of the mathematical model of caspase cascade by Bayesian statistics withMCMC2012

    • Author(s)
      村上陽平
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場(福岡市)
    • Related Report
      2012 Final Research Report
  • [Presentation] Research of Split Point and Fluorescent Recovery of Green Fluorescent Protein by MolecularDynamics Simulation2012

    • Author(s)
      M. Ito
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス(名古屋市)
    • Related Report
      2012 Final Research Report
  • [Presentation] The effect of the internal tension between two heads on the nucleotide binding site of kinesin-1studied by All-atom MD2012

    • Author(s)
      R. Kanada
    • Organizer
      第50回日本生物物理学会年
    • Place of Presentation
      名古屋大学東山キャンパス(名古屋市)
    • Related Report
      2012 Final Research Report
  • [Presentation] ATP Hydrolysis Free Energy Barriers in Kinesin2012

    • Author(s)
      M. J. McGrath
    • Organizer
      JST International Symposium on Multi-scale Simulation ofCondensed-phase Reacting Systems
    • Place of Presentation
      名古屋大学ESホール(名古屋市)
    • Related Report
      2012 Final Research Report
  • [Presentation] ATP Hydrolysis Free Energy Barriers in Kinesin2012

    • Author(s)
      Matthew J. McGrath
    • Organizer
      JST International Symposium on Multi-scale Simulation of Condensed-phase Reacting Systems
    • Place of Presentation
      名古屋大学ESホール(名古屋市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 癌抑制転写因子p53のDNA上の結合部位探索メカニズム: 粗視化分子動力学シミュレーションによる研究2012

    • Author(s)
      寺川 剛
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場(名古屋市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 分子動力学シミュレーションによるSplit型緑色蛍光タンパク質の蛍光回復研究2012

    • Author(s)
      伊藤 真志保
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場(名古屋市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] The effect of the internal tension between two heads on the nucleotide binding site of kinesin-1 studied by All-atom MD2012

    • Author(s)
      Ryo Kanada
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス(名古屋市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Movement of T4 sliding clamp on DNA studied by coarse-grained molecular simulations2012

    • Author(s)
      Itaru Narihara
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス(名古屋市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Research of Split Point and Fluorescent Recovery of Green Fluorescent Protein by Molecular Dynamics Simulation2012

    • Author(s)
      Mashiho Ito
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス(名古屋市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Kinetic parameter analysis of the mathematical model of caspase cascade by Bayesian statistics with MCMC2012

    • Author(s)
      村上陽平
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場(福岡市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Multiscale computational approach to kinesin and F1-ATPase2011

    • Author(s)
      S. Takada
    • Organizer
      Telluride Science Research center meeting(招待講演)
    • Place of Presentation
      Telluride (USA)
    • Year and Date
      2011-08-09
    • Related Report
      2012 Final Research Report
  • [Presentation] 粗視化生体分子シミュレータCafeMol2011

    • Author(s)
      高田彰二
    • Organizer
      蛋白質研究所セミナー(招待講演)
    • Place of Presentation
      大阪大学蛋白質研究所(吹田市)
    • Year and Date
      2011-03-05
    • Related Report
      2012 Final Research Report
  • [Presentation] 粗視化生体分子シミュレータCafeMol2011

    • Author(s)
      高田彰二
    • Organizer
      蛋白質研究所セミナー
    • Place of Presentation
      大阪大学蛋白質研究所(吹田市)(招待講演)
    • Year and Date
      2011-03-05
    • Related Report
      2010 Annual Research Report
  • [Presentation] Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations2011

    • Author(s)
      X-Q. Yao
    • Organizer
      蛋白質研究所セミナー
    • Place of Presentation
      大阪大学蛋白質研究所(吹田市)
    • Year and Date
      2011-03-04
    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Presentation] シミュレーションで観る生体分子機械のゆらぎと機能2011

    • Author(s)
      高田彰二
    • Organizer
      自然科学研究機構プロジェクト 「機能生命科学における揺らぎと決定」(招待講演)
    • Place of Presentation
      生理学研究所(岡崎市)
    • Year and Date
      2011-02-23
    • Related Report
      2012 Final Research Report
  • [Presentation] シミュレーションで観る生体分子機械のゆらぎと機能2011

    • Author(s)
      高田彰二
    • Organizer
      自然科学研究機構プロジェクト「機能生命科学における揺らぎと決定」
    • Place of Presentation
      生理学研究所(岡崎市)(招待講演)
    • Year and Date
      2011-02-23
    • Related Report
      2010 Annual Research Report
  • [Presentation] 全原子シミュレーションによるキネシン-微小管間の界面構造のリファインメント2011

    • Author(s)
      金田亮
    • Organizer
      バイオスーパーコンピューティングサマースクール2011(招待講演)
    • Place of Presentation
      兵庫県立淡路夢舞台国際会議場(淡路市)
    • Related Report
      2012 Final Research Report
  • [Presentation] 粗視化分子モデルによる生体分子機械の作動原理研究2011

    • Author(s)
      高田彰二
    • Organizer
      日本物理学会2011年秋期大会(招待講演)
    • Place of Presentation
      富山大学五福キパス(富山市)
    • Related Report
      2012 Final Research Report
  • [Presentation] FUNCTIONALLY ROTATING MECHANISM OF A MULTIDRUG TRANSPORTER STUDIED BY COARSE-GRAINED SIMULATION: EXPLORING THE BINDING PATHWAYS OF DRUGS2011

    • Author(s)
      X-Q. Yao, H. Kenzaki, S. Takada
    • Organizer
      Biophysical Society 55th Annual Meeting
    • Place of Presentation
      Baltimore(USA)
    • Related Report
      2012 Final Research Report
  • [Presentation] COARSE-GRAINED SIMULATION OF PROTEIN-DNA COMPLEX: MECHANICAL UNZIPPING OF NUCLEOSOME2011

    • Author(s)
      H. Kenzaki, S. Takada
    • Organizer
      Biophys. Soc. 55th Ann. Meeting
    • Place of Presentation
      Baltimore(USA)
    • Related Report
      2012 Final Research Report
  • [Presentation] KINESIN INTERNAL TENSION FOR THE COORDINATED WALK ESTIMATED BY ALL-ATOM MD SIMULATION2011

    • Author(s)
      R. Kanada, T. Makino, M. Tomishige, S. Takada
    • Organizer
      Biophys. Soc. 55th Ann. Meeting
    • Place of Presentation
      20110305-09
    • Related Report
      2012 Final Research Report
  • [Presentation] Kinesin internal tension for the coordinated walk estimated by all-atom MD simulation(全原子MDによる双頭キネシン分子モーターの内部張力評価)、2011

    • Author(s)
      金田亮、牧野司、富重道雄、高田彰二
    • Organizer
      第3回バイオスーパーコンピューティングシンポジウム
    • Place of Presentation
      理化学研究所計算科学研究機構(神戸市)
    • Related Report
      2012 Final Research Report
  • [Presentation] ミトコンドリア依存アポトーシスシグナル伝達系の数理モデル化とその応答2011

    • Author(s)
      村上陽平、高田彰二
    • Organizer
      第33回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド(神戸市)
    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Presentation] 分子シミュレーションによる多剤排出トランスポーターの作動機構研究2011

    • Author(s)
      高田彰二
    • Organizer
      第33回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド(神戸市)
    • Related Report
      2012 Final Research Report
  • [Presentation] 粗視化分子モデルによる生体分子機械の作動原理研究2011

    • Author(s)
      高田彰二
    • Organizer
      日本物理学会2011年秋期大会
    • Place of Presentation
      富山大学五福キャンパス(富山市)
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] 全原子シミュレーションによるキネシン-微小管間の界面構造のリファインメント2011

    • Author(s)
      金田亮
    • Organizer
      バイオスーパーコンピューティングサマースクール2011
    • Place of Presentation
      兵庫県立淡路夢舞台国際会議上(淡路市)
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] 分子シミュレーションによる多剤排出トランスポーターの作動機構研究2011

    • Author(s)
      高田彰二
    • Organizer
      第33回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド(神戸市)(招待講演)
    • Related Report
      2010 Annual Research Report
  • [Presentation] KINESIN INTERNAL TENSION FOR THE COORDINATED WALK ESTIMATED BY ALL-ATOM MD SIMULATION2011

    • Author(s)
      Ryo Kanada, Tsukasa Makino, Michio Tomishige, Shoji Takada
    • Organizer
      Biophysical Society 55th Annual Meeting
    • Place of Presentation
      Baltimore (USA)
    • Related Report
      2010 Annual Research Report
  • [Presentation] COARSE-GRAINED SIMULATION OF PROTEIN-DNA COMPLEX : MECHANICAL UNZIPPING OF NUCLEOSOME2011

    • Author(s)
      Hiroo Kenzaki, Shoji Takada
    • Organizer
      Biophysical Society 55th Annual Meeting
    • Place of Presentation
      Baltimore (USA)
    • Related Report
      2010 Annual Research Report
  • [Presentation] FUNCTIONALLY ROTATING MECHANISM OF A MULTIDRUG TRANSPORTER STUDIED BY COARSE-GRAINED SIMULATION : EXPLORING THE BINDING PATHWAYS OF DRUGS2011

    • Author(s)
      Xin-Qiu Yao, Hiroo Kenzaki, Shoji Takada
    • Organizer
      Biophysical Society 55th Annual Meeting
    • Place of Presentation
      Baltimore (USA)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Kinesin internal tension for the coordinated walk estimated by all-atom MD simulation(全原子MDによる双頭キネシン分子モーターの内部張力評価)2011

    • Author(s)
      金田亮、牧野司、富重道雄、高田彰
    • Organizer
      第3回バイオスーパーコンピューティングシンポジウム
    • Place of Presentation
      理化学研究所計算科学研究機構(神戸市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] タンパク質-DNA複合体の粗視化シミュレーション:ヌクレオソームの力学的なアンジッピング、ポスター発表2011

    • Author(s)
      検崎博生、高田彰二
    • Organizer
      第3回バイオスーパーコンピューティングシンポジウム
    • Place of Presentation
      理化学研究所計算科学研究機構(神戸市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] CafeMolを用いた粗視化シミュレーションによるヌクレオソームの動的構造解析2011

    • Author(s)
      高山真澄、検崎博生、高田彰二
    • Organizer
      第3回バイオスーパーコンピューティングシンポジウム
    • Place of Presentation
      理化学研究所計算科学研究機構(神戸市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation2010

    • Author(s)
      X-Q. Yao, H. Kenzaki, S. Takada
    • Organizer
      揺らぎと生体機能第4回公開シンポジウム
    • Place of Presentation
      滋賀県立県民交流センターピアザ淡海(大津市)
    • Year and Date
      2010-11-30
    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Presentation] ENSEMBLE MODELING OF P53 INTRINSICALLY DISORDERED N-TERMINAL DOMAIN BY COMBINING MULTI-SCALE SIMULATIONS WITH NMR EXPERIMENTS2010

    • Author(s)
      T. Terakawa, S. Takada
    • Organizer
      揺らぎと生体機能第4回公開シンポジウム
    • Place of Presentation
      滋賀県立県民交流センターピアザ淡海(大津市)
    • Year and Date
      2010-11-30
    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Presentation] CG modeling of biomolecular machines: Specificity, non-linearity, and function2010

    • Author(s)
      S. Takada
    • Organizer
      Characterizing Landscapes: From Biomolecules to Cellular Networks(招待講演)
    • Place of Presentation
      Telluride(USA)
    • Year and Date
      2010-07-05
    • Related Report
      2012 Final Research Report
  • [Presentation] Kinesin internal tension for the coordinated walk estimated by all-atom MD simulation2010

    • Author(s)
      R. Kanada, S. Takada
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Presentation] Coarse-grained simulation of protein-DNA complex: mechanical unzipping of nucleosome2010

    • Author(s)
      H. Kenzaki, S. Takada
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2012 Final Research Report
  • [Presentation] Functionally rotating mechanism of a multidrug transporter studied2010

    • Author(s)
      X-Q. Yao, H. Kenzaki, S. Takada
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Presentation] Nucleosome unwrapping dynamic studied by coarse-grained molecular simulations2010

    • Author(s)
      M. Takayama, H. Kenzaki, S. Takada
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2012 Final Research Report
  • [Presentation] Coarse-grained model of RNA-protein complexes based on all-atom simulations2010

    • Author(s)
      N. Hori, W. Li, S. Takada
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular Dynamics Simulation Study of p53 Intrinsically Disordered N Terminal Domain2010

    • Author(s)
      T. Terakawa, S. Takada
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2012 Final Research Report
  • [Presentation] Modeling Rhodopsin active conformation (Meta II) by molecular dynamics simulations2010

    • Author(s)
      F. Sakai, S. Takada
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2012 Final Research Report
  • [Presentation] Modulations of protein allosteric dynamics by physicochemical features2010

    • Author(s)
      W. Li, S. Takada
    • Organizer
      Characterizing Landscapes: From Biomolecules to Cellular Networks
    • Place of Presentation
      Telluride(USA)
    • Related Report
      2012 Final Research Report
  • [Presentation] p53のN末端天然変性ドメインの分子動力学シミュレーション研究2010

    • Author(s)
      寺川剛, 高田彰二
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(札幌市)
    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Presentation] RNA-タンパク質複合体の粗視化シミュレーションモデル:全原子モデルに基づく導出2010

    • Author(s)
      堀直人, Wenfei Li, 高田彰二
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(札幌市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] 分子動力学シミュレーションによるロドプシン活性(MetaII)状態の構造モデルとその活性過程の解析2010

    • Author(s)
      坂井冬樹, 高田彰二
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(札幌市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Modulations of protein allosteric dynamics by physicochemical features2010

    • Author(s)
      Wenfei Li, Shoji Takada
    • Organizer
      Characterizing Landscapes : From Biomolecules to Cellular Networks
    • Place of Presentation
      Telluride (USA)
    • Related Report
      2010 Annual Research Report
  • [Presentation] CG modeling of biomolecular machines : Specificity, non-linearity, and function2010

    • Author(s)
      Shoji Takada
    • Organizer
      Characterizing Landscapes : From Biomolecules to Cellular Networks
    • Place of Presentation
      Telluride (USA)(招待講演)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Coarse-grained simulation of protein-DNA complex : mechanical unzipping of nucleosome2010

    • Author(s)
      Hiroo Kenzaki, Shoji Takada
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Nucleosome unwrapping dynamic studied by coarse-grained molecular simulations2010

    • Author(s)
      Masumi Takayama, Hiroo Kenzaki, Shoji Takada
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Coarse-grained model of RNA-protein complexes based on all-atom simulations2010

    • Author(s)
      Naoto Hori, Wenfei Li, Shoji Takada
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Molecular Dynamics Simulation Study of p53 Intrinsically Disordered N Terminal Domain2010

    • Author(s)
      Tsuyoshi Terakawa, Shoji Takada
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Modeling Rhodopsin active conformation (Meta II) by molecular dynamics simulations2010

    • Author(s)
      Fuyuki Sakai, Shoji Takada
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      東北大学川内キャンパス(仙台市)
    • Related Report
      2010 Annual Research Report
  • [Presentation] Coarse-grained molecular simulations of large biomolecules:

    • Author(s)
      Shoji Takada
    • Organizer
      The 9th Fukui Inst Fundamental Chemistry Seminar
    • Place of Presentation
      Fukui Institute for Fundamental Chemistry(Kyoto)
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Multiscale computational approach to kinesin and F1-ATPase

    • Author(s)
      Shoji Takada
    • Organizer
      Telluride Science Research center meeting
    • Place of Presentation
      Telluride Science Research center(USA)
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Book] アンサンブルvol.12, No.2(ハミルトニアンレプリカ交換法)2010

    • Author(s)
      高田彰二
    • Total Pages
      4
    • Publisher
      分子シミュレーション研究会、
    • Related Report
      2012 Final Research Report
  • [Book] 生物物理2010

    • Author(s)
      高田彰二
    • Total Pages
      2
    • Publisher
      日本生物物理学会、
    • Related Report
      2012 Final Research Report
  • [Book] タンパク質の立体構入門--基礎から構造バイオインフォマティクスへ--, 編集:藤博幸(2章タンパク質構造の物理化学,5章アミノ酸配列からの構造予測とデザイン,6 章分子シミュレーション的な技法)2010

    • Author(s)
      高田彰二
    • Total Pages
      81
    • Publisher
      講談社
    • Related Report
      2012 Final Research Report
  • [Book] アンサンブルvol.12,No.2(ハミルトニアンレプリカ交換法)2010

    • Author(s)
      高田彰二
    • Total Pages
      4
    • Publisher
      分子シミュレーション研究会
    • Related Report
      2010 Annual Research Report
  • [Book] 生物物理vol.50,No.4(郷モデルの35年)2010

    • Author(s)
      高田彰二
    • Total Pages
      2
    • Publisher
      日本生物物理学会
    • Related Report
      2010 Annual Research Report
  • [Book] タンパク質の立体構造入門-基礎から構造バイオインフォマティクスへ-(2章タンパク質構造の物理化学,5章アミノ酸配列からの構造予測とデザイン,6章分子シミュレーション的な技法)(編集:藤博幸)2010

    • Author(s)
      高田彰二
    • Total Pages
      81
    • Publisher
      講談社
    • Related Report
      2010 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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