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2011 Fiscal Year Final Research Report

Functional Funnel of Molecular Motors

Research Project

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Project/Area Number 20244068
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics/Chemical physics
Research InstitutionNagoya University

Principal Investigator

SASAI Masaki  名古屋大学, 工学研究科, 教授 (30178628)

Project Period (FY) 2008 – 2011
Keywords分子モーター / 粗視化モデル / アロステリック変形
Research Abstract

Protein motors show the superior abilities in working efficiently at the mild temperature by responding flexibly to the applied load. In this research project, protein machines were studied theoretically to reveal their physical principles :(1) Coarse-grained models were constructed to analyze the large structural fluctuation of myosins and other proteins, and the theoretical framework to understand allosteric transitions is developed,(2) the millisecond time-scale trajectories of moving proteins were simulated, and(3) the functional funnel hypothesis of molecular motors was proposed and critically examined.

  • Research Products

    (42 results)

All 2012 2011 2010 2009 2008 Other

All Journal Article (14 results) (of which Peer Reviewed: 14 results) Presentation (23 results) Book (5 results)

  • [Journal Article] Dynamical modeling of 3D genome organization in interphase budding yeast2012

    • Author(s)
      N. Tokuda, T. P. Terada, and M. Sasai
    • Journal Title

      Biophys. J.

      Volume: Vol.102, No.2 Pages: 296-304

    • DOI

      DOI:10.1016/j.bpj.2011.12.005

    • Peer Reviewed
  • [Journal Article] The fragment-based consistency score in model quality assessment for de novo prediction of protein structures2011

    • Author(s)
      H. Cetin, T. N. Sasaki, and M. Sasai
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: Vol.11 Pages: 63-81

    • Peer Reviewed
  • [Journal Article] De novo protein structure prediction by dynamic fragment assembly and conformational space annealing2011

    • Author(s)
      J. Lee, J. Lee, T. N. Sasaki, M. Sasai, C. Seok, and J. Lee
    • Journal Title

      Proteins : Structure, Function, and Bioinformatics

      Volume: Vol.79, No.8 Pages: 2403-2417

    • DOI

      DOI:10.1002/prot.23059

    • Peer Reviewed
  • [Journal Article] Statistical mechanics of protein allostery : Roles of backbone and side-chain structural fluctuations2011

    • Author(s)
      K. Itoh and M. Sasai
    • Journal Title

      J. Chem. Phys.

      Volume: Vol.134, No.12 Pages: 125102 : 1-18

    • DOI

      DOI:10.1063/1.3565025.

    • Peer Reviewed
  • [Journal Article] Roles of DNA looping in enhancer-blocking activity2011

    • Author(s)
      N. Tokuda, M. Sasai, and G. Chikenji
    • Journal Title

      Biophys. J.

      Volume: Vol.100, No.1 Pages: 126-134

    • DOI

      DOI:10.1016/j.bpj.2010.11.016

    • Peer Reviewed
  • [Journal Article] Synchronizaion of circadian oscillation of phosphorylation level of KaiC2010

    • Author(s)
      T. Nagai, T. P. Terada, and M. Sasai
    • Journal Title

      Biophys. J.

      Volume: Vol.98, No.11 Pages: 2469-2477

    • DOI

      DOI:10.1016/j.bpj.2010.02.036

    • Peer Reviewed
  • [Journal Article] Entropic mecha-nism of large fluctuation in allosteric transition2010

    • Author(s)
      K. Itoh and M. Sasai
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: Vol.107, No.17 Pages: 7775-7780

    • DOI

      DOI:10.1073/pnas.0912978107

    • Peer Reviewed
  • [Journal Article] Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor2010

    • Author(s)
      M. Takano, T. P. Terada, and M. Sasai
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: Vol.107, No.17 Pages: 7769-7774

    • DOI

      DOI:10.1073/pnas.0911830107

    • Peer Reviewed
  • [Journal Article] Multi-dimensional theory of protein folding2009

    • Author(s)
      K. Itoh and M. Sasai
    • Journal Title

      J. Chem. Phys

      Volume: Vol.130, No.14 Pages: 145104_1-21

    • DOI

      DOI:10.1063/1.3097018

    • Peer Reviewed
  • [Journal Article] Cortical factor feedback model for cellular locomotion and cytofission2009

    • Author(s)
      S. I. Nishimura, M. Ueda, and M. Sasai
    • Journal Title

      PLoS Comp. Biol.

      Volume: Vol.5, No.3 Pages: e1000310_1-11

    • DOI

      DOI:10.1371/journal.pcbi.1000310

    • Peer Reviewed
  • [Journal Article] Mechanism of robust circadian oscillation of KaiC phosphorylation2008

    • Author(s)
      K. Eguchi, M. Yoda, T. P. Terada, and M. Sasai
    • Journal Title

      Biophys. J.

      Volume: Vol.95, No.4 Pages: 1773-1784

    • DOI

      DOI:10.1529/biophysj.107.127555.

    • Peer Reviewed
  • [Journal Article] Cooperativity, connectivity, and folding pathways of multidomain proteins2008

    • Author(s)
      K. Itoh and M. Sasai
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: Vol.105, No.37 Pages: 13865. 13870

    • DOI

      DOI:10.1073/pnas.0804512105

    • Peer Reviewed
  • [Journal Article] A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction2008

    • Author(s)
      T. N. Sasaki, H. Cetin, and M. Sasai
    • Journal Title

      Biochem. Biophys. Research Comm

      Volume: Vol.369, No.2 Pages: 500-506

    • DOI

      DOI:10.1016/j.bbrc.2008.02.048

    • Peer Reviewed
  • [Journal Article] ゆらぎと柔らかさの物理としての生物物理

    • Author(s)
      笹井理生
    • Journal Title

      日本物理学会誌

      Volume: Vol.63, No.10 Pages: 810-811

    • Peer Reviewed
  • [Presentation] Epigenetic switches and network transitions2012

    • Author(s)
      M. Sasai
    • Organizer
      2012 March Meeting of the American Physical Society
    • Place of Presentation
      Boston
    • Year and Date
      2012-02-28
  • [Presentation] ミオシンVIのアクチンフィラメント上の運動の粗視化モデルによる自由エネルギー解析2012

    • Author(s)
      池尾眞人、笹井理生、佐々木尚、寺田智樹
    • Organizer
      2012年生体運動研究合同班会議
    • Place of Presentation
      筑波大学
    • Year and Date
      2012-01-06
  • [Presentation] Cooperativity and flexibility in protein allostery2011

    • Author(s)
      K. Itoh and M. Sasai
    • Organizer
      The 11th KIAS Conference on Protein Structure and Function
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2011-10-06
  • [Presentation] Biological networks : multiple scales and heterogeneities in switching dynamics2011

    • Author(s)
      M. Sasai
    • Organizer
      第49回日本生物物理学会
    • Place of Presentation
      兵庫県立大学
    • Year and Date
      2011-09-16
  • [Presentation] Statistical mechanical per-spective of allosteric transition of proteins2011

    • Author(s)
      M. Sasai
    • Organizer
      The 1st KIAS Conference on Subcellular Dynamics
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2011-07-25
  • [Presentation] The chameleon model : a novel approach to conformational transitions of proteins2011

    • Author(s)
      Tomoki P. Terada, Takahiro Yamashita, Shogo Yokota, Toru Kimura, Masaki Sasai
    • Organizer
      The 1st KIAS Conference on Subcellular Dynamics
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2011-07-25
  • [Presentation] Intrinsic Disorder in Allosteric Transition of Proteins2011

    • Author(s)
      K, Itoh, M. Sasai
    • Organizer
      第11回日本蛋白質科学会
    • Place of Presentation
      大阪
    • Year and Date
      2011-06-06
  • [Presentation] Biological networks : oscillat-ions and transitions2011

    • Author(s)
      M. Sasai
    • Organizer
      International Workshop on "Multiscale Characteriz-ations of Biological Systems : From Molecules to Networks"
    • Place of Presentation
      Nanjing Dongjiao State Guesthouse, China
    • Year and Date
      2011-06-02
  • [Presentation] 計算生物学:分子から細胞そして個体へ2011

    • Author(s)
      笹井理生
    • Organizer
      岡崎統合バイオサイエンスセンター10周年記念シンポジウム
    • Place of Presentation
      岡崎コンファレンスセンター
    • Year and Date
      2011-02-10
  • [Presentation] Statistical mechanics of protein allostery : roles of back-bone and side-chain fluctuations2010

    • Author(s)
      K. Itoh and M. Sasai
    • Organizer
      The 10th KIAS Conference on Protein Structure and Function, Korea Institute for Advanced Study
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2010-10-01
  • [Presentation] Anomalous Dynamics of Eukaryotic Cell Locomotion, Emergent behaviour of biomolecular ensembles and networks2010

    • Author(s)
      M. Sasai
    • Organizer
      Kavli Institute for Theoretical Physics China
    • Place of Presentation
      Beijing, China
    • Year and Date
      2010-08-04
  • [Presentation] Synchronization and Noise in a Protein-Based Circadian Oscillator, Biological Networks. Principles and Dynamics2010

    • Author(s)
      M. Sasai
    • Organizer
      Kavli Institute for Theoretical Physics China
    • Place of Presentation
      Beijing, China
    • Year and Date
      2010-07-27
  • [Presentation] Anomalous Dynamics of Eukaryotic Cell Locomotion2010

    • Author(s)
      M. Sasai
    • Organizer
      Dynamic Days Asia Pacific 6
    • Place of Presentation
      University of New South Wales, Sydney, Australia
    • Year and Date
      2010-07-13
  • [Presentation] Molecular Mechanism of A Protein-Based Circadian Clock2010

    • Author(s)
      M. Sasai
    • Organizer
      Fifty Years of Biophysics Research at Nagoya University
    • Place of Presentation
      Nagoya University
    • Year and Date
      2010-03-13
  • [Presentation] 熱揺らぎのなかで働く分子マシンとしての蛋白質2009

    • Author(s)
      笹井理生
    • Organizer
      第23回分子シミュレーション討論会
    • Place of Presentation
      名古屋市吹上ホール
    • Year and Date
      2009-11-30
  • [Presentation] Harnessing the thermal noise with molecular machines2009

    • Author(s)
      M. Sasai
    • Organizer
      The 9th KIAS-SNU Conference on Protein Structure and Function
    • Place of Presentation
      Seoul National University, Seoul, Korea
    • Year and Date
      2009-10-09
  • [Presentation] Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor, Single molecule experiments and theories2009

    • Author(s)
      M. Sasai
    • Organizer
      International Workshop on Single Molecule Dynamics and Spectroscopy
    • Place of Presentation
      Chung-Ang University Seoul, Korea
    • Year and Date
      2009-10-07
  • [Presentation] A coarse-grained MD approach for de novo prediction of protein structure2009

    • Author(s)
      M. Sasai
    • Organizer
      Asian Workshop for Protein Structure Prediction Methodology
    • Place of Presentation
      Korea Institute for Advanced Study, Seoul, Korea
    • Year and Date
      2009-09-19
  • [Presentation] Stochastic gene expression in developing embryos2009

    • Author(s)
      M. Sasai
    • Organizer
      International Symposium on Reaction Dynamics of Many-body Chemical Systems
    • Place of Presentation
      Kyoto
    • Year and Date
      2009-06-22
  • [Presentation] Energy landscape theory of protein allostery2009

    • Author(s)
      M. Sasai
    • Organizer
      Korea-Japan seminars on biomolecular sciences-Experiments and simulations
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2009-02-27
  • [Presentation] タンパク質のダイナミックな構造と機能に果たす水の役割2008

    • Author(s)
      笹井理生
    • Organizer
      日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2008-12-03
  • [Presentation] Consistency among local and global structures in protein folding and structure prediction2008

    • Author(s)
      M. Sasai
    • Organizer
      The 8th KIAS-Yonsei Conference on Protein Structure and Function
    • Place of Presentation
      Yonsei University, Seoul, Korea
    • Year and Date
      2008-10-10
  • [Presentation] Noise and coherent dynamics in biomolecular networks, Noise in complex systems : From molecular dynamics to stochastic modeling2008

    • Author(s)
      M. Sasai
    • Organizer
      WORKSHOP 2008, in KAIST Daejeon
    • Place of Presentation
      Korea
    • Year and Date
      2008-10-07
  • [Book] 論文にみる最重要概念と革新実験データ,巨大分子系の計算化学2012

    • Author(s)
      笹井理生
    • Total Pages
      38-41
    • Publisher
      日本化学会編
  • [Book] 細胞の物理生物学2011

    • Author(s)
      ロブ・フィリップス他著,笹井理生,伊藤一仁,千見寺浄慈,寺田智樹訳
    • Total Pages
      1-957
    • Publisher
      共立出版
  • [Book] タンパク質の論理,超多自由度系の新しい科学,笹井理生編,(計算科学講座第10巻)2010

    • Author(s)
      笹井理生,伊藤一仁,佐々木尚
    • Total Pages
      181-216
    • Publisher
      共立出版
  • [Book] 計算科学の考え方,超多自由度系の新しい科学,笹井理生編,(計算科学講座第10巻)2010

    • Author(s)
      笹井理生
    • Total Pages
      9-18
    • Publisher
      共立出版
  • [Book] 蛋白質の柔らかなダイナミクス2008

    • Author(s)
      笹井理生
    • Total Pages
      1-192
    • Publisher
      培風館

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Published: 2013-07-31  

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