Flexible dynamics and reactions in biomolecules

• Project/Area Number: 18066005
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: Nagoya University
• Principal Investigator: SASAI Masaki Nagoya University, 大学院・工学研究科, 教授 (30178628)
• Project Period (FY): 2006 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥18,300,000 (Direct Cost: ¥18,300,000); Fiscal Year 2009: ¥3,200,000 (Direct Cost: ¥3,200,000); Fiscal Year 2008: ¥5,500,000 (Direct Cost: ¥5,500,000); Fiscal Year 2007: ¥5,500,000 (Direct Cost: ¥5,500,000); Fiscal Year 2006: ¥4,100,000 (Direct Cost: ¥4,100,000)
• Keywords: 生物物理 / 化学物理 / 自己組織化 / 生体分子 / 蛋白質

Research Abstract

Flexible dynamics of the large scale conformational change of proteins is essential in many biochemical reactions. In order to solve the principles of flexible dynamics and to bridge between quantum chemical understanding of reactions and the observed physiological phenomena, we studied the energy landscape models of protein conformation change. Also important is the flexible stochastic kinetics of reactions among biomolecules which are confined in a meso-scopic i.e. cellular size space. We studied the stochastic processes in such meso-scopic systems by developing models of biochemical reactions.

Research Products

• [Journal Article] Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor (2010)
  • Author(s): M. Takano, T.P. Terada, M. Sasai
  • Journal Title: Proc. Natl. Acad. Sci. USA
  • NAID: 120005475997
  • Peer Reviewed
• [Journal Article] Entropic mechanism of large fluctuation in allosteric transition (2010)
  • Author(s): K. Itoh, M. Sasai
  • Journal Title: Proc. Natl. Acad. Sci. USA
  • NAID: 120005475996
  • Peer Reviewed
• [Journal Article] Synchronizaion of circadian oscillation of phosphorylation level of KaiC in vitro (2010)
  • Author(s): T. Nagai, T.P. Terada, M. Sasai
  • Journal Title: Biophys. J. 98,No.11
  • Peer Reviewed
• [Journal Article] de Novo Protein Structure Prediction using Fragment Based Potential and Conformational Space Annealing (2010)
  • Author(s): Juyong Lee, M. Sasai, C. Seok, Jooyoung Lee
  • Journal Title: Biophys. J. 98,Issue3
• [Journal Article] de Novo Protein Structure Prediction using Fragment Based Potential and Conformational Space Annealing (2010)
  • Author(s): Juyong Lee, M.Sasai, C.Seok, Jooyoung Lee
  • Journal Title: Biophys.J. 98
• [Journal Article] Multi-dimensional theory of protein folding (2009)
  • Author(s): K. Itoh, M. Sasai
  • Journal Title: J. Chem. Phys. 130,No.14
  • NAID: 120001804820
  • Peer Reviewed
• [Journal Article] Stable, precise, and reproducible patterning of bicoid and hunchback molecules in the early Drosophila embryo (2009)
  • Author(s): Y. Okabe-Oho, H. Murakami, S. Oho, M. Sasai
  • Journal Title: PLoS Comp. Biol. 5,No.8
  • NAID: 120005475994
  • Peer Reviewed
• [Journal Article] Cortical factor feedback model of cellular locomotion and cytofission (2009)
  • Author(s): S.I. Nishimura, M. Ueda, M. Sasai
  • Journal Title: PLoS Comp. Biol. 5,No.3
  • Peer Reviewed
• [Journal Article] Stable, precise, and reproducible patterning of bicoid and hunchback molecules in the early Drosophila embryo (2009)
  • Author(s): Y.Okabe-Oho, H.Murakami, S.Oho, M.Sasai
  • Journal Title: PLoS Comp.Biol. 5
  • NAID: 120005475994
  • Peer Reviewed
• [Journal Article] Multi-dimensional theory of protein folding (2009)
  • Author(s): K.Itoh, M.Sasai
  • Journal Title: J.Chem.Phys. 130
  • NAID: 120001804820
  • Peer Reviewed
• [Journal Article] Cortical factor feedback model of cellular locomotion and cytofission (2009)
  • Author(s): S. I. Nishimura, M. Ueda and M. Sasai
  • Journal Title: PLoS Computational Biology 5
  • Peer Reviewed
• [Journal Article] Cooperativity, connectivity, and folding pathways of multidomain proteins (2008)
  • Author(s): K. Itoh, M. Sasai
  • Journal Title: Proc. Natl. Acad. Sci. USA. 105 Pages: 13865-13870
  • NAID: 120005475995
  • Peer Reviewed
• [Journal Article] A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction (2008)
  • Author(s): T.N. Sasaki, H. Cetin, M. Sasai
  • Journal Title: Biochem. Biophys. Research Comm. 369 Pages: 500-506
  • NAID: 120005475992
  • Peer Reviewed
• [Journal Article] Cooperativity, connectivity, and folding pathways of multidomain proteins (2008)
  • Author(s): K.Itoh and M.Sasai
  • Journal Title: Proc.Natl.Acad.Sci.USA. 105 Pages: 13865-13870
  • NAID: 120005475995
  • Peer Reviewed
• [Journal Article] A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction (2008)
  • Author(s): T.N.Sasaki, H.Cetin, and M.Sasai
  • Journal Title: Biochem.Biophys.Research Comm. 369 Pages: 500-506
  • NAID: 120005475992
  • Peer Reviewed
• [Journal Article] Cooperativity, connectivity, and folding pathways of multidomain proteins (2008)
  • Author(s): K. Itoh and M. Sasai
  • Journal Title: Proc. Natl. Acad. Sci. USA 105 Pages: 13865-13870
  • NAID: 120005475995
  • Peer Reviewed
• [Journal Article] Mechanism of robust circadian oscillation of KaiC phosphorylation in vitro (2008)
  • Author(s): K. Eguchi, M. Yoda, T. P. Terada and M. Sasai
  • Journal Title: Biophysical Journal 95 Pages: 1773-1784
  • Peer Reviewed
• [Journal Article] Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene (2007)
  • Author(s): Y. Okabe, Y. Yagi, M. Sasai
  • Journal Title: J. Chem. Phys. 127
  • Peer Reviewed
• [Journal Article] Monomer-shuffling and allosteric transition in circadian oscillation of KaiC phosphorylation (2007)
  • Author(s): M. Yoda, K. Eguchi, T.P. Terada, M. Sasai
  • Journal Title: PLoS ONE 2
  • Peer Reviewed
• [Journal Article] Fluctuating hydration structure around nanometer-size hydrophobic solutes II -Caging and drying around single-wall carbon nanotubes- (2007)
  • Author(s): T. Hotta, M. Sasai
  • Journal Title: J. Phys. Chem. C 111 Pages: 2861-2871
  • Peer Reviewed
• [Journal Article] Roles of noise in single and coupled multiple genetic oscillators (2007)
  • Author(s): M. Yoda, T. Ushikubo, W. Inoue, M. Sasai
  • Journal Title: J. Chem. Phys. 126
  • NAID: 120002410545
  • Peer Reviewed
• [Journal Article] Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene (2007)
  • Author(s): Y.Okabe, Y.Yagi, and M.Sasai
  • Journal Title: J.Chem.Phys. 127
  • Peer Reviewed
• [Journal Article] Monomer-shuffling and allosteric transition in circadian oscillation of KaiC phosphorylation (2007)
  • Author(s): M.Yoda, K.Eguchi, T.P.Terada, and M.Sasai
  • Journal Title: PLoS ONE 2 e408-1-8
  • Peer Reviewed
• [Journal Article] Fluctuating hydration structure around nanometer-size hydrophobic solutes II -Caging and drying around single-wall carbon nanotubes- (2007)
  • Author(s): T.Hotta, and M.Sasai
  • Journal Title: J.Phys.Chem. C 111 Pages: 2861-2871
  • Peer Reviewed
• [Journal Article] Roles of noise in single and coupled multiple genetic oscillators (2007)
  • Author(s): M.Yoda, T.Ushikubo, W.Inoue, and M.Sasai
  • Journal Title: J.Chem.Phys. 126
  • NAID: 120002410545
  • Peer Reviewed
• [Journal Article] Monomer-shuffling and allosteric transition in circadian oscillation of KaiC phosphorylation (2007)
  • Author(s): M. Yoda, K. Eguchi, T.P. Terada, and M. Sasai
  • Journal Title: PLoS ONE 2
  • Peer Reviewed
• [Journal Article] Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene (2007)
  • Author(s): Y. Okabe, Y. Yagi, and M. Sasai
  • Journal Title: J. Chem. Phys 127
  • Peer Reviewed
• [Journal Article] Roles of noise in single and coupled multiple genetic oscillators (2007)
  • Author(s): M.Yoda, T.Ushikubo, W.Inoue, M.Sasai
  • Journal Title: J. Chem. Phys. 126
  • NAID: 120002410545
• [Journal Article] Modulation of the reaction rate of regulating protein induces large morphological and motional change of amoebic cell (2007)
  • Author(s): S.I.Nishimura, M.Sasai
  • Journal Title: J. Theor. Biol. 245・2 Pages: 230-237
• [Journal Article] Testing the transition state theory in stochastic dynamics of a genetic switch (2006)
  • Author(s): T. Ushikubo, W. Inoue, M. Yoda, M. Sasai
  • Journal Title: Chem. Phys. Lett. 430 Pages: 139-143
  • Peer Reviewed
• [Journal Article] Flexibly varying folding mechanism of a nearly symmetrical protein: B domain of protein A (2006)
  • Author(s): K. Itoh, M. Sasai
  • Journal Title: Proc. Natl. Acad. Sci. USA 103 Pages: 7298-7303
  • Peer Reviewed
• [Journal Article] Testing the transition state theory in stochastic dynamics of a genetic switch (2006)
  • Author(s): T.Ushikubo, W.Inoue, M.Yoda, and M.Sasai
  • Journal Title: Chem.Phys.Lett. 430 Pages: 139-143
  • Peer Reviewed
• [Journal Article] Flexibly varying folding mechanism of a nearly symmetrical protein : B domain of protein A (2006)
  • Author(s): K.Itoh and M.Sasai
  • Journal Title: Proc.Natl.Acad.Sci.USA 103 Pages: 7298-7303
  • Peer Reviewed
• [Journal Article] Testing the transition state theory in stochastic dynamics of a genetic switch (2006)
  • Author(s): T.Ushikubo, W.Inoue, M.Yoda, M.Sasai
  • Journal Title: Chem. Phys. Lett. 430・1 Pages: 139-143
• [Presentation] Harnessing the thermal noise with molecular machines (2010)
  • Author(s): M.Sasai
  • Organizer: International Symposium on Molecular Theory for Real Systems
  • Place of Presentation: Fukui Institute(京都市)
  • Year and Date: 2010-01-08
• [Presentation] Molecular Mechanism of A Protein-Based Circadian Clock (2010)
  • Author(s): M. Sasai
  • Organizer: Fifty Years of Biophysics Research at Nagoya University
  • Place of Presentation: Nagoya University
• [Presentation] Entropic mechanism of large fluctuation in allosteric transition (2010)
  • Author(s): K. Itoh, M. Sasai
  • Organizer: Gordon Research Conference on Protein Folding Dynamics
  • Place of Presentation: Ventura, California
• [Presentation] Harnessing the thermal noise with molecular machines, International Symposium on Molecular Theory for Real Systems (2010)
  • Author(s): M. Sasai
  • Organizer: Fukui Institute
  • Place of Presentation: Kyoto
• [Presentation] Harnessing the thermal noise with molecular machines (2009)
  • Author(s): M.Sasai
  • Organizer: The 9th KIAS-SNU Conference on Protein Structure and Function
  • Place of Presentation: Seoul National Universi(ソウル)
  • 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 theories (2009)
  • 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] Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor (2009)
  • Author(s): M.Sasai
  • Organizer: International Workshop on Single Molecule Dynamics and Spectroscopy
  • Place of Presentation: Chung-Ang University(ソウル)
  • Year and Date: 2009-10-07
• [Presentation] Harnessing the thermal noise with molecular machines (2009)
  • Author(s): M. Sasai
  • Organizer: The 9th KIAS-SNU Conference on Protein Structure and Function
  • Place of Presentation: Seoul National University, Seoul, Korea
• [Presentation] Stochastic gene expression in developing embryos (2009)
  • Author(s): M. Sasai
  • Organizer: International Symposium on Reaction Dynamics of Many-body Chemical Systems
  • Place of Presentation: Kyoto
• [Presentation] Energy landscape theory of protein allostery (2009)
  • Author(s): M. Sasai
  • Organizer: Korea-Japan seminars on biomolecular sciences - Experiments and simulations
  • Place of Presentation: Seoul, Korea
• [Presentation] Energy landscape theory of protein allostery (2009)
  • Author(s): M.Sasai
  • Organizer: Korea-Japan seminars on biomolecular sciences - Experiments and simulations
  • Place of Presentation: Seoul,Korea
• [Presentation] Monte Carlo simulation of transcriptional control in 6 kbp DNA (2009)
  • Author(s): Naoko Tokuda, Masaki Sasai and George Chikenii
  • Organizer: The 53 rd Annual Meeting of Biophysical Society
  • Place of Presentation: Boston
• [Presentation] Energy landscape theory of protein allostery (2009)
  • Author(s): Masaki Sasai
  • Organizer: First Korea-Japan. Seminars on Biomolecular Sciences
  • Place of Presentation: First Korea-Japan. Seminars on Biomolecular Sciences
• [Presentation] Consistency among local and global structures in protein folding and structure prediction (2008)
  • Author(s): M. Sasai
  • Organizer: The 8th KIAS - Yonsei Conference on Protein Structure and Function
  • Place of Presentation: Yonsei University, Seoul, Korea
• [Presentation] Noise and coherent dynamics in biomolecular networks (2008)
  • Author(s): M. Sasai
  • Organizer: Noise in complex systems: From molecular dynamics to stochastic modeling WORKSHOP 2008
  • Place of Presentation: KAIST Daejeon, Korea
• [Presentation] Noise and coherent dynamics in biomolecular networks (2008)
  • Author(s): M.Sasai
  • Organizer: Noise in complex systems : From molecular dynamics to stochastic modeling WORKSHOP 2008
  • Place of Presentation: KAIST Daejeon, Korea
• [Presentation] Consistency among local and global structures in proteinfolding and structure prediction (2008)
  • Author(s): M. Sasai
  • Organizer: The 8 th KIAS-Yonsei Conference on Protein Structure and Function
  • Place of Presentation: Yonsei University, Seoul
• [Presentation] Precise spatial patterns of Bicoid and Hunchback in the early Drosophila embryo (2008)
  • Author(s): Yurie Okabe, Hiroki Murakami, Masaki Sasai
  • Organizer: Frontiers in Developmental Biology(フランス発生生物学会/日本発生生物学会合同年会)
  • Place of Presentation: Giens, France
• [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
• [Presentation] Monte Carlo Simulation of Transcriptional Regulation in Linear DNA of Eukaryotes (2008)
  • Author(s): Naoko Tokuda, Masaki Sasai, George Chikenji
  • Organizer: Joint Meeting of the Biophysical Society 52nd Annual Meeting & 16th International Biophysics Congress
  • Place of Presentation: Long Beach, California
• [Presentation] Energy landscape perspective of protein functioning (2007)
  • Author(s): M. Sasai
  • Organizer: The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry
  • Place of Presentation: Beijing
• [Presentation] Energy landscape perspective of protein functioning (2007)
  • Author(s): Masaki Sasai
  • Organizer: The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry
  • Place of Presentation: 北京,中華人民共和国
• [Presentation] Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene (2007)
  • Author(s): Yurie Okabe, Yuu Yagi, and Masaki Sasai
  • Organizer: The 8th International Conference on Systems Biology
  • Place of Presentation: Long Beach, California
• [Presentation] A unified mechanism of amoeboid cel locomotion and cell fission (2007)
  • Author(s): Shin I. Nishimura and Masaki Sasai
  • Organizer: The Joint Annual Meetings of the Society for Mathematical Biology and the Japanese Society for Mathematical Biology
  • Place of Presentation: San Jose, California
• [Presentation] 細胞運動及び細胞分裂の統一モデル (2007)
  • Author(s): 西村信一郎, 笹井理生
  • Organizer: 細胞性粘菌研究会
  • Place of Presentation: 弘前大学
• [Presentation] シャッフリングとアロステリック転移を用いたKaiC概日リズムのモデル化 (2007)
  • Author(s): 依田充正, 江口浩平, 寺田智樹, 笹井理生
  • Organizer: 第14回日本時間生物学会
  • Place of Presentation: 京王プラザホテル
• [Presentation] 蛋白質の構造変化ダイナミクス-1分子統計力学の視点からの考察 (2007)
  • Author(s): 伊藤一仁, 笹井理生
  • Organizer: 第45回生物物理学会年会
  • Place of Presentation: パシフィコ横浜
• [Presentation] 拡張された郷-likeモデルによるモータータンパク質の構造変化 (2007)
  • Author(s): 検崎博生, 笹井理生
  • Organizer: 第45回生物物理学会年会
  • Place of Presentation: パシフィコ横浜
• [Presentation] 細胞運動及び細胞分裂の統一モデル (2007)
  • Author(s): 西村 信一郎, 笹井 理生
  • Organizer: 第45回生物物理学会年会
  • Place of Presentation: パシフィコ横浜
• [Presentation] ショウジョウバエ胚においてBicoidの確率的拡散と協同的結合がhunchbackの発現に及ぼす影響 (2007)
  • Author(s): 岡部ゆりえ, 村上博紀, 笹井理生
  • Organizer: 第45回生物物理学会年会
  • Place of Presentation: パシフィコ横浜
• [Presentation] ショウジョウバエ初期胚においてBicoidの確率的拡散と協同的結合がhunchbackの発現に及ぼす影響 (2007)
  • Author(s): 村上 博紀, 岡部ゆりえ, 笹井理生
  • Organizer: 第45回生物物理学会年会
  • Place of Presentation: パシフィコ横浜
• [Presentation] シャッフリングとアロステリック転移を用いたKaiC概日リズムのモデル化 (2007)
  • Author(s): 依田 充正, 江口 浩平, 寺田 智樹, 笹井 理生
  • Organizer: 第45回生物物理学会年会
  • Place of Presentation: パシフィコ横浜
• [Book] 蛋白質の柔らかなダイナミクス (2008)
  • Author(s): 笹井理生
  • Total Pages: 192
  • Publisher: 培風館