タンパク質物性から振動の理論生物学へ

• Project Area: Dynamical ordering of biomolecular systems for creation of integrated functions
• Project/Area Number: 26102520
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: Nagoya University
• Principal Investigator: 笹井 理生 名古屋大学, 工学(系)研究科(研究院), 教授 (30178628)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000); Fiscal Year 2015: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000); Fiscal Year 2014: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
• Keywords: アロステリック転移 / 概日周期 / １分子運動論 / 反応システム理論 / 1分子運動論

Outline of Annual Research Achievements

本研究は、タンパク質のアロステリック構造転移の転移経路と自由エネルギーランドスケープを計算する新しい方法を開発し、その成果をタンパク質間相互作用のシステム生物学と結び付け、分子から細胞機能への融合分野を開拓することを目的としている。このため、２７年度は以下のテーマに取り組んだ。
その１つは、タンパク質アロステリック転移を表現する自己無撞着な粗視化モデル（カメレオンモデル）の開発である。カメレオンモデルをNtrCに適用し、遷移状態で構造の乱れがおきる様子を計算で示した。
もう１つは、KaiABC系の１分子レベルのモデルである。２７年度に明らかになった、生化学的実験データ、原子間力顕微鏡観測データ、構造データをもとに２６年度までに構築した１分子モデルを再検討し、合理的なモデルに向けて整備を行った。

Research Progress Status

27年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

27年度が最終年度であるため、記入しない。

Research Products

• [Int'l Joint Research] State University of New York(米国)
• [Journal Article] Importance of consensus region of multiple-ligand templates in a virtual screening method (2016)
  • Author(s): Tatsuya Okuno, Koya Kato, Shintaro Minami, Tomoki P. Terada, Masaki Sasai, and George Chikenji
  • Journal Title: Biophysics and Physicobiology Volume: 未定
  • NAID: 130005165373
  • Peer Reviewed / Open Access
• [Journal Article] Multiple coupled landscapes and non-diabatic dynamics with applications to self activating genes (2015)
  • Author(s): Cong Chen, Kun Zhang, Haidong Feng, Masaki Sasai and Jin Wang
  • Journal Title: Phys. Chem. Chem. Phys. Volume: 17 Issue: 43 Pages: 29036-29044
  • DOI: 10.1039/c5cp04780c
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Effects of collective histone state dynamics on epigenetic landscape and kinetics of cell reprogramming (2015)
  • Author(s): S. S. Ashwin and Masaki Sasai
  • Journal Title: Scientific Reports Volume: 5 Issue: 1
  • DOI: 10.1038/srep16746
  • NAID: 120005822508
  • Peer Reviewed / Open Access
• [Journal Article] Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin (2014)
  • Author(s): Nie, QM., Togashi, A., Sasaki, TN., Takano, M., Sasai, M., Terada, TP
  • Journal Title: PLoS Comput Biol Volume: 10 Issue: 4 Pages: e1003552-e1003552
  • DOI: 10.1371/journal.pcbi.1003552
  • NAID: 120005476003
  • Peer Reviewed / Open Access
• [Journal Article] Folding pathway of a multidomain protein depends on its topology of domain connectivity (2014)
  • Author(s): Takashi Inanami, Tomoki P. Terada, and Masaki Sasai
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 111 Issue: 45 Pages: 15969-15974
  • DOI: 10.1073/pnas.1406244111
  • Peer Reviewed / Open Access
• [Presentation] Dynamical energy landscape perspective on protein functioning (2015)
  • Author(s): Masaki Sasai, Tomoki P Terada, Qing-Miao Nie
  • Organizer: The International Chemical Congress of Pacific Basin Societies 2015 (PACIFICHEM2015)
  • Place of Presentation: ホノルル
  • Year and Date: 2015-12-15
  • Int'l Joint Research / Invited
• [Presentation] A stochastic simulation study on circadian oscillation and ATPase activity of KaiC hexamer (2015)
  • Author(s): Sumita Das, Shota Hashimoto, Tomoki P. Terada, Masaki Sasai
  • Organizer: 日本生物物理学会第53回年会
  • Place of Presentation: 金沢大学
  • Year and Date: 2015-09-13
• [Presentation] Interdomain communication as the mechanism of correlation between circadian oscillation of KaiC phosphorylation and ATPase activity (2015)
  • Author(s): Shota Hashimoto, Das Sumita, Masaki Sasai, Tomoki P. Terada
  • Organizer: 日本生物物理学会第53回年会
  • Place of Presentation: 金沢大学
  • Year and Date: 2015-09-13
• [Presentation] タンパク質物性から振動の理論生物学へ (2015)
  • Author(s): Sumita Das、橋本翔多、寺田智樹、笹井理生
  • Organizer: 新学術領域「動的秩序と機能」全体班会議
  • Place of Presentation: 兵庫県淡路
  • Year and Date: 2015-08-04
• [Presentation] 分子モーターの時空間スケール (2015)
  • Author(s): 笹井理生
  • Organizer: 第６回分子モーター討論会
  • Place of Presentation: 東京大学
  • Year and Date: 2015-06-13
  • Invited
• [Presentation] Multi-funnel view of protein folding (2015)
  • Author(s): Masaki Sasai
  • Organizer: The First Korean-Polish Conference on "Protein Folding: Theoretical and Experimental Approaches"
  • Place of Presentation: ソウル
  • Year and Date: 2015-05-24
  • Int'l Joint Research / Invited
• [Presentation] KaiCタンパク質のリン酸化リズムとATP加水分解のカップリングの確率シミュレーション (2015)
  • Author(s): 寺田智樹，成田建樹，笹井理生
  • Organizer: 日本物理学会第70回年次大会
  • Place of Presentation: 早稲田大学
  • Year and Date: 2015-03-21 – 2015-03-24
• [Presentation] From molecules to system: Multiscale modeling of reactions, structural changes, and rhythm of KaiABC system (2015)
  • Author(s): Kenjyu Narita, Masaki Sasai, Tomoki P. Terada
  • Organizer: The 3rd International Symposium "Dynamical ordering of biomolecular systems for creation of integrated functions"
  • Place of Presentation: 三重県志摩市
  • Year and Date: 2015-01-10 – 2015-01-11
• [Presentation] Interplay between the ATPase activity and the structural change of KaiC protein studied by stochastic simulation (2014)
  • Author(s): Kenju Narita, Masaki Sasai, Tomoki P. Terada
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2014-09-25 – 2014-09-27
• [Presentation] タンパク質物性から振動の理論生物学へ (2014)
  • Author(s): 笹井理生
  • Organizer: 新学術領域「動的秩序と機能」領域班会議
  • Place of Presentation: 石川県
  • Year and Date: 2014-08-04 – 2014-08-07
• [Presentation] Allosteric dynamics of proteins, (2014)
  • Author(s): Masaki Sasai
  • Organizer: Macromolecular dynamics: structure, function and diseases
  • Place of Presentation: Beijing
  • Year and Date: 2014-07-01
  • Invited
• [Presentation] Dynamical Landscapes of motors and enzymes (2014)
  • Author(s): Masaki Sasai
  • Organizer: Macromolecular dynamics: structure, function and diseases
  • Place of Presentation: Beijing
  • Year and Date: 2014-06-27
  • Invited