Water roles in functioning of ATP-driven proteins: Analyses based on statistical mechanics

2012 Fiscal Year Final Research Report

• Project Area: Water plays a key role in ATP hydrolysis and ATP-driven functions of proteins
• Project/Area Number: 20118004
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Complex systems
• Research Institution: Kyoto University
• Principal Investigator: KINOSHITA Masahiro 京都大学, エネルギー理工学研究所, 教授 (90195339)
• Project Period (FY): 2008 – 2012
• Keywords: ATP / 蛋白質 / 水和 / エントロピー / 自己組織化 / 積分方程式論

Research Abstract

We have performed statistical-mechanical analyses on the assist to protein folding by chaperonin, multi-drug efflux by ABC transporter, unidirectional rotation of the γ-subunit in F_1-ATPase, and unidirectional movement of myosin along F-actin. We have constructed a novel, unified physical picture of the functioning of ATP-driven proteins which utilizes the binding of ATP to a receptor, ATP hydrolysis within the receptor, and release of ADP and Pi.

Research Products

• [Journal Article] Entropic Release of a Big Sphere from a Cylindrical Vessel (2013)
  • Author(s): H. Mishima, H. Oshima, S. Yasuda, K. Amano, and M. Kinoshita
  • Journal Title: Chem. Phys. Lett Volume: 561-562 Pages: 159-165
  • DOI: DOI:10.1016/j.cplett.2013.01.045
  • Peer Reviewed
• [Journal Article] タンパク質水和理論の新機軸III.理論的考察 (2012)
  • Author(s): 木下正弘,永山國昭
  • Journal Title: 生物物理 Volume: 52 Pages: 300-303
  • URL: https://www.jstage.jst.go.jp/article/biophys/52/6/52_300/_pdf
  • Peer Reviewed
• [Journal Article] タンパク質水和理論の新機軸II.新理論の応用展開 (2012)
  • Author(s): 木下正弘,永山國昭
  • Journal Title: 生物物理 Volume: 52 Pages: 250-253
  • URL: https://www.jstage.jst.go.jp/article/biophys/52/5/52_250/_pdf
  • Peer Reviewed
• [Journal Article] タンパク質水和理論の新機軸I.朝倉-大沢理論を越えて (2012)
  • Author(s): 木下正弘,永山國昭
  • Journal Title: 生物物理 Volume: 52 Pages: 203-205
  • URL: https://www.jstage.jst.go.jp/article/biophys/52/4/52_203/_pdf
  • Peer Reviewed
• [Journal Article] Physical Origin of Hydrophobicity Studied in terms of Cold Denaturation of Proteins: Comparison between Water and Simple Fluids (2012)
  • Author(s): T. Yoshidome and M. Kinoshita
  • Journal Title: Phys. Chem. Chem. Phys Volume: 14 Pages: 14554-14566
  • DOI: DOI:10.1039/c2cp41738c
  • Peer Reviewed
• [Journal Article] Structural Characteristics of Yeast F1-ATPase before and after 16-Degree Rotation of the . Subunit: Theoretical Analysis Focused on the Water-Entropy Effect (2012)
  • Author(s): T. Yoshidome, Y. Ito, N. Matubayasi, M. Ikeguchi, and M. Kinoshita
  • Journal Title: J. Chem. Phys Volume: 137 Pages: 035102(1-8)
  • DOI: DOI:10.1063/1.4734298
  • Peer Reviewed
• [Journal Article] Potential of Mean Force between a Large Solute and a Biomolecular Complex: A Model Analysis on Protein Flux through Chaperonin System (2011)
  • Author(s): K. Amano, H. Oshima, and M. Kinoshita
  • Journal Title: J. Chem. Phys Volume: 135 Pages: 185101(1-14)
  • DOI: DOI:10.1063/1.3657856
  • Peer Reviewed
• [Journal Article] Rotational Mechanism of F1-ATPase: Crucial Importance of Water-Entropy Effect (2011)
  • Author(s): T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita
  • Journal Title: J. Am. Chem. Soc Volume: 133 Pages: 4030-4039
  • DOI: DOI:10.1021/ja109594y
  • Peer Reviewed
• [Journal Article] Entropic Potential Field Formed for a Linear-Motor Protein near a Filament: Statistical-Mechanical Analyses Using Simple Models (2010)
  • Author(s): K. Amano, T. Yoshidome, M. Iwaki, M. Suzuki, and M. Kinoshita
  • Journal Title: J. Chem. Phys Volume: 133 Pages: 045103(1-11)
  • DOI: DOI:10.1063/1.3462279
  • Peer Reviewed
• [Presentation] Roles of Water and ATP in Functioning of ATP-Driven Proteins (2011)
  • Author(s): M. Kinoshita
  • Organizer: The 7th Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
  • Place of Presentation: Waseda University, Tokyo, Japan
  • Year and Date: 20110902-08
• [Presentation] 「疎水性」の本当の物理起源:その温度依存性を通しての考察 (2011)
  • Author(s): 木下正弘
  • Organizer: 第56回低温生物工学会大会セミナー
  • Place of Presentation: いわて県民情報交流センター
  • Year and Date: 20110707-08
• [Presentation] 生命現象発現における水分子並進移動の役割 (2011)
  • Author(s): 木下正弘
  • Organizer: 新世代研究所第6回合同研究会
  • Place of Presentation: 明治大学紫紺館
  • Year and Date: 2011-11-29
• [Presentation] 分子認識などの生命現象における水の並進エントロピーの重要性 (2011)
  • Author(s): 木下正弘
  • Organizer: 日本学術振興会回折構造生物第169委員会第36回研究会
  • Place of Presentation: ゆうぽうと,東京都品川区
  • Year and Date: 2011-10-04
• [Presentation] Importance of Translational Entropy of Water in Biological Self-Assembly (2009)
  • Author(s): M. Kinoshita
  • Organizer: International Symposium on Multi-Scale Dynamics of Protein Complex Formation and Function
  • Place of Presentation: Sanjo Conference Hall, The University of Tokyo, Japan
  • Year and Date: 20090714-16
• [Presentation] アクトミオシンのような大規模系に対応可能な計算法はあるか? (2008)
  • Author(s): 木下正弘
  • Organizer: 日本生物物理学会第46回年会シンポジウム「水を主役とした化学力学エネルギー変換論-ATPから運動へ-」
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 20081203-05
• [Book] 「表面の水和の統計力学理論」,日本化学会・コロイドおよび界面化学部会35周年記念出版,「現代界面コロイド科学の事典-シャンプーから宇宙まで-」,10章 6節 (2010)
  • Author(s): 木下正弘
  • Total Pages: 244-245
  • Publisher: 丸善
• [Remarks] 木下研究室-京都大学エネルギー理工学研究所
  • URL: http://www.iae.kyoto-u.ac.jp/centerbunya/kinoshita