Free-Energy Analysis of ATP Hydrolysis

2010 Fiscal Year Self-evaluation Report

• Project Area: Water plays a key role in ATP hydrolysis and ATP-driven functions of proteins
• Project/Area Number: 20118002
• 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: MATUBAYASI Nobuyuki Kyoto University, 化学研究所, 准教授 (20281107)
• Project Period (FY): 2008 – 2012
• Keywords: ATP / 自由エネルギー / 加水分解 / 水和 / 溶媒和 / 分子シミュレーション

Research Abstract

ATP加水分解は、生体エネルギー代謝に中心的な役割を果たしている。本研究では、ATPとそれに関連する分子の分子間相互作用と自由エネルギーの計算によって、「なぜATPが水を環境母体とする生体内でエネルギー通貨として有用なのか」という問に分子論的アプローチを試みる。全原子型の自由エネルギー計算によって、統計熱力学的に理解することが目的である。
ATPは、糖・核酸塩基・リン酸の部分からなる。これらの構成部分の役割を明らかにするために、まず、バルク水中でのピロリン酸や様々なアナログの加水分解との比較を行う。NMRや誘電測定で得られる構造形成・破壊の知見と水和自由エネルギーの関連についても検討する。次いで、F1型ATPアーゼ存在下での解析に進む。ATPとADPの結合自由エネルギーの解析である。結合自由エネルギーをタンパク質と水からの寄与に分割し、タンパク質構造変化と基質結合の補償作用の解析によって、化学力学エネルギー変換の分子論を展開する。

Research Products

• [Journal Article] Energetic Origin of Proton Affinity to the Air/Water Interface (2011)
  • Author(s): H.Takahashi, K.Maruyama, Y.Karino, A.Morita, M.Nakano, P.Jungwirth, N.Matubayasi
  • Journal Title: J.Phys.Chem.B 115 Pages: 4745-4751
• [Journal Article] Free-energy analysis of hydration effect on protein with explicit solvent : Equilibrium fluctuation of cytochrome c (2011)
  • Author(s): Y.Karino, N.Matubayasi
  • Journal Title: J.Chem.Phys.(Communication) 134 Pages: 041105(4)
• [Journal Article] Hydration property of globular proteins : An analysis of solvation free energy by energy representation method (2010)
  • Author(s): H.Saito, N.Matubayasi, K.Nishikawa, H.Nagao
  • Journal Title: Chem.Phys.Lett. 497 Pages: 218-222
• [Journal Article] End-point calculation of solvation free energy of amino-acid analogs by molecular theories of solution (2010)
  • Author(s): Y.Karino, M.V.Fedorov, N.Matubayasi
  • Journal Title: Chem.Phys.Lett. 496 Pages: 351-355
• [Journal Article] Controlling the Equilibrium of Formic Acid with Hydrogen and Carbon Dioxide Using Ionic Liquid (2010)
  • Author(s): Y.Yasaka, C.Wakai, N.Matubayasi, M.Nakahara
  • Journal Title: J.Phys.Chem.A 114 Pages: 3510-3515
• [Presentation] Free-Energy Analysis of Biomolecular Solvation in the Energetic Perspective (2010)
  • Author(s): N.Matubayasi
  • Organizer: Gordon Research Conference on Water and Aqueous Solutions
  • Place of Presentation: Holderness, USA
  • Year and Date: 20100808-20100813
• [Presentation] Free-Energy Analysis of Nano-Organized Systems in Solution (2010)
  • Author(s): N. Matubayasi
  • Organizer: 21st IUPAC International Conference on Chemical Thermodynamics
  • Place of Presentation: つくば
  • Year and Date: 20100801-06
• [Presentation] Free-Energy Analysis of Solvation in the Energetic Perspective (2010)
  • Author(s): N.Matubayasi
  • Organizer: Trilateral Scientific Seminar "Solvation in Complex Liquids : Bridging Length Scales by Theory and Experiment
  • Place of Presentation: Leipzig, Germany
  • Year and Date: 20100623-20100625
• [Presentation] Free-Energy Analysis of Solvation in the Energetic Perspective (2009)
  • Author(s): N.Matubayasi
  • Organizer: Mini-Symposium on Computation of Interactions in Biological Systems
  • Place of Presentation: Nove Hrady, Czech Republic
  • Year and Date: 20091212-20091213
• [Presentation] Free Energy of Solvation in the Energetic Perspective (2009)
  • Author(s): N.Matubayasi
  • Organizer: International Symposium on Multi-Scale Dynamics of Protein Complex Formation and Function
  • Place of Presentation: 東京
  • Year and Date: 20090714-20090716
• [Book] Advances in QuantumChemistry, vol59 (2010)
  • Author(s): H.Takahashi, N.Matubayasi, M.Nakan
  • Total Pages: 283-351
  • Publisher: Development of a Quantum ChemicalMethod Combined with a Theory ofSolutions -- Free-Energy Calculation forChemical Reactions by Condensed PhaseSimulations
• [Book] 熱測定(ISSN: 0386-2615), 36 (3) (2009)
  • Author(s): 松林伸幸
  • Total Pages: 165-172
  • Publisher: エネルギー表示法による溶媒和の自由エネルギー解析
• [Book] Frontiers in Bioscience 14 (2009)
  • Author(s): N.Matubayasi
  • Total Pages: 3536-3549
  • Publisher: Free-Energy Analysis ofSolvation with the Method of EnergyRepresentation