Free-Energy Analysis of ATP Hydrolysis

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: 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 京都大学, 化学研究所, 准教授 (20281107)
• Co-Investigator(Kenkyū-buntansha): NAKAHARA Masaru 京都大学, 化学研究所, 教授 (20025480) ; WAKAI Chihiro 京都大学, 化学研究所, 助教 (40293948)
• Project Period (FY): 2008 – 2012
• Keywords: ATP / 水和 / 溶媒和 / 加水分解 / 自由エネルギー / 溶液理論 / タンパク質構造

Research Abstract

ATP is a key compound to bridge material science and life science. In the present project, all-atom analysis of free energy is conducted for the hydrolysis of ATP. It is found that the hydration free energies of ATP and its related compounds are comparable in magnitude to the energies of covalent bonds. The interaction component responsible for the solvation effect on ATP and protein systems is further identified, and an analysis scheme for cosolvent effect is established.

Research Products

• [Journal Article] Anion-Dependence of Fast Relaxation Component in Na-, K-Halide Solutions at Low Concentrations Measured by High-Resolution Microwave Dielectric Spectroscopy (2013)
  • Author(s): G. Mogami, T. Miyazaki, T. Wazawa, N. Matubayasi, and M. Suzuki
  • Journal Title: J. Phys. Chem. A Volume: 117(in press)
  • DOI: DOI:10.1021/jp4012119
  • Peer Reviewed
• [Journal Article] Effect of heavy hydrogen isotopes on the vibrational line shape for supercritical water through rotational couplings (2013)
  • Author(s): K. Yoshida, N. Matubayasi, Y. Uosaki, and M. Nakahara
  • Journal Title: J. Chem. Phys Volume: 138 Pages: 134508 (12 pages)
  • DOI: DOI:10.1063/1.4798933
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Simulations of Yeast F_<1-> ATPase before and after 16° Rotation of the γ Subunit (2013)
  • Author(s): Y. Ito, T. Yoshidome, N. Matubayasi, M. Kinoshita, and M. Ikeguchi
  • Journal Title: J. Phys. Chem. B Volume: 117 Pages: 298-3307
  • DOI: DOI:10.1021/jp312499u
  • Peer Reviewed
• [Journal Article] Solvent Effect on Pathways and Mechanisms for D-Fructose Conversion to 5-Hydroxymethyl-2-furaldehyde: In Situ^<13>C NMR Study (2013)
  • Author(s): H. Kimura, M. Nakahara, and N. Matubayasi
  • Journal Title: J. Phys. Chem. A Volume: 117 Pages: 2102-2113
  • DOI: DOI:10.1021/jp312002h
  • Peer Reviewed
• [Journal Article] Interaction-component analysis of the urea effect on amino acid analogs (2013)
  • Author(s): Y. Karino and N. Matubayasi
  • Journal Title: Phys. Chem. Chem. Phys Volume: 15 Pages: 4377-4391
  • DOI: DOI:10.1039/c3cp43346c
  • Peer Reviewed
• [Journal Article] A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method (2013)
  • Author(s): T. Ishikawa, R. R. Burri, Y. O. Kamatari, S. Sakuraba, N. Matubayasi, A. Kitao, and K. Kuwata
  • Journal Title: Phys. Chem. Chem. Phys Volume: 15 Pages: 3646-3654
  • DOI: DOI:10.1039/c3cp42761g
  • Peer Reviewed
• [Journal Article] Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation (2013)
  • Author(s): K. Takemura, R. R. Burri, T. Ishikawa, T. Ishikura, S. Sakuraba, N. Matubayasi, K. Kuwata, and A. Kitao
  • Journal Title: Chem. Phys. Lett Volume: 559 Pages: 94-98
  • DOI: DOI:10.1016/j.cplett.2012.12.063
  • Peer Reviewed
• [Journal Article] High-Energy X-ray Diffraction Study on the Intramolecular Structure of 2-Aminoethanol in the Liquid State (2013)
  • Author(s): Y. Kameda, H. Deguchi, Y. Kubota, H. Furukawa, Y. Yagi, Y. Imai, M. Tatsumi, N. Yamazaki, N. Watari, T. Hirata, N. Matubayasi
  • Journal Title: Bull. Chem. Soc. Japan Volume: 86 Pages: 99-103
  • DOI: DOI:10.1246/bcsj.20120222
  • Peer Reviewed
• [Journal Article] Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation (2012)
  • Author(s): T. Kawakami, I. Shigemoto, and N. Matubayasi
  • Journal Title: J. Chem. Phys Volume: 137 Pages: 234903 (9pages)
  • DOI: DOI:10.1063/1.4770334
  • Peer Reviewed
• [Journal Article] Molecular dynamics study of fast dielectric relaxation of water around a molecular-sized ion (2012)
  • Author(s): Y. Kubota, A. Yoshimori, N. Matubayasi, M. Suzuki, and R. Akiyama
  • Journal Title: J. Chem. Phys Volume: 137 Pages: 224502(4 pages)
  • DOI: DOI:10.1063/1.4769972
  • Peer Reviewed
• [Journal Article] Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation (2012)
  • Author(s): K. Takemura, H. Guo, S. Sakuraba, N. Matubayasi, and A. Kitao
  • Journal Title: J. Chem. Phys Volume: 137 Pages: 215105 (10 pages)
  • DOI: DOI:10.1063/1.4768901
  • Peer Reviewed
• [Journal Article] Density effect on infrared spectrum for supercritical water in the low- and medium-density region studied by molecular dynamics simulation (2012)
  • Author(s): K. Yoshida, N. Matubayasi, Y. Uosaki, and M. Nakahara
  • Journal Title: J. Chem. Phys Volume: 137 Pages: 194506 (10pages)
  • DOI: DOI:10.1063/1.4767352
  • Peer Reviewed
• [Journal Article] Nuclear magnetic resonance study on rotational dynamics of water and benzene in a series of ionic liquids: Anion and cation effects (2012)
  • Author(s): H. Kimura, Y. Yasaka, M. Nakahara, and N. Matubayasi
  • Journal Title: J. Chem. Phys Volume: 137 Pages: 194503 (10 pages)
  • DOI: DOI:10.1063/1.4766258
  • Peer Reviewed
• [Journal Article] Non-catalytic Hydrothermal Elimination of Terminal D-Glucose Unit from Malto- and Cello-oligosaccharides through Transformation to D-Fructose (2012)
  • Author(s): H. Kimura, M. Nakahara, and N. Matubayasi
  • Journal Title: J. Phys. Chem. A Volume: 116 Pages: 10039-10049
  • DOI: DOI:10.1021/jp3034165
  • Peer Reviewed
• [Journal Article] Structural characteristics of yeast F_<1->ATPase before and after 16-deg rotation of the γ 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 (8 pages)
  • DOI: DOI:10.1063/1.4734298
  • Peer Reviewed
• [Journal Article] Interaction of naphthalene derivatives with lipid in membrane studied by 1H-nuclear Overhauser effect and molecular dynamics simulation (2012)
  • Author(s): M. Shintani, Y. Matsuo, S. Sakuraba, and N. Matubayasi
  • Journal Title: Phys. Chem. Chem. Phys Volume: 14 Pages: 14049-14060
  • DOI: DOI:10.1039/c2cp41984j
  • Peer Reviewed
• [Journal Article] A possible molecular mechanism for the pressure reversal of general anaesthetics: aggregation of halothane in POPC bilayers at high pressure (2012)
  • Author(s): K. M. Tu, N. Matubayasi, K. K. Liang, I. T. Todorov, S. L. Chan, and P.-L. Chau
  • Journal Title: Chem. Phys. Lett Volume: 542 Pages: 148-154
  • DOI: DOI:10.1016/j.cplett.2012.06.044
  • Peer Reviewed
• [Journal Article] Simple and exact approach to the electronic polarization effect on the solvation free energy: Formulation for QM/MM system and its applications to aqueous solutions (2012)
  • Author(s): H. Takahashi, A. Omi, A. Morita, and N. Matubayasi
  • Journal Title: J. Chem. Phys Volume: 136 Pages: 214503(12 pages)
  • DOI: DOI:10.1063/1.4722347
  • Peer Reviewed
• [Journal Article] Free-Energy and Structural Analysis of Ion Solvation and Contact Ion-Pair Formation of Li^+ with BF_4^- and PF_6^- in Water and Carbonate Solvents (2012)
  • Author(s): M. Takeuchi, N. Matubayasi, Y. Kameda, B. Minofar, S. Ishiguro, and Y. Umebayashi
  • Journal Title: J. Phys. Chem. B Volume: 116 Pages: 6476-6487
  • DOI: DOI:10.1021/jp3011487
  • Peer Reviewed
• [Journal Article] The effect of pressure on halothane binding to hydrated DMPC bilayers (2012)
  • Author(s): P.-L. Chau, K. M. Tu, K. K. Liang, I. T. Todorov, S. J. Roser, R. Barker, and N. Matubayasi
  • Journal Title: Mol. Phys Volume: 110 Pages: 1461-1467
  • DOI: DOI:10.1080/00268976.2012.659682
  • Peer Reviewed
• [Journal Article] Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T_1 measurements (2012)
  • Author(s): Y. Yasaka, M. L. Klein, M. Nakahara, and N. Matubayasi
  • Journal Title: J. Chem. Phys Volume: 136 Pages: 074508 (12 pages)
  • DOI: DOI:10.1063/1.3685100
  • Peer Reviewed
• [Journal Article] Free-energy analysis of the electron-density fluctuation in the QM/MM simulation combined with the theory of energy representation (2012)
  • Author(s): N. Matubayasi and H. Takahashi
  • Journal Title: J. Chem. Phys Volume: 136 Pages: 044505 (10pages)
  • DOI: DOI:10.1063/1.3677184
  • Peer Reviewed
• [Journal Article] Pathways and Kinetics of Anisole Pyrolysis Studied by NMR and Selective ^<13>C Labeling. Heterolytic Carbon Monoxide Generation (2012)
  • Author(s): Y. Tsujino, Y. Yasaka, N. Matubayasi, and M. Nakahara
  • Journal Title: Bull. Chem. Soc. Japan Volume: 85 Pages: 124-132
  • DOI: DOI:10.1246/bcsj.20110334
  • Peer Reviewed
• [Journal Article] In Situ Kinetic Study on Hydrothermal Transformation of D-Glucose into 5-Hydroxymethylfurfural through D-Fructose with ^<13>C NMR (2012)
  • Author(s): H. Kimura, M. Nakahara, and N. Matubayasi
  • Journal Title: J. Phys. Chem. A Volume: 115 Pages: 14013-14021
  • DOI: DOI:10.1021/jp206355e
  • Peer Reviewed
• [Journal Article] Frequency-domain investigation of the ionic mobility of triflate salts in tetrahydrofuran (2011)
  • Author(s): T. Yamaguchi, Y. Yamada, T. Matsuoka, S. Koda, Y. Yasaka, and N. Matubayasi
  • Journal Title: J. Phys. Chem. B Volume: 115 Pages: 12558-12565
  • DOI: DOI:10.1021/jp208317f
  • Peer Reviewed
• [Journal Article] Hydration structure around CO_2 captured in aqueous amine solutions observed by high energy X-ray scattering (2011)
  • Author(s): H. Deguchi, Y. Kubota, H. Furukawa, Y. Yagi, Y. Imai, M. Tatsumi, N. Yamazaki, N. Watari, T. Hirata, N. Matubayasi, Y. Kameda
  • Journal Title: Int. J. Greenhouse Gas Control Volume: 5 Pages: 1533-1539
  • DOI: DOI:10.1016/j.ijggc.2011.08.010
  • Peer Reviewed
• [Journal Article] Distribution-function approach to free energy computation (2011)
  • Author(s): S. Sakuraba and N. Matubayasi
  • Journal Title: J. Chem. Phys Volume: 135 Pages: 114108(11 pages)
  • DOI: DOI:10.1063/1.3637036
  • Peer Reviewed
• [Journal Article] NMR-NOE and MD Simulation Study on Phospholipid Membranes: Dependence on Membrane Diameter and Multiple Time Scale Dynamics (2011)
  • Author(s): M. Shintani, K. Yoshida, S. Sakuraba, M. Nakahara, and N. Matubayasi
  • Journal Title: J. Phys. Chem. B Volume: 115 Pages: 9106-9115
  • DOI: DOI:10.1021/jp204051f
  • Peer Reviewed
• [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, and N. Matubayasi
  • Journal Title: J. Phys. Chem. B Volume: 115 Pages: 4745-4751
  • DOI: DOI:10.1021/jp2015676
  • Peer Reviewed
• [Journal Article] Exploring the reorientation of benzene in an ionic liquid via molecular dynamics: Effect of temperature and solvent effective charge on the slow dynamics (2011)
  • Author(s): Y. Yasaka, M. L. Klein, M. Nakahara, and N. Matubayasi
  • Journal Title: J. Chem. Phys Volume: 134 Pages: 191101 (4 pages)
  • DOI: DOI:10.1063/1.3592530
  • Peer Reviewed
• [Journal Article] Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c (2011)
  • Author(s): Y. Karino and N. Matubayasi
  • Journal Title: J. Chem. Phys Volume: 134 Pages: 041105(4 pages)
  • DOI: DOI:10.1063/1.3535560
  • Peer Reviewed
• [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, and H. Nagao
  • Journal Title: Chem. Phys. Lett Volume: 497 Pages: 218-222
  • DOI: DOI:10.1016/j.cplett.2010.08.008
  • Peer Reviewed
• [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, and N. Matubayasi
  • Journal Title: Chem. Phys. Lett Volume: 496 Pages: 351-355
  • DOI: DOI:10.1016/j.cplett.2010.07.054
  • Peer Reviewed
• [Journal Article] Scaled Polynomial Expression for Self-Diffusion Coefficients for Water, Benzene, and Cyclohexane over a Wide Range of emperatures and Densities (2010)
  • Author(s): K. Yoshida, N. Matubayasi, Y. Uosaki, and M. Nakahara
  • Journal Title: J. Chem. Eng. Data Volume: 55 Pages: 2815-2823
  • DOI: DOI:10.1021/je100206s
  • Peer Reviewed
• [Journal Article] Insights into the Origins of Configurational Stability of Axially Chiral Biaryl Amines with an Intramolecular N-H-N Hydrogen Bond (2010)
  • Author(s): K. Hayashi, N. Matubayasi, C. Jiang, T. Yoshimura, S. Majumdar, T. Sasamori, N. Tokitoh, and T. Kawabata
  • Journal Title: J. Org. Chem Volume: 75 Pages: 5031-5036
  • DOI: DOI:10.1021/jo100586b
  • Peer Reviewed
• [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, and M. Nakahara
  • Journal Title: J. Phys. Chem. A Volume: 114 Pages: 3510-3515
  • DOI: DOI:10.1021/jp908174s
  • Peer Reviewed
• [Journal Article] Newly Designed Neutron Diffraction Cell for Fluids at High Temperatures and High Pressures (2010)
  • Author(s): H. Iwase, N. Matubayasi, Y. Kameda, K. Itoh, T. Otomo, and M. Nakahara
  • Journal Title: Japanese Journal of Applied Physics Volume: 49 Pages: 016602 (3 pages)
  • DOI: DOI:10.1143/JJAP.49.016602
  • Peer Reviewed
• [Journal Article] Self-diffusion coefficients for water and organic solvents in extremely low-density supercritical states (2009)
  • Author(s): K. Yoshida, N. Matubayasi, and M. Nakahara
  • Journal Title: J. Mol. Liq Volume: 147 Pages: 96-101
  • DOI: DOI:10.1016/j.molliq.2008.10.006
  • Peer Reviewed
• [Journal Article] Water as an In-situ NMR Indicator for Impurity Acids in Ionic Liquids (2009)
  • Author(s): Y. Yasaka, C. Wakai, N. Matubayasi, and M. Nakahara
  • Journal Title: Anal. Chem Volume: 81 Pages: 400-407
  • DOI: DOI:10.1021/ac801767u
  • Peer Reviewed
• [Presentation] Effects of water and cosolvents on functional molecules in solution (2012)
  • Author(s): N. Matubayasi
  • Organizer: EMLG/JMLG Annual Meeting 2012 "Molecular association in fluid phases and at fluid interfaces",
  • Place of Presentation: Eger, Hungary
  • Year and Date: 20120905-09
• [Presentation] Extended Concept of Solvation toward Unified Understandings of Molecular Binding in Weakly Ordered Systems (2012)
  • Author(s): N. Matubayasi
  • Organizer: JST International Symposium on Multi-scale Simulation of Condensed-phase Reacting Systems
  • Place of Presentation: 名古屋
  • Year and Date: 20120510-12
• [Presentation] Extended Concept of Solvation toward Unified Treatment of Molecular Binding in Weakly Ordered Systems (2012)
  • Author(s): N. Matubayasi
  • Organizer: The 2nd AICS (Advanced Institute for Computational Science) International Symposium
  • Place of Presentation: 神戸
  • Year and Date: 20120301-02
• [Presentation] Free-energy analysis of water and cosolvent effects on functional molecules in solution (2012)
  • Author(s): N. Matubayasi
  • Organizer: RCAS Thursday Seminar
  • Place of Presentation: Taipei, Taiwan
  • Year and Date: 2012-12-13
• [Presentation] Extended Concept of Solvation toward Unified Analysis of Molecular Binding in Weakly Ordered Systems (2011)
  • Author(s): N. Matubayasi
  • Organizer: The Seventh Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
  • Place of Presentation: 東京
  • Year and Date: 20110902-08
• [Presentation] Free-energy Analysis of urea effect on amino-acid analogs and proteins (2011)
  • Author(s): N. Matubayasi
  • Organizer: Telluride Science Research Center workshop "The Physics, Chemistry, and Biology of Ions and Osmolytes in Solution"
  • Place of Presentation: Telluride, CO, USA
  • Year and Date: 20110711-15
• [Presentation] Free-Energy Analysis of Biomolecular Solvation in the Energetic Perspective (2010)
  • Author(s): N. Matubayasi
  • Organizer: Gordon Research Conference on Water & Aqueous Solutions
  • Place of Presentation: Holderness, NH, USA
  • Year and Date: 20100808-13
• [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: 20100623-25
• [Presentation] Free-energy analysis of functional, self-organizing systems in solution (2010)
  • Author(s): N. Matubayasi
  • Organizer: Workshop "Solvation of bioactive compounds: bridging theory, computation and experiment"
  • Place of Presentation: Leipzig, Germany
  • Year and Date: 20100107-09
• [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
  • Year and Date: 20091212-13
• [Book] 超臨界水と脂質膜,巨大分子系の計算化学超大型計算機時代の理論化学の新展開11章 (2012)
  • Author(s): 松林伸幸
  • Publisher: CSJカレントレビュー, 化学同人
• [Book] Development of a Quantum ChemicalMethod Combined with a Theory of Solutions--Free-Energy Calculation fbr ChemicalReactions by Condensed Phase Simulations (2010)
  • Author(s): H. Takahashi, N. MatUbayasi, and M. Nakano
  • Total Pages: 283-351
  • Publisher: Advances in Quantum Chemistry, vol 59
• [Remarks] 本研究で用いた自由エネルギー計算ソフト Ermodを公開
  • URL: http://sourceforge.net/projects/ermod/
• [Patent(Industrial Property Rights)] 細胞・微生物の NMR測定方法および NMR用プローブ並びに NMR制御装置 (2012)
  • Inventor(s): 池田武義、中原勝、松林伸幸、若井千尋
  • Industrial Property Rights Holder: 池田武義、中原勝、松林伸幸、若井千尋
  • Industrial Property Number: 特許、登録第5046319号
  • Acquisition Date: 2012-07-27
• [Patent(Industrial Property Rights)] 水熱反応を利用した水素の製造方法 (2010)
  • Inventor(s): 中原勝、松林伸幸、若井千尋、吉田健
  • Industrial Property Rights Holder: 中原勝、松林伸幸、若井千尋、吉田健
  • Industrial Property Number: 特許、登録第4481060号
  • Acquisition Date: 2010-03-26
• [Patent(Industrial Property Rights)] 水素の製造方法 (2009)
  • Inventor(s): 中原勝、松林伸幸、八坂能郎
  • Industrial Property Rights Holder: 中原勝、松林伸幸、八坂能郎
  • Industrial Property Number: 特許、PCT/JP2009/063427
  • Acquisition Date: 2009-07-28
  • Overseas
• [Patent(Industrial Property Rights)] 高温測定用 NMRプローブ (2009)
  • Inventor(s): 中原勝、松林伸幸、若井千尋、池田武義
  • Industrial Property Rights Holder: 中原勝、松林伸幸、若井千尋、池田武義
  • Industrial Property Number: 特許、登録第4330076号
  • Acquisition Date: 2009-06-26