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2012 Fiscal Year Final Research Report

MD and NMR Analysis of Drug Distribution and Aggregationin Lipid Bilayer

Research Project

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Project/Area Number 21300111
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionKyoto University

Principal Investigator

MATUBAYASI Nobuyuki  京都大学, 化学研究所, 准教授 (20281107)

Co-Investigator(Kenkyū-buntansha) WAKAI Chihiro  京都大学, 化学研究所, 助教 (40293948)
Project Period (FY) 2009 – 2012
Keywordsコンピュータシミュレーション / 脂質二重膜 / 溶液理論 / 自由エネルギー / NOE
Research Abstract

The insight of the molecular binding into lipid bilayer is crucial in understanding the drug and anesthesia actions. In the present project, an approach is established which combines the theoretical/computational method (large-scale molecular simulation and solution theory in the energy representation) and the experimental method (NMR-NOE). The binding strength and mode are analyzed for a variety of molecules ranging from small anesthetic to transmembrane protein of ~20 residues.

  • Research Products

    (57 results)

All 2013 2012 2011 2010 2009 Other

All Journal Article (39 results) (of which Peer Reviewed: 39 results) Presentation (11 results) Book (2 results) Remarks (1 results) Patent(Industrial Property Rights) (4 results) (of which Overseas: 1 results)

  • [Journal Article] Anion-Dependence of Fast Relaxation Component in Na-, K-Halide Solutions at Low Concentrations Measured by High-Resolution Microwave Dielectric Spectroscopy2013

    • 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 couplings2013

    • Author(s)
      K. Yoshida, N. Matubayasi, Y. Uosaki, and M. Nakahara
    • Journal Title

      J.Chem. Phys.

      Volume: 138 Pages: 134508(12)

    • 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 Subunit2013

    • Author(s)
      Y. Ito, T. Yoshidome, N. Matubayasi, M. Kinoshita, and M. Ikeguchi
    • Journal Title

      J. Phys. Chem. B

      Volume: 117 Pages: 3298-3307

    • 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 13C NMR Study2013

    • 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 analogs2013

    • 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 method2013

    • 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 representation2013

    • 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 State2013

    • 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 representation2012

    • Author(s)
      T. Kawakami, I. Shigemoto, and N. Matubayasi
    • Journal Title

      J. Chem. Phys

      Volume: 137 Pages: 234903(9)

    • DOI

      DOI:10.1063/1.4770334

    • Peer Reviewed
  • [Journal Article] Molecular dynamics study of fast dielectric relaxation of water around a molecular-sized ion2012

    • Author(s)
      Y. Kubota, A. Yoshimori, N. Matubayasi, M. Suzuki, and R. Akiyama
    • Journal Title

      J. Chem. Phys.

      Volume: 137 Pages: 224502(4)

    • 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 representation2012

    • Author(s)
      K. Takemura, H. Guo, S. Sakuraba, N. Matubayasi, and A. Kitao
    • Journal Title

      J. Chem. Phys.

      Volume: 137 Pages: 215105(10)

    • 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 simulation2012

    • Author(s)
      K. Yoshida, N. Matubayasi, Y. Uosaki, and M. Nakahara
    • Journal Title

      J. Chem. Phys

      Volume: 137 Pages: 194506(10)

    • 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 effects2012

    • Author(s)
      H. Kimura, Y. Yasaka, M. Nakahara, and N. Matubayasi
    • Journal Title

      J. Chem. Phys

      Volume: 137 Pages: 194503(10)

    • 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-Fructose2012

    • 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 effect2012

    • Author(s)
      T. Yoshidome, Y. Ito, N. Matubayasi, M. Ikeguchi, and M. Kinoshita
    • Journal Title

      J. Chem. Phys

      Volume: 137 Pages: 035102(8)

    • 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 simulation2012

    • 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 pressure2012

    • 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: 543 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 solutions2012

    • Author(s)
      H. Takahashi, A. Omi, A. Morita, and N. Matubayasi
    • Journal Title

      J. Chem. Phys

      Volume: 136 Pages: 214503(12)

    • 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 Solvents2012

    • 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 bilayers2012

    • 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_1measurements2012

    • Author(s)
      Y. Yasaka, M. L. Klein, M. Nakahara, and N. Matubayasi
    • Journal Title

      J. Chem. Phys.

      Volume: 136 Pages: 074508(12)

    • 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 representation2012

    • Author(s)
      N. Matubayasi and H. Takahashi
    • Journal Title

      J. Chem. Phys

      Volume: 136 Pages: 044505(10)

    • DOI

      DOI:10.1063/1.3677184

    • Peer Reviewed
  • [Journal Article] Pathways and Kinetics of Anisole Pyrolysis Studied by NMR and Selective 13C Labeling. Heterolytic Carbon Monoxide Generation2012

    • 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 13C NMR2011

    • 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 tetrahydrofuran2011

    • 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 CO2 captured in aqueous amine solutions observed by high energy X-ray scattering2011

    • 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 computation2011

    • Author(s)
      S. Sakuraba and N. Matubayasi
    • Journal Title

      J. Chem. Phys.

      Volume: 135 Pages: 114108(11)

    • 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 Dynamics2011

    • 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 Interface2011

    • 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 dynamics2011

    • Author(s)
      Y. Yasaka, M. L. Klein, M. Nakahara, and N. Matubayasi
    • Journal Title

      J. Chem. Phys.

      Volume: 134 Pages: 191101(4)

    • 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 c2011

    • Author(s)
      Y. Karino and N. Matubayasi
    • Journal Title

      J. Chem. Phys

      Volume: 134 Pages: 041105(4)

    • DOI

      DOI:10.1063/1.3535560

    • Peer Reviewed
  • [Journal Article] Hydration property of globular proteins: An analysis of solvation free energy by energy representation method2010

    • 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 solution2010

    • 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 Temperatures and Densities2010

    • 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 HydrogenBond2010

    • 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 Liquid2010

    • 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)

    • DOI

      DOI:10.1143/JJAP.49.016602

    • Peer Reviewed
  • [Journal Article] Self-diffusion coefficients for water and organic solvents in extremely low-density supercritical states2009

    • 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 Liquids2009

    • 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 solution2012

    • 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 Systems2012

    • 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 Systems2012

    • 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 solution2012

    • 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 Systems2011

    • 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 proteins2011

    • 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 Perspective2010

    • 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 Solution2010

    • 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 Perspective2010

    • 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 solution2010

    • 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 Perspective2009

    • 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,CSJカレントレビュー2012

    • Author(s)
      松林 伸幸
    • Publisher
      化学同人
  • [Book] Development of a Quantum Chemical Method Combined with a Theory of Solutions -- Free-Energy Calculation for Chemical Reactions by Condensed Phase Simulations,Advances in Quantum Chemistry, vol 592010

    • Author(s)
      H. Takahashi, N. Matubayasi, and M. Nakano
    • Total Pages
      283-351
  • [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
      登録第5046319号
    • Filing 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
      登録第4481060号
    • Filing 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
      PCT/JP2009/063427
    • Filing 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
      登録第4330076号
    • Filing Date
      2009-06-26

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Published: 2014-08-29  

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