Theoretical Study on Conjugated Dynamics of Protein and Solvent

2012 Fiscal Year Final Research Report

• Project Area: Molecular Science of Fluctuations toward Biological Functions
• Project/Area Number: 20107008
• 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: Ritsumeikan University (2012); Institute for Molecular Science (2008-2011)
• Principal Investigator: HIRATA Fumio 立命館大学, 生命科学部, 教授 (90218785)
• Co-Investigator(Kenkyū-buntansha): YOSHIDA Norio 九州大学, 理学(系)研究科(院), 准教授 (10390650)
• Project Period (FY): 2008 – 2012
• Keywords: 3D-RISM/RISM / 蛋白質構造揺らき / 分子認識 / 自由エネルギー / 一般化ランジェヴァン理論 / 分散・共分散行列 / 知的創薬 / 化合物スクリーニンク

Research Abstract

The research program which aims to construct a theory to describe the molecular recognition process correlated with the structural fluctuation of protein was carried out along the four subjects listed below, and the goal of the research program was successfully achieved.
1. Statistical mechanics theory of molecular recognition (Equilibrium theory)
2. Application of the statistical mechanics of molecular recognition to "drug design"
3. Quasi dynamics of protein in solution based on the 3D-RISM and the molecular dynamics simulation
4. A new theory for structural fluctuation of protein, created by combining the 3D-RISM/RISM with the generalized Langevin theories

Research Products

• [Journal Article] (2012)
  • Author(s): Bongsoo Kim and Fumio Hirata
  • Journal Title: J. Chem. Phys Volume: 138 Pages: 054108-1-054108-11
  • Peer Reviewed
• [Journal Article] (2012)
  • Author(s): Maruyama, Yutaka; Hirata, Fumio
  • Journal Title: J. Chem. Theory Comput Volume: 8 Pages: 3015 - 3021
  • Peer Reviewed
• [Journal Article] (2012)
  • Author(s): Hong, Jooyeon; Yoshida, Norio; Chong, Song-Ho; Lee, Chewook; Ham, Sihyun; Hirata, Fumio
  • Journal Title: J. Chem. Theory Comput Volume: 8 Pages: 2239-2246
  • Peer Reviewed
• [Journal Article] (2012)
  • Author(s): Sindhikara, Daniel; Yoshida, Norio; Hirata, Fumio
  • Journal Title: J. Comp. Chem Volume: 33 Pages: 1536-1543
  • Peer Reviewed
• [Journal Article] (2011)
  • Author(s): Y. Kiyota, N. Yoshida, and F. Hirata
  • Journal Title: J. Chem. Theor. Comp Volume: 7 Pages: 3803-3815
  • Peer Reviewed
• [Journal Article] (2011)
  • Author(s): Danniel J. Sindhikara, Norio Yoshida, Mikio Kataoka, Fumio Hirata
  • Journal Title: J. Mol. Liq Volume: 164 Pages: 120-122
  • Peer Reviewed
• [Journal Article] (2011)
  • Author(s): Imai, Takashi; Miyashita, Naoyuki; Sugita, Yuji; Kovalenko, Andriy; Hirata, Fumio; Kidera, Akinori
  • Journal Title: J. Phys. Chem. B Volume: 115 Pages: 8288-8295
  • Peer Reviewed
• [Journal Article] (2011)
  • Author(s): Tatsuhiko Miyata, Yasuhiro Ikuta, and Fumio Hirata
  • Journal Title: J. Chem. Phys Volume: 134 Pages: 44127-44144
  • Peer Reviewed
• [Journal Article] (2011)
  • Author(s): Yutaka Maruyama, Taku Matsushita, Ryuichi Ueoka, and Fumio Hirata
  • Journal Title: J. Phys. Chem. B Volume: 115 Pages: 2408-2416
  • Peer Reviewed
• [Journal Article] (2010)
  • Author(s): Tatsuhiko Miyata, Yasuhiro Ikuta, and Fumio Hirata
  • Journal Title: J. Chem. Phys Volume: 113 Pages: 044114
  • Peer Reviewed
• [Journal Article] (2010)
  • Author(s): Saree Phongphonphanee, Thanyada Rungromongkol, Norio Yoshida, Supot Hannongbua, and Fumio Hirata
  • Journal Title: J. Am. Chem. Soc Volume: 132 Pages: 9782-9788
  • Peer Reviewed
• [Journal Article] (2010)
  • Author(s): Saree Phongphonphanee, Norio Yoshida, and Fumio Hirata
  • Journal Title: J. Phys. Chem. B Volume: 114 Pages: 7967
  • Peer Reviewed
• [Journal Article] (2010)
  • Author(s): Yutaka Maruyama, Norio Yoshida, and Fumio Hirata
  • Journal Title: J. Phys. Chem. B Volume: 114 Pages: 6464-6471
  • Peer Reviewed
• [Journal Article] (2009)
  • Author(s): Yui, Toshifumi; Shiiba, Hirohide; Tsutsumi, Yuya; Hayashi, Sachio; Miyata, Tatsuhiko; Hirata, Fumio
  • Journal Title: J. Phys. Chem. B Volume: 114 Pages: 49-58
  • Peer Reviewed
• [Journal Article] (2009)
  • Author(s): Takashi Imai, Koji Oda, Andriy Kovalenko, Fumio Hirata, and Akinori Kidera
  • Journal Title: J. Am. Chem. Soc Volume: 131 Pages: 12430-12440
  • Peer Reviewed
• [Journal Article] (2009)
  • Author(s): Takashi Imai, Andriy Kovalenko, Fumio Hirata, and Akinori Kidera
  • Journal Title: Interdiscip. Sci. Comput. Life Sic Volume: 1 Pages: 156-160
  • Peer Reviewed
• [Journal Article] (2009)
  • Author(s): Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, and Fumio Hirata
  • Journal Title: J. Am. Chem. Soc Volume: 131 Pages: 3852-3853
  • Peer Reviewed
• [Journal Article] (2009)
  • Author(s): Norio Yoshida, Takashi Imai, Saree Phongphanphanee, Andriy Kovalenko, and Fumio Hirata
  • Journal Title: J. Phys. Chem. B Volume: 113 Pages: 873-886
  • Peer Reviewed
• [Journal Article] (2009)
  • Author(s): Katusra Nishiyama, Tsuyoshi Yamaguchi, and Fumio Hirata
  • Journal Title: J. Phys. Chem. B Volume: 113 Pages: 2800-2804
  • Peer Reviewed
• [Journal Article] (2008)
  • Author(s): Yoshiteru Yonetani, Yutaka Maruyama, Fumio Hirata, and Hidetoshi Kono
  • Journal Title: J. Chem. Phys Volume: 128 Pages: 185102-1-185102-9
  • Peer Reviewed
• [Journal Article] (2008)
  • Author(s): Y. Ikuta, S. Karita, Y. Kitago, N. Watanabe, and F. Hirata
  • Journal Title: Chem. Phys. Lett Volume: 465 Pages: 279-284
  • Peer Reviewed
• [Journal Article] (2008)
  • Author(s): N. Yoshida, T. Ishida, and F. Hirata
  • Journal Title: J. Phys. Chem Volume: 112 Pages: 433-440
  • Peer Reviewed
• [Presentation] Structural Fluctuation of Proetin in Water around Its Native State: A New Statistical Mechanics Formulation (2013)
  • Author(s): Fumio Hirata
  • Organizer: Fifth Korea-Japan Seminars on Biomolecular Sciences - Experiments and Simulations
  • Place of Presentation: Gohan, Korea
  • Year and Date: 2013-02-26
• [Presentation] Ligand Binding by Protein Probed with the 3D-RISM Microscope (2013)
  • Author(s): 平田文男
  • Organizer: 「次世代の物質科学・ナノサイエンスを探る」研究会
  • Place of Presentation: 北海道大学百年記念会館、北海道
  • Year and Date: 2013-01-11
• [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution (2012)
  • Author(s): Fumio Hirata
  • Organizer: The 71^<st> Okazaki International Conference: New perspectives on molecular science of glycoconjugate
  • Place of Presentation: 岡崎コンファレンスセンター(愛知県)
  • Year and Date: 20121012-14
• [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution (2012)
  • Author(s): Fumio Hirata
  • Organizer: Asian Core symposium on "The 4^<th> Japan-Korea Seminar on Biomolecular Sciences: Experiment and Simulation
  • Place of Presentation: 国際会議場(奈良県)
  • Year and Date: 20120109-11
• [Presentation] Exploring life phenomena with a theory featuring chemical 'specificity' and physical 'universality' (2012)
  • Author(s): Fumio Hirata
  • Organizer: "Israel -Japan Joint Symposium on Biophysics: Protein Dynamics: From single molecules to whole cell" in Biophysics Society meeting in Japan
  • Place of Presentation: 兵庫県立大学(兵庫県)
  • Year and Date: 2012-09-16
• [Presentation] Ligand Binding by Protein Probed with the 3D-RISM Microscope (2012)
  • Author(s): Fumio Hirata
  • Organizer: The ACS Symposium on "Continuum Solvation Modeling in Biological Systems
  • Place of Presentation: Philadelphia, USA
  • Year and Date: 2012-08-20
• [Presentation] Ligand Binding by Protein Probed with 3D-RISM Microscope (2012)
  • Author(s): Fumio Hirata
  • Organizer: Foundation of Molecular Modeling and Simulation(FOMMS)
  • Place of Presentation: Mt. Hood, Oregon, USA
  • Year and Date: 2012-07-25
• [Presentation] Exploring life phenomena with a Theory Featuring Chemical Specificity and Physical Universality (2012)
  • Author(s): Fumio Hirata
  • Organizer: International Conference on Pure and Applied Chemistry: The key for our Future
  • Place of Presentation: Flic-en-Flac, Mauritius
  • Year and Date: 2012-07-04
• [Presentation] 分子認識の統計力学(3D-RISM/RISM)と構造生物学 (2012)
  • Author(s): 平田文男
  • Organizer: 第12回蛋白質科学シンポジウム「YouTube 時代の構造生物学」
  • Place of Presentation: 名古屋国際会議場(愛知県)
  • Year and Date: 2012-06-22
• [Presentation] Theory of Molecular Recognition and Its Application to Pharmaceutical Design (2012)
  • Author(s): Fumio Hirata
  • Organizer: 12^<th> Eurasia Conference on Chemical Sciences EuAsC2S-12
  • Place of Presentation: Corfu, Greece
  • Year and Date: 2012-04-20
• [Presentation] Statistical Mechanics of Molecular Liquids Reveals Elementary Processes in Life Phenomena (2011)
  • Author(s): Fumio Hirata
  • Organizer: Third Korea-Japan Seminars on Biomolecular Sciences: - Experiments and Simulations
  • Place of Presentation: Jeju, Korea
  • Year and Date: 20110226-0301
• [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution (2011)
  • Author(s): Fumio Hirata
  • Organizer: 32th International Conference on Solution Chemistry
  • Place of Presentation: La Grande Motte, France
  • Year and Date: 2011-08-28
• [Presentation] Statistical Mechanics Theory of Molecular Recognition and its Application to Pharmaceutical Design (2011)
  • Author(s): Fumio Hirata
  • Organizer: Telluride Wrokshop on Free Energy Simulation
  • Place of Presentation: Telluride, Colorado, USA
  • Year and Date: 2011-07-03
• [Presentation] Collaboration between computer and computational scientists make high performance computing on the K-computer a reality (2011)
  • Author(s): Fumio Hirata
  • Organizer: ISC'11 HPC in Asia Workshop
  • Place of Presentation: Hamburg, Germany
  • Year and Date: 2011-06-18
• [Presentation] Exploring life phenomena with a theory featuring chemical 'specificity' and physical 'universality' (2011)
  • Author(s): Fumio Hirata
  • Organizer: Statistical Mechanics Approaches to Biomolecular Applications
  • Place of Presentation: Seoul, Korea
  • Year and Date: 2011-06-13
• [Presentation] Theory of Molecular Recognition and its Application to Drug Design (2011)
  • Author(s): Fumio Hirata
  • Organizer: International Conference on Computer Science (ICCS) 2011
  • Place of Presentation: Singapore
  • Year and Date: 2011-06-02
• [Presentation] 分子認識の統計力学と生体機能 (2011)
  • Author(s): 平田文男
  • Organizer: 自然科学研究機構岡崎統合バイオサイエンスセンター「10周年記念シンポジウム」
  • Place of Presentation: 岡崎コンファレンスセンター(愛知県)
  • Year and Date: 2011-02-12
• [Presentation] Ligand binding and escaping pathway in myoglobin studied by the 3D-RISM theory (2010)
  • Author(s): Fumio Hirata
  • Organizer: Dynamics and Mechanisms of Photochemical Reactions of Biological Proteins, Pacifichem 2010
  • Place of Presentation: Honolulu, USA
  • Year and Date: 20101215-20
• [Presentation] Molecular Recognition in Biological Functions Revealed by Statistical mechanics of Molecular Liquids (2010)
  • Author(s): Fumio Hirata
  • Organizer: 4th International symposium on "Molecular Science of Fluctuations toward Biological Functions
  • Place of Presentation: ピアザ淡海(滋賀県)
  • Year and Date: 2010-12-01
• [Presentation] Statistical Mechanics of Molecular Liquids Reveals Elementary Processes in Life Phenomena (2010)
  • Author(s): Fumio Hirata
  • Organizer: EMLG-JMLG joint meeting 2010
  • Place of Presentation: Lviv, Ukraine
  • Year and Date: 2010-09-07
• [Presentation] On the origin of energy produced by the hydrolysis reaction of ATP:3D-RISM-SCF study (2010)
  • Author(s): Fumio Hirata
  • Organizer: ICPOC-20: 20th International Conference on Physical Organic Chemistry
  • Place of Presentation: Busan, Republic of Korea
  • Year and Date: 2010-08-25
• [Presentation] A Statistical Mechanics Study of Molecular Recognition and Drug Design (2009)
  • Author(s): Fumio Hirata
  • Organizer: 2^<nd> Japan-Korea Seminar on Biomolecular Science - Experiments and Simulations
  • Place of Presentation: 名古屋大学(愛知県)
  • Year and Date: 2009-12-23
• [Presentation] Biomolecules in water and water in biomolecules on the Physics, Chemistry, and Biology of Water 2009 (2009)
  • Author(s): Hirata
  • Organizer: the Fourth Annual Conference
  • Place of Presentation: Snow Mountain, USA
  • Year and Date: 2009-10-22
• [Presentation] Model Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids (2009)
  • Author(s): Fumio Hirata
  • Organizer: International Workshop on "Continuum Modeling of Biomolecules
  • Place of Presentation: Beijin, China
  • Year and Date: 2009-09-14
• [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids (2009)
  • Author(s): Fumio, Hirata
  • Organizer: EMLG/JMLG Annual Meeting "Intermolecular Interactions and Liquid Structure,"
  • Place of Presentation: Salzburg, Austlia
  • Year and Date: 2009-09-11
• [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids (2009)
  • Author(s): Fumio Hirata
  • Organizer: 6^<th> International Discussion Meeting on Relaxations in Complex Systems
  • Place of Presentation: Roma, Italy
  • Year and Date: 2009-09-03
• [Presentation] Statistical mechanics reached at the point where it can explain elementary processes in life phenomena (2009)
  • Author(s): Fumio Hirata
  • Organizer: Statistical Physics: Modern Trends and Applications dedicated to the 100-th anniversary of Prof. M.M.Bogolyubov
  • Place of Presentation: Lviv, Ukraine
  • Year and Date: 2009-06-24
• [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids (2009)
  • Author(s): Fumio Hirata
  • Organizer: The 6^<th> Open Workshop on "Water and Biomolecules," and The 2^<nd> Open Workshop on "Fluctuation and Function,"
  • Place of Presentation: 岡崎コンファレンスセンター(愛知県)
  • Year and Date: 2009-03-16
• [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids (2009)
  • Author(s): Fumio Hirata
  • Organizer: Asian Core symposium "First Korea-Japan Seminars on Biomolecular Sciences - Experiments and Simulations"
  • Place of Presentation: Seoul, Korea
  • Year and Date: 2009-02-28
• [Presentation] 生体分子および溶媒の構造揺らぎと共役した機能発現過程の理論的解明 (2009)
  • Author(s): 平田文男
  • Organizer: 新学術領域「揺らぎと生体機能」第一回公開シンポジウム
  • Place of Presentation: 京都テルサ(京都府)
  • Year and Date: 2009-01-06
• [Presentation] Molecular Recognition in Life Phenomena Probed with the Statistical Mechanics of Liquids (2008)
  • Author(s): F. Hirata
  • Organizer: IMA Annual Program Tear Workshop "Solvation,"
  • Place of Presentation: Minneapolis, USA
  • Year and Date: 2008-12-10
• [Presentation] Statistical-mechanics theory of molecular recognition: water and other molecules recognized by protein (2008)
  • Author(s): F. Hirata
  • Organizer: Water in Biological System, A French-Japanese Workshop
  • Place of Presentation: 京都大学(京都府)
  • Year and Date: 2008-11-26
• [Presentation] Molecular Recognition in Life Phenomena Probed with the Statistical Mechanics of Liquids (2008)
  • Author(s): F. Hirata
  • Organizer: The 8^<th> KIAS-Yonsei Conference on Protein Structure and Function
  • Place of Presentation: Seoul, Korea
  • Year and Date: 2008-10-10
• [Presentation] Molecular Recognition Realized by the Statistical Mechanics Theory of Liquids (2008)
  • Author(s): F. Hirata
  • Organizer: Theory and Applications of Computational Chemistry (TACC)
  • Place of Presentation: Shanghai, China
  • Year and Date: 2008-09-25
• [Presentation] Theory of molecular recognition and it's application to the enzymatic reaction (2008)
  • Author(s): F. Hirata
  • Organizer: The grand challenge to Next Generation Integrated Nano-science
  • Place of Presentation: 未来科学館(東京都)
  • Year and Date: 2008-06-04
• [Presentation] Statistical theory of molecular recognition, and it's application to aquaporin (2008)
  • Author(s): F. Hirata
  • Organizer: The 5^<th> Open Workshop on "Chemistry of Biological Processes Created by Water and Biomolecules
  • Place of Presentation: 能楽堂(奈良県)
  • Year and Date: 2008-01-24
• [Presentation] A Statistical Mechanics Study of Molecular Recognition and Anesthesia (0)
  • Author(s): Fumio Hirata
  • Organizer: 第47回生物物理学会シンポジウム"麻酔作用の分子機構:生物物理から明らかにされる生体分子と麻酔 薬の相互作用
  • Place of Presentation: 文理大学(徳島県)
  • Year and Date: 00001101
• [Presentation] An attempt toward the generalized Langevin dynamics simulation (0)
  • Author(s): Fumio Hirata
  • Organizer: KIAS meeting on "Recent Progress in Computer Simulations in Molecular Sciences,"
  • Place of Presentation: Seoul, Korea
  • Year and Date: 00000615
• [Book] 「水と生体分子のハーモニー」。日本化学会編「巨大分子系の計算科学」第15章 (2012)
  • Author(s): 吉田紀生、丸山豊、清田泰臣、平田文男、今井隆志
  • Total Pages: 147-158
  • Publisher: 化学同人
• [Book] 「新しい分子統計力学・統計的動力学記述法」、日本化学会編「巨大分子系の計算科学」第7章 (2012)
  • Author(s): 平田文男
  • Total Pages: 88-99
  • Publisher: 化学同人
• [Book] Statistical-mechanics theory of molecular recognition: water and other molecules recognized by protein, in Bihan and Fukuyama(Ed.): "Water, the forgotten biological molecule." (2010)
  • Author(s): Norio Yoshida, Yasuomi Kiyota, Saree Phongphanphanee, Takashi Imai and Fumio Hirata
  • Publisher: Pan Stanford Publishing, Singapore
• [Book] "Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids," in "Modeling Solvent Environment," Ed. M. Feig (2009)
  • Author(s): N. Yoshida, Y. Kiyota, Y. Ikuta, T. Imai, and F. Hirata
  • Publisher: Wiley-VCH
• [Book] "A Statistical Mechanics Theory of Molecular Recognition," in "Water and Biomolecules," Eds, K. Kuwajima, Y. Goto, F. Hirata, M. Kataoka, and M, Terazima (2009)
  • Author(s): T. Imai, N. Yoshida, A. Kovalenko, and F. Hirata
  • Publisher: Springer
• [Patent(Industrial Property Rights)] 溶液中の生体高分子の構造揺らぎとダイナミクスを 記述する方程式 (2013)
  • Inventor(s): 平田文男;Kim,Bongsoo
  • Industrial Property Rights Holder: 平田文男; Kim Bongsoo
  • Industrial Property Number: 特許、PCT/ JP2013/ 051940
  • Filing Date: 2013-01-23
  • Overseas
• [Patent(Industrial Property Rights)] Analysis of Biomolecular Solvation site by the 3D-RISM Theory (2013)
  • Inventor(s): Hirata, Fumio; Sindhikara, Daniel, Jon
  • Industrial Property Rights Holder: Hirata, Fumio; Sindhikara, Daniel, Jon
  • Industrial Property Number: 特許、PCT/JP2013/060996
  • Filing Date: 2013-04-05
  • Overseas