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Theortical study of free energy landscapes of biological macromolecules by the hybrid computation for electronic structure and molecular structure sampling

Research Project

Project/Area Number 18370063
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionOsaka University

Principal Investigator

NAKAMURA Haruki  Osaka University, Institute for Protein Research, Professor (80134485)

Co-Investigator(Kenkyū-buntansha) YONEZAWA Yasushige  Osaka University, Institute hr Protein Research, Specially Appointed Researcher (40248753)
TAKANO Yu  Osaka University, Institute for Protein Research, Assistant Professor (30403017)
OSHIMA Kanji  Osaka Uniyersity, The Center for Adanced Medital Engineering and Informatics, Specially Appointed Assistant Professor (40437330)
Project Period (FY) 2006 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥5,420,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥720,000)
Fiscal Year 2007: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2006: ¥2,300,000 (Direct Cost: ¥2,300,000)
KeywordsBiophysics / Enzymatic reaction / Biological macromolecules / Quantum chemistry / Molecular dynamics / Molecular simulation / Electron state / Reaction free energy
Research Abstract

1. Development of the hybrid-QM/MM calculation method
The hybrid-QM/MM method combines the advantages in the quantum chemistry and the molecular mechanics for the accurate simulation of a protein-solvent system, by treating the essential region of a protein by quantum mechanics and applying the classical Newtonian equations to the rest of the target system. We have developed a software program for the novel hybrid-QM/MM simulations.
2. The hybrid-QM/MM simulation study on the mechanism of proline cis-trans isomerization of human Pin 1 protein
Pin1 is one of human peptidyl-prolyl isomerases, which catalyzes the cis-trans isomerization of a proline residue. This enzyme is associated with a cancerous change of cells and apoptosis, and its close relationships with Alzheimer's disease has also been reported. We have studied the isomerization mechanism of this enzyme, by calculating the electronic structure of the peptide bond at the proline in the ligand and sampling the protein and the surrou … More nding solvent molecular structures. Finally, we have revealed the reaction and conformation free energy change including the entropy effect.
3. Molecular orbital and molecular dynamics studies of the reaction mechanism of the enzyme-catalyzed hydrolysis
To understand how the conformational factors are related to enzyme-catalyzed hydrolysis by lipases, conformational analysis was performed by molecular dynamics simulations for the tetrahedral intermediates bound to lipases. Consequently, we found the similar conformational preference to the intermediates of the transacylation of methyl acetate computed by molecular orbital theory. In molecular dynamics simulation for the two-metal mechanism of the RNase H catalysis, the distance between two Mg^<2+> ions in the active site drifted apart due to the electrostatic repulsion, resulting in the disruption of the active site. Density functional calculation shows that esters of cyclopropanecarboxylic acid demonstrate a substantial increase in stability under base-catalyzed hydrolysis compared to other esters. Less

Report

(3 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • Research Products

    (108 results)

All 2008 2007 2006 Other

All Journal Article (35 results) (of which Peer Reviewed: 17 results) Presentation (73 results)

  • [Journal Article] Protein-inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free-energy barrier distrinsuishing the native complex from the others.2008

    • Author(s)
      Kamiya, Narutoshi
    • Journal Title

      PROTEINS 70

      Pages: 41-53

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Cyclopropanecarboxylic Acid Esters as Porential Prodrugs with Enhanced Hydrolytic Stability.2008

    • Author(s)
      Bender, David M.
    • Journal Title

      Organic Letters 10

      Pages: 509-511

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems.2008

    • Author(s)
      Kikugawa, Gota
    • Journal Title

      Journal of Computational Chemistry 29(印刷中)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Protein-inhibitor flexible docking by a multicanonical sampling : Native complex structure with the lowest free energy and a free-energy barrier distrinsuishing the native complex from the others2008

    • Author(s)
      N., Kamiya, Y., Yonezawa, H., Nakamura, J., Higo
    • Journal Title

      PROTEINS 70 (1)

      Pages: 41-53

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Cyclopropanecarboxylic Acid Esters as Porential Prodrugs with Enhanced Hydrolytic Stability2008

    • Author(s)
      D. M., Bender, J. A., Peterson, J. R., McCarthy, H., Gunaydin, Y., Takano, K. N., Houk
    • Journal Title

      Organic Letters 10 (3)

      Pages: 509-511

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems2008

    • Author(s)
      G., Kikugawa, R., Apostolov, N., Kamiya, M., Taiji, R., Himeno, H., Nakamura, Y., Yonezawa
    • Journal Title

      Journal of Computational Chemistry 29 (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Protein-inhibitor flexible docking by a multicanonical sampling: Nativecomplex structure with the lowest free energy and a free-energy barrierdistrinsuishing the native complex from the others.2008

    • Author(s)
      Narutoshi Kamiya
    • Journal Title

      PROTEINS 70

      Pages: 41-53

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cyclopropanecarboxylic Acid Esters as Porential Prodrugs with Enhanced Hydrolytic Stability.2008

    • Author(s)
      David M. Bender
    • Journal Title

      Organic Letters 10

      Pages: 509-511

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks.2007

    • Author(s)
      Patil, Ashwini
    • Journal Title

      Biophysics 3

      Pages: 27-35

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Conformational sampling of a 40-residue protein consisting of α and β secondary-structure elements in explicit solvent.2007

    • Author(s)
      Ikebe, Jinzen
    • Journal Title

      Chemical Physics Letters 443

      Pages: 364-368

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of the protein environment and structural asymmetry.2007

    • Author(s)
      Yamasaki, Hideki
    • Journal Title

      Chemical Physics Letters 447

      Pages: 324-329

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks2007

    • Author(s)
      A., Patil, H., Nakamura
    • Journal Title

      Biophysics 3 (1)

      Pages: 27-35

    • NAID

      130000091817

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Conformational sampling of a 40-residue protein consisting of α and β secondary-structure elements in explicit solvent2007

    • Author(s)
      J., Ikebe, N., Kamiya, H., Shindo, H., Nakamura, J., Higo
    • Journal Title

      Chemical Physics Letters 443 (4-6)

      Pages: 364-368

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center : Effect of the protein environment and structural asymmetry2007

    • Author(s)
      H., Yamasaki, H., Nakamura, Y., Takano
    • Journal Title

      Chemical Physics Letters 447 (4-6)

      Pages: 324-329

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks.2007

    • Author(s)
      Ashwini Patil
    • Journal Title

      BIOPHYSICS 3

      Pages: 27-35

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational sampling of a 40-residue protein consisting of α and βsecondary-structure elements in explicit solvent.2007

    • Author(s)
      Jinzen Ikebe
    • Journal Title

      Chemical Physics Letters 443

      Pages: 364-368

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of the protein environment and structural asymmetry.2007

    • Author(s)
      Hideki Yamasaki
    • Journal Title

      Chemical Physics Letters 447

      Pages: 324-329

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes2006

    • Author(s)
      Takahashi, Hideo
    • Journal Title

      Journal of Biomolecular NMR 34

      Pages: 167-177

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] PreBI: Prediction of biological interfaces of proteins in crystals2006

    • Author(s)
      Tsuchiya, Yuko
    • Journal Title

      Nucleic Acids Research 34

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity2006

    • Author(s)
      Tsuchiya, Yuko
    • Journal Title

      Protein Engineering, Design and Screening 19

      Pages: 421-429

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Simulation Study on Water Associated with π-electrons of Benzene by using QM/MM Potential.2006

    • Author(s)
      Yonezawa, Yasushige
    • Journal Title

      Chemical Physics Letters 428

      Pages: 73-77

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Quantum mechanical study of the proton transfer via a peptide bond in the novel proton translocation pathway of cytochrome c oxidase.2006

    • Author(s)
      Takano, Yu
    • Journal Title

      Chemical Physics Letters 430

      Pages: 149-155

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Effect of Hunter Disease mutations on molecular phenotypes of iduronate-2-sulfonate: Enzymatic activity, protein processing and structural analysis.2006

    • Author(s)
      Sukegawa-Hayasaka, Kazuko
    • Journal Title

      Journal of Inherited Metabolic Disease 29

      Pages: 755-761

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes2006

    • Author(s)
      H., Takahashi, M., Miyazawa, Y., Ina, Y., Fukunishi, Y., MIzukoshi, H., Nakamura, I., Shimada
    • Journal Title

      Journal of Biomolecular NMR 34 (12)

      Pages: 167-177

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] PreBI : Prediction of biological interfaces of proteins in crystals2006

    • Author(s)
      Y., Tsuchiya, K., Kinoshita, N., Ito, H., Nakamura
    • Journal Title

      Nucleic Acids Research, 34 (Web Service issue)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity2006

    • Author(s)
      Y., Tsuchiya, K., Kinoshita, H., Nakamura
    • Journal Title

      Protein Engineering, Design and Screening 19 (9)

      Pages: 421-429

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Molecular Dynamics Simulation Study on Water Associated with π-electrons of Benzene by using QM/MM Potential2006

    • Author(s)
      Y., Yonezawa, K, Nakata, T., Takada, H., Nakamura
    • Journal Title

      Chemical Physics Letters 428 (1-3)

      Pages: 73-77

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Quantum mechanical study of the proton transfer via a peptide bond in the novel proton translocation pathway of cytochrome c oxidase2006

    • Author(s)
      Y., Takano, H., Nakamura
    • Journal Title

      Chemical Physics Letters 430 (1-3)

      Pages: 149-155

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Effect of Hunter Disease mutations on molecular phenotypes of iduronate-2-sulfonate : Enzymatic activity, protein processing and structural analysis2006

    • Author(s)
      K., Sukegawa-Hayasaka, Z., Kato, H., Nakamura, S., Tomatsu, T., Fukao, K., Kawata, T., Orii, N., Kondo
    • Journal Title

      Journal of Inherited Metabolic Disease 29 (6)

      Pages: 755-761

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes.2006

    • Author(s)
      H.Takahashi, M.Miyazawa, Y.Ina, Y.Fukunishi, Y.MIzukoshi, H.Nakamura, I.Shimada
    • Journal Title

      Journal of Biomolecular NMR Vol. 34, No. 3

      Pages: 167-177

    • Related Report
      2006 Annual Research Report
  • [Journal Article] PreBI : Prediction of biological interfaces of proteins in crystals.2006

    • Author(s)
      Y.Tsuchiya, K.Kinoshita, N.Ito, H.Nakamura
    • Journal Title

      Nucleic Acids Research Vol. 34, Web Service issue

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity.2006

    • Author(s)
      Y.Tsuchiya, K.Kinoshita, H.Nakamura
    • Journal Title

      Protein Engineering, Design and Screening Vol. 19, No. 9

      Pages: 421-429

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Molecular Dynamics Simulation Study on Water Associated with π-electrons of Benzene by using QM/MM Potential.2006

    • Author(s)
      Y.Yonezawa, K, Nakata, T.Takada, H.Nakamura
    • Journal Title

      Chemical Physics Letters Vol. 428, No. 1-3

      Pages: 73-77

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Quantum mechanical study of the proton transfer via a peptide bond in the novel proton translocation pathway of cytochrome c oxidase.2006

    • Author(s)
      Y.Takano, H.Nakamura
    • Journal Title

      Chemical Physics Letters Vol. 430, No. 1-3

      Pages: 149-155

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Effect of Hunter Disease mutations on molecular phenotypes of iduronate-2-sulfonate : Enzymatic activity, protein processing and structural analysis.2006

    • Author(s)
      K.Sukegawa-Hayasaka, Z.Kato, H.Nakamura, S.Tomatsu, T.Fukao, K.Kawata, T.Orii, N.Knodo
    • Journal Title

      Journal of Inherited Metabolic Disease Vol. 29

      Pages: 755-761

    • Related Report
      2006 Annual Research Report
  • [Presentation] ウシシトクロムc酸化酵素のヘムaの酸化還元状態における電子構造2008

    • Author(s)
      中村春木
    • Organizer
      日本化学会第88回春期年会
    • Place of Presentation
      立教大学,東京
    • Year and Date
      2008-03-29
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Electronic structure of heme a in bovine cytochrome c oxidase in the redox state2008

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      88'th Spring Meeting of The Chemical Society of Japan
    • Place of Presentation
      Rikkyo University, Tokyo
    • Year and Date
      2008-03-29
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] ウシシトクロムc酸化酵素のヘムαの酸化還元状態における電子構造2008

    • Author(s)
      中村春木
    • Organizer
      日本化学会第88回春期年会
    • Place of Presentation
      立教大学(東京)
    • Year and Date
      2008-03-29
    • Related Report
      2007 Annual Research Report
  • [Presentation] Dynamical Aspects of MAOA funcfion: Membrane Attachment Facilitates Ligand Access,2008

    • Author(s)
      中村春木
    • Organizer
      Perspective in Structural Biology of Membrane Proteins and Biological Macromolecules
    • Place of Presentation
      大阪大学蛋白質研究所,大阪
    • Year and Date
      2008-03-22
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Dynamical Aspects of MAOA function: Membrane Attachment Facilitates Ligand Access2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      Perspective in Structural Biology of Membrane Proteins and Biological Macromolecules
    • Place of Presentation
      大阪大学蛋白質研究所(大阪)
    • Year and Date
      2008-03-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] Theoretical study of the roles of heme side chains and axial ligands2008

    • Author(s)
      Nakamura, Haruki
    • Organizer
      48th Sanibel Symposium
    • Place of Presentation
      The King and Prince Golf & Beach Resort, Georgia,米国
    • Year and Date
      2008-02-26
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Theoretical study of the roles of heme side chains and axial ligands2008

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      48'th Sanibel Symposium
    • Place of Presentation
      The King and Prince Golf & Beach Resort, Georgia, U.S.A
    • Year and Date
      2008-02-26
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Theoretical study of the roles of heme side chains and axial ligands2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      48th Sanibel Symposium
    • Place of Presentation
      The King and Prince Golf& Beach Resort, Georgia, USA
    • Year and Date
      2008-02-26
    • Related Report
      2007 Annual Research Report
  • [Presentation] ウシシトクロムc酸化酵素のヘムaの酸化還元状態における電子構造2008

    • Author(s)
      中村春木
    • Organizer
      スーパーコンピュータワークショップ2008「大規模計算と分子のダイナミクス」
    • Place of Presentation
      分子科学研究所,岡崎
    • Year and Date
      2008-02-18
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 光合成反応中心スペシャルペアの電子非対称性の理論解析2008

    • Author(s)
      中村春木
    • Organizer
      スーパーコンピュータワークショップ2008「大規模計算と分子のダイナミクス」
    • Place of Presentation
      分子科学研究所,岡崎
    • Year and Date
      2008-02-18
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Electronic structure of heme a in bovine cytochrome c oxidase in the redox state2008

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      Supercomputer Workshop 2008 : Large-scale computation and molecular dynamics
    • Place of Presentation
      Institute for Molecular Science, Okazaki
    • Year and Date
      2008-02-18
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A theoretical analysis of electronic asymmetry of the special pari in photosynthetic reaction center2008

    • Author(s)
      H., Yamasaki, Y., Takano, H., Nakamura
    • Organizer
      Supercomputer Workshop 2008 : Large-scale computation and molecular dynamics
    • Place of Presentation
      Institute for Molecular Science, Okazaki
    • Year and Date
      2008-02-18
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] ウシシトクロムc酸化の酵素のヘムαの酸化還元状態における電子構造2008

    • Author(s)
      中村春木
    • Organizer
      スーパーコンピュータワークショップ2008 「大規模計算と分子のダイナミクス」
    • Place of Presentation
      分子科学研究所(岡崎)
    • Year and Date
      2008-02-18
    • Related Report
      2007 Annual Research Report
  • [Presentation] 光合成反応中心スペシャルペアの電子非対称性の理論解析2008

    • Author(s)
      中村春木
    • Organizer
      スーパーコンピュータワークショップ2008「大規模計算と分子のダイナミクス」
    • Place of Presentation
      分子科学研究所(岡崎)
    • Year and Date
      2008-02-18
    • Related Report
      2007 Annual Research Report
  • [Presentation] Quantum chemical study of the spin density distribution of the special pair cation radical in the photosynthetic reaction center2008

    • Author(s)
      Nakamura, Haruki
    • Organizer
      The lst International Global COE Symposium on Bio-Environmental Chemistry
    • Place of Presentation
      ホテル阪急EXPOパーク,大阪
    • Year and Date
      2008-01-28
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Quantum chemical study of the spin density distribution of the special pair cation radical in the photosynthetic reaction center2008

    • Author(s)
      H., Yamasaki, Y., Takano, H., Nakamura
    • Organizer
      The 1st International Global COE Symposium on Bio-Environmental Chemistry
    • Place of Presentation
      Hotel Hankyu EXPO park, Osaka
    • Year and Date
      2008-01-28
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Quantum chemical study of the spin density distribution of the special paircation radical in the photosynthetic reaction center2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 1st International Global COE Symposium on Bio-Environmental Chemistry
    • Place of Presentation
      Hotel Hankyu EXPO Park, Osaka
    • Year and Date
      2008-01-28
    • Related Report
      2007 Annual Research Report
  • [Presentation] チトクロムc酸化酵素の新しいプロトン輸送機構への理論的アプローチ-heme αの酸化還元における電子構造とペプチドを介したプロトン移動の関係-2007

    • Author(s)
      中村春木
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜,横浜
    • Year and Date
      2007-12-23
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A theoretical approach to a novel proton transfer pathway of cytochrome c oxidase2007

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      45'th Annual Meeting of Biophysical Society of Japan
    • Place of Presentation
      Pacifico Yokohama, Yokohama
    • Year and Date
      2007-12-23
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] チトクロムc酸化酵素の新しいプロトン輸送機構への理論的アプローチ -heme αの酸化還元における電子構造とペプチドを介したプロトン移動の関係-2007

    • Author(s)
      中村春木
    • Organizer
      第45回日本生物物理学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2007-12-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] アルファとベータの二次構造を含む40残基の蛋白質H-NSのfolding simulation2007

    • Author(s)
      中村春木
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜,横浜
    • Year and Date
      2007-12-22
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 光合成活性中心スペシャルペアカチオンラジカルのスピン密度分布に関する理論的研究2007

    • Author(s)
      中村春木
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜,横浜
    • Year and Date
      2007-12-22
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Folding simulation of a 40-residue protein, H-NS, involving alpha and beta secondary structures in explicit water2007

    • Author(s)
      J., Higo, J., Ikebe, N., Kamiya, H., Nakamura, H., Shindo
    • Organizer
      45'th Annual Meeting of Biophysical Society of Japan
    • Place of Presentation
      Pacifico Yokohama, Yokohama
    • Year and Date
      2007-12-22
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Quantum chemical study of the spin density distribution of the special pair cation radical in the bacterial photosynthetic reaction center2007

    • Author(s)
      H., Yamasaki, Y., Takano, H., Nakamura
    • Organizer
      45'th Annual Meeting of Biophysical Society of Japan
    • Place of Presentation
      Pacifico Yokohama, Yokohama
    • Year and Date
      2007-12-22
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] アルファとベータの二次構造を含む40残基の蛋白質H-NSのfolding simulation2007

    • Author(s)
      中村春木
    • Organizer
      第45回日本生物物理学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2007-12-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] 光合成活性中心スペシャルペアカチオンラジカルのスピン密度分布に関する理論的研究2007

    • Author(s)
      中村春木
    • Organizer
      第45回日本生物物理学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2007-12-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] タンパク質-リガンド複合体予測構造の分子シミュレーションによる評価2007

    • Author(s)
      中村春木
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜,横浜
    • Year and Date
      2007-12-21
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] QM/MMシミュレーションによるPinl蛋白質のCis-Trans異性化酵素活性研究2007

    • Author(s)
      中村春木
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜,横浜
    • Year and Date
      2007-12-21
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A Computational Study of Monoamine Oxidase A Dynamics2007

    • Author(s)
      中村春木
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      パシフィコ横浜,横浜
    • Year and Date
      2007-12-21
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Molecular simulations of protein-ligand structures constructed by computational doking2007

    • Author(s)
      A., Oda, Y., Takano, H., Nakamura, N., Yamaotsu, S., Hirono, O., Takahashi, H., Matsuzaki
    • Organizer
      45'th Annual Meeting of Biophysical Society of Japan
    • Place of Presentation
      Pacifico Yokohama, Yokohama
    • Year and Date
      2007-12-21
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] QM/MM simulation study on the mechanism of cis-trans isomerization of human Pinl protein2007

    • Author(s)
      Y., Yonezwa, N., Kamiya, H., Nakamura
    • Organizer
      45'th Annual Meeting of Biophysical Society of Japan
    • Place of Presentation
      Pacifico Yokohama, Yokohama
    • Year and Date
      2007-12-21
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A Computational Study of Monoamine Oxidase A Dynamics2007

    • Author(s)
      R., Apostolov, Y., Yonezawa, H., Nakamura
    • Organizer
      45'th Annual Meeting of Biophysical Society of Japan
    • Place of Presentation
      Pacifico Yokohama, Yokohama
    • Year and Date
      2007-12-21
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] タンパク質-リガンド複合体予測構造の分子シミュレーションによる評価2007

    • Author(s)
      中村春木
    • Organizer
      第45回日本生物物理学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2007-12-21
    • Related Report
      2007 Annual Research Report
  • [Presentation] QM/MMシミュレーションによるPinl蛋白質のCis-Trans異性化酵素活性研究2007

    • Author(s)
      中村春木
    • Organizer
      第45回日本生物物理学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2007-12-21
    • Related Report
      2007 Annual Research Report
  • [Presentation] A Computational Study of Monoamine Oxidase A Dynamics2007

    • Author(s)
      中村春木
    • Organizer
      第45回日本生物物理学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2007-12-21
    • Related Report
      2007 Annual Research Report
  • [Presentation] 大腸菌エンドヌクレアーゼ の基質認識機構の計算化学的研究2007

    • Author(s)
      中村春木
    • Organizer
      第30回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜,横浜
    • Year and Date
      2007-12-13
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Computational studies of the substrate recognition mechanism of Escherichia coil endonuclease III2007

    • Author(s)
      K., Manabe, Y., Takano, K., Hitomi, J.A., Tainer, H., Nakamura, N., Iwai
    • Organizer
      BMB 2007
    • Place of Presentation
      Pacifico Yokohama, Yokohama
    • Year and Date
      2007-12-13
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] 大腸菌エンドヌクレアーゼIIIの基質認識機構の計算化学的研究2007

    • Author(s)
      中村春木
    • Organizer
      分子生物学会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2007-12-13
    • Related Report
      2007 Annual Research Report
  • [Presentation] Molecular orbital study of the proton transfer through a peptide bond-A theoretical approach to a novel pathway of proton translocation of cytochrome coxidase-2007

    • Author(s)
      Nakamura, Haruki
    • Organizer
      ICCMSE2007
    • Place of Presentation
      Marbella Corfu Hotel,ギリシャ
    • Year and Date
      2007-09-26
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Molecular orbital study of the proton transfer through a peptide bond-A theoretical approach to a novel pathway of proton translocation of cytochrome c oxidase-2007

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      ICCMSE2007
    • Place of Presentation
      Marbella Corfu Hotel, Greece
    • Year and Date
      2007-09-26
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] チトクロムc酸化酵素のheme αの酸化還元における電子構造変化とプロトン移動との関係2007

    • Author(s)
      中村春木
    • Organizer
      第1回分子科学討論会2007仙台
    • Place of Presentation
      東北大学川内北キャンパス,仙台
    • Year and Date
      2007-09-18
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Relationship between electronic structural change and proton transfer of heme a in cytochrome c oxidase in the redox state2007

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      1'st meeting of Japan Society of Molecular Science 2007 at Sendai
    • Place of Presentation
      Tohoku University
    • Year and Date
      2007-09-18
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] チトクロムc酸化酵素のheme aの酸化還元における電子構造変化とプロトン移動との関係2007

    • Author(s)
      中村春木
    • Organizer
      第1回分子科学討論会2007仙台
    • Place of Presentation
      東北大学川内北キャンパス
    • Year and Date
      2007-09-18
    • Related Report
      2007 Annual Research Report
  • [Presentation] A theoretical approach to a novel proton transfer pathway of cytochromc coxidase2007

    • Author(s)
      Nakamura, Haruki
    • Organizer
      International Symposium on Molecular Theory for Real Systems
    • Place of Presentation
      京都大学桂キャンパス,京都
    • Year and Date
      2007-07-28
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A theoretical approach to a novel proton transfer pathway of cytochrome c oxidase2007

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      International Symposium on Molecular Theory for Real Systems
    • Place of Presentation
      Kyoto University
    • Year and Date
      2007-07-28
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A theoretical approach to a novel proton transfer pathway of cytochrome coxidase2007

    • Author(s)
      Haruki Nakamura
    • Organizer
      International Symposium on Molecular Theory for Real Systems
    • Place of Presentation
      Kyoto University (Katsuracampus)
    • Year and Date
      2007-07-28
    • Related Report
      2007 Annual Research Report
  • [Presentation] チトクロムc酸化酵素のheme αの酸化還元状態における電子構造2007

    • Author(s)
      中村春木
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター,仙台
    • Year and Date
      2007-05-25
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] プロリン異性化酵素Pin1のQM/MM錬成計算シミュレーション研究2007

    • Author(s)
      中村春木
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター,仙台
    • Year and Date
      2007-05-25
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A Computational Study of Monoamine Oxidase A Dynamics2007

    • Author(s)
      中村春木
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター,仙台
    • Year and Date
      2007-05-25
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] マルチカノニカル分子動力学法による酵素-阻害剤間のフレキシブルドッキング2007

    • Author(s)
      中村春木
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター,仙台
    • Year and Date
      2007-05-25
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Electronic structure of heme a in cytochrome c oxidase in the redox state2007

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      7'th Annual Meeting of Protein Science Society of Japan
    • Place of Presentation
      Sendai International Center, Sendai
    • Year and Date
      2007-05-25
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A QM/MM molecular dynamics study on peptidyl-prolyl isomerase Pinl2007

    • Author(s)
      Y., Yonezawa, N., Kamiya, T., Takada, H., Nakamura
    • Organizer
      7'th Annual Meeting of Protein Science Society of Japan
    • Place of Presentation
      Sendai International Center, Sendai
    • Year and Date
      2007-05-25
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] A Computational Study of Monoamine Oxidase A Dynamics2007

    • Author(s)
      R., Apostolov, Y., Yonezawa, H., Nakamura
    • Organizer
      7'th Annual Meeting of Protein Science Society of Japan
    • Place of Presentation
      Sendai International Center, Sendai
    • Year and Date
      2007-05-25
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Flexible docking between enzyme and inhibitor by multicanonical molecular dynamics2007

    • Author(s)
      N., Kamiya, Y., Yonezawa, H., Nakamura, J., Higo
    • Organizer
      7'th Annual Meeting of Protein Science Society of Japan
    • Place of Presentation
      Sendai International Center, Sendai
    • Year and Date
      2007-05-25
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] プロリン異性化酵素PinlのQM/MM錬成計算シミュレーション研究2007

    • Author(s)
      中村春木
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター(仙台)
    • Year and Date
      2007-05-25
    • Related Report
      2007 Annual Research Report
  • [Presentation] チトクロムc酸化酵素のheme aの酸化還元状態における電子構造2007

    • Author(s)
      中村春木
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター(仙台)
    • Year and Date
      2007-05-25
    • Related Report
      2007 Annual Research Report
  • [Presentation] A Computational Study of Monoamine Oxidase A Dynamics2007

    • Author(s)
      中村春木
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター(仙台)
    • Year and Date
      2007-05-25
    • Related Report
      2007 Annual Research Report
  • [Presentation] マルチカノニカル分子動力学法による酵素-阻害剤間のフレキシブルドッキング2007

    • Author(s)
      中村春木
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台国際センター(仙台)
    • Year and Date
      2007-05-25
    • Related Report
      2007 Annual Research Report
  • [Presentation] Structural Features of Hubs in Protein-Protein Interaction Networks2007

    • Author(s)
      Nakamura, Haruki
    • Organizer
      上海大学セミナー
    • Place of Presentation
      上海大学 Institute of Systems Biology,上海
    • Year and Date
      2007-03-29
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Structural Features of Hubs in Protein-Protein Interaction Networks2007

    • Author(s)
      H., Nakamura
    • Organizer
      Shanghai University Seminar
    • Place of Presentation
      Institute of Systems Biology, Shanghai University, Shanghai
    • Year and Date
      2007-03-29
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Structural Features of Hubs in Protein-Protein Interaction Networks2007

    • Author(s)
      Nakamura, Haruki
    • Organizer
      PROTEIN ASSEMBLY, DYNAMICS AND FUNCTION
    • Place of Presentation
      Institut des Haute Etudes Scientifiques,パリ
    • Year and Date
      2007-01-11
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Structural Features of Hubs in Protein-Protein Interaction Networks2007

    • Author(s)
      H., Nakamura
    • Organizer
      PROTEIN ASSEMBLY, DYNAMICS AND FUNCTION
    • Place of Presentation
      Institut des Haute Etudes Scientifiques, Paris
    • Year and Date
      2007-01-11
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Protein fhnction analyses from structural bioinformatics approach2006

    • Author(s)
      Nakamura, Haruki
    • Organizer
      EABS & BSJ 2006
    • Place of Presentation
      沖縄コンベンションセンター沖縄県宜野湾市
    • Year and Date
      2006-11-15
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Protein function analyses from structural bioinformatics approach2006

    • Author(s)
      H., Nakamura
    • Organizer
      EABS &BSJ
    • Place of Presentation
      Okinawa Convention Center, Ginowan, Okinawa
    • Year and Date
      2006-11-15
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] QM/MM study on catalytic mechanism of PPIase protein Pin12006

    • Author(s)
      Nakamura, Haruki
    • Organizer
      EABS & BSJ 2006
    • Place of Presentation
      沖縄コンベンションセンター沖縄県宜野湾市
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Large-scale molecular dynamics simulations with the pariwise electrostatic interaction method for protein-solvent systems2006

    • Author(s)
      Nakamura, Haruki
    • Organizer
      EABS & BSJ 2006
    • Place of Presentation
      沖縄コンベンションセンター沖縄県宜野湾市
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Quantum mechanical study of the proton transfer via a peptide bond in the novel pathway of proton translocation of cytochrome c oxidase2006

    • Author(s)
      Nakamura, Haruki
    • Organizer
      EABS & BSJ 2006
    • Place of Presentation
      沖縄コンベンションセンター沖縄県宜野湾市
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Theoretical analysis of electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of protein environment2006

    • Author(s)
      Nakamura, Haruki
    • Organizer
      EABS & BSJ 2006
    • Place of Presentation
      沖縄コンベンションセンター沖縄県宜野湾市
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] QM/MM study on catalytic mechanism of PPIase protein Pinl2006

    • Author(s)
      Y., Yonezawa, N., Kamiya, H., Nakamura
    • Organizer
      EABS &BSJ
    • Place of Presentation
      Okinawa Convention Center, Ginowan, Okinawa
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Large-scale molecular dynamics simulations with the pariwise electrostatic interaction method for protein-solvent systems2006

    • Author(s)
      G., Kikugwa, Y., Yonezawa, H., Nakamura, R., Himeno
    • Organizer
      EABS &BSJ
    • Place of Presentation
      Okinawa Convention Center, Ginowan, Okinawa
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Quantum mechanical study of the proton transfer via a peptide bond in the novel pathway of proton translocation of cytochrome c oxidase2006

    • Author(s)
      Y., Takano, H., Nakamura
    • Organizer
      EABS &BSJ
    • Place of Presentation
      Okinawa Convention Center, Ginowan, Okinawa
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Theoretical analysis of electronic asymmetry of the special pair in the photosynthetic reaction center : Effect of protein environment2006

    • Author(s)
      H., Yamasaki, Y., Takano, H., Nakamura
    • Organizer
      EABS &BSJ
    • Place of Presentation
      Okinawa Convention Center, Ginowan, Okinawa
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Dynamical Aspects of MAOA function : Membrane Attachment Facilitates Ligand Access

    • Author(s)
      R., Apostolov, Y., Yonezawa, H., Nakamura
    • Organizer
      Perspective in Structural Biology of Membrane Proteins and Biological Macromolecules
    • Place of Presentation
      Osaka University, Osaka
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary

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Published: 2006-04-01   Modified: 2016-04-21  

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