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Prediction of Protein Fold and Analysis of Protein Folding Procedure

Research Project

Project/Area Number 12680657
Research Category

Grant-in-Aid for Scientific Research (C)

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

Principal Investigator

NAKAMURA Haruki  Institute for Protein Research, Osaka University, Professor, たんぱく質研究所, 教授 (80134485)

Co-Investigator(Kenkyū-buntansha) NAKAJIMA Nobuyuki  Institute for Protein Research, Osaka University, Research Associate, たんぱく質研究所, 助手 (60324852)
Project Period (FY) 2000 – 2001
Project Status Completed (Fiscal Year 2001)
Budget Amount *help
¥3,600,000 (Direct Cost: ¥3,600,000)
Fiscal Year 2001: ¥1,200,000 (Direct Cost: ¥1,200,000)
Fiscal Year 2000: ¥2,400,000 (Direct Cost: ¥2,400,000)
KeywordsSimulation Computation / Molecular Dynamics / Peptide Conformation / Conformation Sampling / Quantum Chemistry / Disordered Structure / Tsallis Statistics / Multicanonical ensemble / β-ヘアピン / 水素結合
Research Abstract

Our purpose is to predict the protein fold by computing the major free energy landscape of a protein molecule, since native conformations of proteins assume the conformations with low free energy values. In addition, the analysis of protein folding procedures are investigated.
First, we chose two kinds of peptides with about 10 amino acids, and draw the free energy landscapes after enhanced conformational search. The resulted landscapes were consistent with the experiments of CD and NMR spectra.
Further, we noticed that the landscapes were strongly dependent on the force field parameters, and so we made our effort on this problem. We developed a new algorithm to calibrate the free energy landscapes by the quantum chemical calculations, and we succeeded to calibrate several free energy landscapes, which were given by using different force fields, into the common landscape.
In addition, we developed another method for the enhanced conformational search, by applying Tsallis statistics. When the parameter q in Tsallis statistics was treated as one of the variables for the motion of equation, the wide energy region can be covered by this new method for a simple peptide system composed of five amino acids.

Report

(3 results)
  • 2001 Annual Research Report   Final Research Report Summary
  • 2000 Annual Research Report
  • Research Products

    (23 results)

All Other

All Publications (23 results)

  • [Publications] Higo, Junichi: "Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin and other disordered conformations"Protein Science. vol.10, No.6. 1160-1171 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Higo, Junichi: "Energy landscape of a beta-hairpin peptide in explicit water studied by multicanonical molecular dynamics"Chemical Physics Letters. vol.377, No.1. 169-175 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Higo, Junichi: "Large vortex-like structure of dipole field in computere models of liquid water and dipole-bridge between biomolecules"Proceedings of National Academy of Science USA. vol.98, No.11. 5961-5964 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Hitomi, Kenichi: "Role of two histidines in the (6-4) photolyase reaction"Journal of Biological Chemistry. vol.276, No.13. 10103-10109 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Yamagata, Yuriko: "Entropic stabilization of the tryptophan synthase α-subunit from a hyperthermophile, Pyrococcus furiosus"Journal of Biological Chemistry. vol.276, No.14. 11062-11071 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ono, Satoshi: "Calibration of force-field dependency in free energy landscapes of peptide caonformations by quantum chemical calculations"Journal of Compututational Chemistry. vol.23, No.4. 470-476 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Higo, Junichi et al.: "Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations"Protein Science. Vol. 10, No. 6. 1160-1171 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Higo, Junichi et al: "Energy landscape of a beta-hairpin peptide in explicit water studied by multicanonical molecular dynamics"Chemical Physics Letters. Vol. 377, No. 1. 169-175 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Higo, Junichi et al: "Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules"Proceedings of National Academy of Science USA. Vol. 98, No. 11. 5961-5964 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Hitomi, Kenichi et al: "Role of two histidines in the (6-4) photolyase reaction"Journal of Biological Chemistry. Vol. 276, No. 13. 10103-10109 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Yamagata, Yuriko et al: "Entropic stabilization of the tryptophan synthase a-subunit from a hyperthermophile, Pyrococcus furiosus"Journal of Biological Chemistry. Vol. 276, No. 14. 11062-11071 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ono, Satoshi et al: "Calibration of. force-field dependency in free energy landscapes of peptide caonformations by quantum chemical calculations"Journal of Compututational Chemistry. Vol. 23, No. 4. 470-476 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Higo, Junichi: "Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations"Protein Science. vol.10, No.6. 1160-1171 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Higo, Junichi: "Energy landscape of a beta-hairpin peptide in explicit water studied by multicanonical molecular dynamics"Chemical Physics Letters. vol.377, No.1. 169-175 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Higo, Junichi: "Large vortex-like structure of dipole field in computer models of liquid Water and dipole-bridge between biomolecules"Proceedings of National Academy of Science USA. vol.98, No.11. 5961-5964 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Furukawa, Koji: "A role of the third complementarity-determining region in the affinity maturation of an antibody"Journal of Biological Chemistry. vol.276, No.29. 27622-27628 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Ono, Satoshi: "Calibration of force-field dependency in free energy landscapes of peptide caonformations by quantum chemical calculations"Journal of Compututational Chemistry. vol.23, No.4. 470-476 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Fukuda, Ikuo: "Tsallis Dynamics using Nose-Hoover approach"Physical Review E. vol.65(in press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Nakajima,Nobuyuki: "Free energy landscapes of peptides by enhanced conformational sampling."Journal of Molecular Biology. 296. 197-216 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Ono,Satoshi: "Peptide free energy profile is strongly dependent on the force field : Comparison of C96 and AMBER95."Journal of Computational Chemistry. 9. 748-762 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Galzitskaya,Oxana V.: "β-hairpin folds by molecular dynamics simulations"Chem.Phys.Lett.. 326. 421-429 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Higo,Junichi: "Energy landscape of a beta-hairpin peptide in explicit water studied by multicanonical molecular dynamics."Chem.Phys.Lett.. (in press). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Higo,Junichi: "Energy landscape of a peptide consisting of α-helix, 3_<10>-helix, β-turn, β-hairpin, and other disordered conformations."Protein Science. (in press). (2001)

    • Related Report
      2000 Annual Research Report

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Published: 2000-04-01   Modified: 2016-04-21  

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