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Study of Vibrational Energy Transfer in Proteins

Research Project

Project/Area Number 14540474
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionYokohama City University

Principal Investigator

KIDERA Akinori  Yokohama City University, Graduate School of Integrated Science, Professor, 大学院・総合理学研究科, 教授 (00186280)

Co-Investigator(Kenkyū-buntansha) IKEGUCHI Mitsunori  Yokohama City University, Graduate School of Integrated Science, Associate Professor, 大学院・総合理学研究科, 助教授 (60261955)
Project Period (FY) 2002 – 2003
Project Status Completed (Fiscal Year 2003)
Budget Amount *help
¥3,400,000 (Direct Cost: ¥3,400,000)
Fiscal Year 2003: ¥1,600,000 (Direct Cost: ¥1,600,000)
Fiscal Year 2002: ¥1,800,000 (Direct Cost: ¥1,800,000)
Keywordsprotein dynamics / molecular dynamics / anharmonic motions / vibration / diffusion / normal modes / mode coupling / principal component / タンパク質ダイナミクス / 基準振動モード / 非線型振動 / 主成分解析 / 多様体
Research Abstract

Anharmonic dynamics of a protein molecule was studied by molecular dynamics simulations, (1)in terms of the intramolecular vibrational energy transfer, and (2)second through moving normal mode coordinates.
(1)A small excess kinetic energy was added to a specified normal mode, and the process of the energy transfer to other modes was observed. It was found that the vibrational energy was transferred by two distinct mechanisms depending on temperature. At near zero temperature, the vibrational energy is transferred ass a process of the Fermi resonance. As the temperature increases, the resonance type transfer is dominated by the off-resonance energy transfer through various mode coupling terms.
(2)A set of normal mode coordinates is defined at each time instant of the trajectory by principal component analysis (PCA) with a small time window. The time evolution of the normal mode coordinates defines the moving normal mode coordinates. Translation of he origin of he coordinates was decomposed into diffusion and vibrational motions. Significant parts of both types of motions occur in the large-amplitude normal mode space. Rotation of the large-amplitude normal mode space was characterized by fast relaxation completed within the time window of PCA, but was confined in a small space spanned by a limited number of large-amplitude normal modes.

Report

(3 results)
  • 2003 Annual Research Report   Final Research Report Summary
  • 2002 Annual Research Report
  • Research Products

    (21 results)

All Other

All Publications (21 results)

  • [Publications] R.Koike, K.Kinoshita, A.Kidera: "Ring and zipper formation is the key to understanding the structural variety in all beta proteins"EBS Letters. 533. 9-13 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] K.Moritsugu, O.Miyashita, A.Kidera: "Temperature Dependence of Vibrational Energy Transfer in a Protein Molecule"J.Phys.Chem.B. 107. 3309-3317 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] J.G.Kim, Y.Fukunishi, A.Kidera, H.Nakamura: "Determination of multicanonical weight based on a stochastic model of sampling dynamics"Physical Review E. 68. 021110 1-021110 8 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] J.G.Kim, Y.Fukunishi, A.Kidera, H.Nakamura: "Stochastic formulation of sampling dynamics in generalized ensemble methods"Physical Review E. 69. 021101 1-021101 10 (2004)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] K.Moritsugu, A.Kidera: "Protein motions represented in moving normal mode coordinates"J.Phys.Chem.B. 108. 3890-3898 (2004)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Y.Joti M.Nakasako, Kidera, N.Go: "Nonlinear temperature dependence of crystal structure of Lysozyme : Correlation between coordinate shifts and thermal factors"Acta Cryst.Sect.D. 58. 1421-1432 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] T.Terada, Y.Matsuo, A.Kidera: "A method for evaluationg multicanonical potential function without iterative refinement : Application to conformational sampling of a globular protein in water"J.Chem.Phys. 118. 4306-4311 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] K.Moritsugu, O.Miyashita, A.Kidera: "Temperature Dependence of Vibrational Energy Transfer in a Protein Molecule"J.Phys.Chem.B. 107. 3309-3317 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] J.G.Kim, Y.Fukunishi, A.Kidera, H.Nakamura: "Determination of multicanonical weight based on a stochastic model of sampling dynamics"Physical Review, E. 68. 021110 1-021110 8 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] J.G.Kim, Y.Fukunishi, A.Kidera, H.Nakamura: "Stochastic formulation of sampling dynamics in generalized ensemble methods"Physical Review, E. 69. 021101 1-021101 10 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] K.Moritsugu, A.Kidera: "Protein motions represented in moving normal mode coordinates"J.Phys.Chem.B.. 108. 3890-3898 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] S.Nakamura, M.Ikeguchi, K.Shimizu: "Dynamical Analysis of tRNAGln-GlnRS Complex using Normal Mode Calculation"Chem.Phys.Lett.. 372. 423-431 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] S.Nakamura, D.Kyono, M.Ikeguchi, K.Shimizu: "A New Method for Parallel Computation of Hessian Matrix of Conformational Energy Function in Internal Coordinates"J.Comput.Chem.. 23. 463-469 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] M.Ikeguchi: "Partial Rigid-Body Dynamics in NPT, NPAT and NPγT Ensembles for Proteins and Membranes"J.Comput.Chem. 23. 463-469 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] R.Koike, K.Kinoshita, A.Kidera: "Ring and zipper formation is the key to understanding the structural variety in all beta proteins"FEBS Letters. 533. 9-13 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] K.Moritsugu, O.Miyashita, A.Kidera: "Temperature Dependence of Vibrational Energy Transfer in a Protein Molecule"J.Phys.Chem.B. 107. 3309-3317 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] J.G.Kim, Y.Fukunishi, A.Kidera, H.Nakamura: "Determination of multicanonical weight based on a stochastic model of sampling dynamics"Physical Review E. 68. 021110 1-021110 8 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] J.G.Kim, Y.Fukunishi, A.Kidera, H.Nakamura: "Stochastic formulation of sampling dynamics in generalized ensemble methods"Physical Review B. 69. 021101 1-021101 10 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] K.Moritsugu, A.Kidera: "Protein motions represented in moving normal mode coordinates"J.Phys.Chem.B. 108. 3890-3898 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Y.Joti M.Nakasako, A.Kidera, N.Go: "Nonlinear temperature dependence of crystal structure of Lysozyme : Correlation between coordinate shifts and thermal factors"Acta Crystallographica Section D. 58. 1421-1432 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] K.Moritsugu, O.Miyashita, A.Kidera: "Temperature Dependence of Vibrational Energy Transfer in a Protein Molecule"Journal of Physical Chemistry B. 107. (2003)

    • Related Report
      2002 Annual Research Report

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Published: 2002-04-01   Modified: 2016-04-21  

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