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Administration of reseaches on principles of protein architecture

Research Project

Project/Area Number 09044076
Research Category

Grant-in-Aid for international Scientific Research

Allocation TypeSingle-year Grants
SectionJoint Research
Research Field Biophysics
Research InstitutionKYOTO UNIVERSITY

Principal Investigator

GO Nobuhiro  Grad.Schl.Sci., Kyoto Univ., Professor, 大学院・理学研究科, 教授 (50011549)

Co-Investigator(Kenkyū-buntansha) PARAK Fritz  Inst.Phys., Teh.Univ.Muenchen, Professor, 物理学科, 教授
KIDERA Akinori  Grad.Schl.Sci., Kyoto Univ., Assoc.Prof., 大学院・理学研究科, 助教授 (00186280)
FRITZ Parak  ミュンヘン工科大学, 物理学科, 教授
Project Period (FY) 1997 – 1998
Project Status Completed (Fiscal Year 1998)
Budget Amount *help
¥2,300,000 (Direct Cost: ¥2,300,000)
Fiscal Year 1998: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 1997: ¥1,200,000 (Direct Cost: ¥1,200,000)
Keywordsprotein / dynamics / glass-transition / relaxation time / X-ray crystallography / Mossbauer spectroscopy / normal modes / conformational substates
Research Abstract

Proteins, the molecule which play crucially important biological functions, possess its own pattern of conformational fluctuations depending on the three dimensional structure. The fluctuations are suppressed with decreasing temperature, and show a glass transition-like phenomenon at about 200 K.Below 200 K, the protein function is usually lost. Such observations indicate that the fluctuations acquired above the glass transition temperature is crucial for the biological functions. In principle, the glass transition phenomenon can be detected to the atomic detail by a cryo X-ray crystallographic study, as well as various spectroscopic techniques.
This work was done by the cooperation between two groups, Go and Kidera in Kyoto University and Parak in Technical University Muenchen. Muenchen group did cryo X-ray measurements at various cryo-temperatures for myoglobin crystals. Kyoto group did analyses of diffraction data provided by Parak using an elaborated refinement method called the nor … More mal mode refinement. We have had close communication including each of two times visits from Kyoto to Muenchen and from Muenchen to Kyoto. Last December when Parak visited Japan, he presented a lecture on this topics in the 5-th workshop of "Principles of protein architectures".
The results of the cooperative work is summarized as follows. The internal fluctuations,
<R^<**>2>int, derived from the normal mode refinement of X-ray diffraction from myoglobin crystals was found to have temperature dependence of
<R^<**>2>int = AT + B
where T is absolute temperature, and A an B are constants. The value of A has a good agreement with the value predicted by a normal mode analysis. This means that the conformational substates available below the glass transition temperature is the same as those above the transition temperature. This is why we do not observe abrupt increase in <R^<**>2>int at the glass transition temperature. Therefore, the value B represents the static disorder. This is the view of X-ray diffraction detecting the coherent scattering, which is totally different from the other spectroscopic techniques detecting the incoherent scattering, like
Mossbauer absorption spectroscopy. Less

Report

(3 results)
  • 1998 Annual Research Report   Final Research Report Summary
  • 1997 Annual Research Report
  • Research Products

    (21 results)

All Other

All Publications (21 results)

  • [Publications] G.Basu: "Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. 1.Theory" J.Phys.Chem.B102. 2076-2076 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] G.Basu: "Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. 2.Application to Ru-Modified Cytochrome c" J.Phys.Chem.B102. 2085-2094 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] O.Miyashita: "Pressure Dependence of Protein Electron Transfer Reactions: Theory and Simulation" J.Phys.Chem.B103. 562-571 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] C.Keppler: "Determination of the photon spectrum of iron in myoglobin using inelastic X-ray scattering of synchrotron radiation." Eur.Biophys.J.25. 221-224 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] D.C.Lamb: "From metmyoglobin to deoxy myoglobin: relaxations of an intermediate state." Eur.Biophys.J.27. 113-125 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] F.Parak: "Biomolecules: Flucuations and relaxations" Proceeding of The third international symposium on biological physics. in press. (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] G.Basu, et al.: "Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis.1.Theory" J.Phys.Chem.B102. 2076-2084 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] G.Basu, et al.: "Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis.2.Application to Ru-Modifieo Cytochrome c" J.Phys.Chem.B102. 2085-2094 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] O.Miyashita and N.Go: "Pressure Dependence of Protein Electron Transfer Reactions : Theory and Simulation" J.Phys.Chem.B103. 562-571 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] C.Keppler, et al.: "Determination of the photon spectrum of iron in myoglobin using inelastic X-ray scattering of synchrotron radiation." Eur.Biophys.J.25. 221-224 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] D.C.Lamb, et al.: "From metmyoglobin to deoxy myoglobin : relaxations on an intermediate stte" Eur.Biophys.J.27. 113-125 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] F.Parak, etal.: "Biomolicules : Fluctuations and relaxations" Proceedings of The third international symposium on biological physics. (in press). (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] F.Parak: "Biomolecules:Fluctuations and relaxations" Proceeding of American Physical Society. (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] A.Matsumoto: "Dynamical Properties of Double-Standed DNA by Normal Mode Analysis." Eur.Biophys.J.(in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] K.Kinoshita: "Structural Motif of Phosphate Binding Site Common to Various Protein Superfamilies: An All-against-all Structural Comparison of Protein-Mononucleiotide Complexes." Protein Eng.1. 11-14 (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] D.C.Lamb: "From metmyoglobin to deoxy myoglobin: relaxations of an intermediate state." Eur.Biophys.J.27. 113-125 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] L.Cordone: "biophysics leter: A reduction of protein specific motions in co-ligated myoglobin embedded in a trehalose glass." Eur.Biophys.J.27. 173-176 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] H.Ishida: "Canonical molecular dynamics of a protein in water by higu-order decomposition of Liouville oprator." J.Chem.Phys.109. 3276-3284 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] D.Lin: "Normal mode analysis of a double-starnded DNA dodecamer" J.Chem.Phys.107. 3684-3690 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] N.Nakajima: "Flexible docking of a ligand peptide to a receptor protein by multicanocnical molecular dynamics simulation" Chem.Phys.Lett.278. 297-301 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] C.Keppler: "Determination of the phonon spectrum of iron in myoglobin using inelastic X-ray scattering of synchrotron radiation" Eur.Biophys.J.25. 221-224 (1997)

    • Related Report
      1997 Annual Research Report

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Published: 1997-04-01   Modified: 2016-04-21  

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