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Deducing dynamic protein 3D structural information from X-ray crystallography and NMR

Research Project

Project/Area Number 04453166
Research Category

Grant-in-Aid for General Scientific Research (B)

Allocation TypeSingle-year Grants
Research Field 生物物性学
Research InstitutionKYOTO UNIVERSITY

Principal Investigator

GO Nobuhiro  Kyoto University Chemistry Professor, 理学部, 教授 (50011549)

Project Period (FY) 1992 – 1993
Project Status Completed (Fiscal Year 1993)
Budget Amount *help
¥7,100,000 (Direct Cost: ¥7,100,000)
Fiscal Year 1993: ¥1,700,000 (Direct Cost: ¥1,700,000)
Fiscal Year 1992: ¥5,400,000 (Direct Cost: ¥5,400,000)
KeywordsProtein / 3D structure / Dynamics / X-ray Crystallography / NMR / Diffuse scattering / Mutant protein / タンパク質 / 変異タンパク質
Research Abstract

Dynamic 3D structural information of proteins is essential for elucidation of molecular mechanism of protein function. The purpose of this reseach project is firstly to develop new methods of analyzes of experimental X-ray crystallographic and NMR data and secondly to apply the developed methods for real systems to deduce such dynamic information. At first, we applied the new method of protein X-ray crystallographic refinement based on the normal mode concept to human lysozyme and its site-specific mutant, and demonstrated that information about anisotropic temperature factors of protein atoms and their concerted motions could be deduced. Furthermore interesting information was obtained about correlation of changes of 3D structure and fluctuation and also about molecular mechanism of enzymatic function by analyzing changes of 3D structure and fluctuation accompanied with site-derected mutation. At second, we developed a new method to deduce new information about collective motions in protein by analyzing X-ray diffuse scattering. At third, we derived a formula of expressing up to second order changes of protein atomic Cartesian coordinates for small changes of dihedral angles, and applied this formula for developing method of obtaining Lipari-Szabo order parameters from the normal mode analysis. This method will enable us to develop a new method by which dynamic as well as static protein 3D structural information can be deduced from experimental NMR data.

Report

(3 results)
  • 1993 Annual Research Report   Final Research Report Summary
  • 1992 Annual Research Report
  • Research Products

    (24 results)

All Other

All Publications (24 results)

  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure Applied to Human Lysozyme" Biopolymers. 32. 315-319 (1992)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure I.Theory and Test by Simulated Diffraction Data" J.Mol.Biol.225. 457-475 (1992)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure II.Application to Human Lysozyme" J.Mol.Biol.225. 477-486 (1992)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] K.Mizuguchi: "Collective Motions in Proteins Investigated by X-ray Diffuse Scattering" Proteins:Structure,Function,and Genetics. 18. 34-48 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] A.Kidera: "Response of Dynamic Structure to Removal of a Disulfide Bond:Normal Mode Refinement of C77A/C95A Mutant of Human Lysozyme" Protein Science. 3. 92-102 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] S.Sunada: "Comparison of Normal Mode Analysis on a Small Globular Protein in Dihedral Angle Space and Cartesian Coordinate Space" J.Computational Chemistry. (in press).

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] A.Kidera, K.Inaka, M.Matsushima and N.Go: "Normal Mode Refinement : Crystallographic Refinement of Protein Dynamic Structure Applied to Human Lysozyme" Biopolymers. 32. 315-319 (1992)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] A.Kidera and N.Go: "Normal Mode Refinement : Crystallographic Refinement of Protein Dynamic Structure I.Theory and Test by Simulated Diffraction Data" Journal of Molecular Biology. 225. 457-475 (1992)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] A.Kidera, K.Inaka, M.Matsushima and N.Go: "Normal Mode Refinement : Crystallographic Refinement of Protein Dynamic Structure II.Application to Human Lysozyme" Journal of Molecular Biology. 225. 477-486 (1992)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] K.Mizuguchi, A.Kidera and N.Go: "Collective Motions in Proteins Investigated by X-Ray Diffuse Scattering" Proteins : Structure, Function and Genetics. 18. 34-48 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] A.Kidera, K.Inaka, M.Matsushima and N.go: "Response of Dynamics Structure to Removal of a Disulfide Bond : Normal Mode Refinement of C77/95A Mutant of Human Lysozyme" Protein Science. 3. 92-102 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] S.Sunada and N.Go: "Small Amplitude Protein Conformational Dynamics : Second Order Analytic Relation Between Cartesian Coordinates and Dihedral Angles" Journal of Computational Chemistry. (in press).

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1993 Final Research Report Summary
  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure Applied to Human Lysozyme" Biopolymers. 32. 315-319 (1992)

    • Related Report
      1993 Annual Research Report
  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure I.Theory and Test by Simulated Diffraction Data" J.Mol.Biol.225. 457-475 (1992)

    • Related Report
      1993 Annual Research Report
  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure II.Application to Human Lysozyme" J.Mol.Biol.225. 477-486 (1992)

    • Related Report
      1993 Annual Research Report
  • [Publications] K.Mizuguchi: "Collective motions in proteins investigated by X-ray diffuse scattering" Proteins:Structure,Function,and Genetics. 18. 34-48 (1994)

    • Related Report
      1993 Annual Research Report
  • [Publications] A.Kidera: "Response of Dyramic Structure to Removal of a Disulfide Bord:Normal Mode Refinement of C77A/C95A Mutant of Human Lysozyme" Protein Science. 3. 92-102 (1994)

    • Related Report
      1993 Annual Research Report
  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure Applied to Human Lysozyme" Biopolymers. 32. 315-319 (1992)

    • Related Report
      1992 Annual Research Report
  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure I.Theory and Test by Simulated Diffraction Data" J.Mol.Biol.225. 457-475 (1992)

    • Related Report
      1992 Annual Research Report
  • [Publications] A.Kidera: "Normal Mode Refinement:Crystallographic Refinement of Protein Dynamic Structure II.Application to Human Lysozyme" J.Mol.Biol.225. 477-486 (1992)

    • Related Report
      1992 Annual Research Report
  • [Publications] T.Yamato: "Conformational Deformation in Deoxymyoglobin by Hydrostatic Pressure" Proteins.

    • Related Report
      1992 Annual Research Report
  • [Publications] S.Hayward: "Effect of Solvent on Collective Motions in Globular Protein" J.Mol.Biol.

    • Related Report
      1992 Annual Research Report
  • [Publications] K.Mizuguchi: "Collective Motions in proteins investigated by X-ray diffuse scattering" Proteins.

    • Related Report
      1992 Annual Research Report
  • [Publications] 倭 剛久: "化学総説「生物無機化学の新展開、計算機実験」" 丸善出版,

    • Related Report
      1992 Annual Research Report

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Published: 1992-04-01   Modified: 2016-04-21  

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