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Administration of researches on principles of protein architecture

Research Project

Project/Area Number 07280102
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Research InstitutionKYOTO UNIVERSITY

Principal Investigator

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

Co-Investigator(Kenkyū-buntansha) KUWAJIMA Kunihiro  Kuwajima Grad. Schi. Sci.., Univ. Tokyo, Assoc. Prof, 大学院・理学研究科, 教授 (70091444)
WAKO Hiroshi  Schi. Soc. Sci., Waseda Univ., Professor, 社会科学部, 教授 (60158607)
YUTANI Katsuhide  Inst. Protein Res., Osaka Univ., Assoc, 蛋白質研究所, 助教授 (90089889)
KITAO Akio  Grad. Schl. Sci., Kyoto Univ., Assistant, 大学院・理学研究科, 助手 (30252422)
KIDERA Akinori  Grad. Schl. Sci., Kyoto Univ., Assoc. Prof, 大学院・理学研究科, 助教授 (00186280)
中村 春木  生物分子工学研究所, 情報解析研究部門, 部門長
大島 泰郎  東京薬科大学, 生命科学部, 教授 (60167301)
阿久津 秀雄  横浜国立大学, 工学部, 教授 (60029965)
郷 通子  名古屋大学, 大学院・理学研究科, 教授 (70037290)
野口 俊之  名古屋大学, 理学部, 助教授 (90172775)
Project Period (FY) 1995 – 1999
Project Status Completed (Fiscal Year 1999)
Budget Amount *help
¥49,700,000 (Direct Cost: ¥49,700,000)
Fiscal Year 1999: ¥3,000,000 (Direct Cost: ¥3,000,000)
Fiscal Year 1998: ¥10,600,000 (Direct Cost: ¥10,600,000)
Fiscal Year 1997: ¥11,500,000 (Direct Cost: ¥11,500,000)
Fiscal Year 1996: ¥12,300,000 (Direct Cost: ¥12,300,000)
Fiscal Year 1995: ¥12,300,000 (Direct Cost: ¥12,300,000)
KeywordsProtein / Three-dimensional structure / Folding / Stability / Structural prediction / Design / Dynamics / Principle of architecture / タンパク質 / 出版 / 公開講演会 / 進化 / 機能 / 折れたたみ / 比較・分類 / 比較分類
Research Abstract

The research project, "Principle of Protein Architecture," has continued its activity during FY1995-1998 for the purpose of pursuing an evolutional and/or physicochemical solution to the question "how the information of protein's three dimensional structure and function is coded in its amino acid sequence."
When starting this project, we had relied on the hypothesis that the variety of protein folds is limited to a rather small number, about one thousand. Based on such a hypothesis, we imagined a realization of the prediction of protein structures using the 'threading' method. The results of the research done for the four years show adual and significant improvements in terms of the practical goal of prediction, but with no clear-cut success, indicating the essentially complex nature of the problem.
Together with organizing such forefront research efforts, we contributed significantly to the activation of the related fleldsin Japan. To the open workshop we organized annually, more than 4 … More 00 participants and more than 200 poster presentations were contributed.
In FY1999, we carried out of activities of organizing the research results made during the four years and disseminating them widely to academic and more general public. In particular we (1) prepared publication of a monograph covering the research results, and (2) organized an open workshop. (1) We have carried out planning of publication of the research results as a special volume of "Protein, Enzyme and Nucleic Acid," which is one of the most important review journal in Japan. We had editorial meetings twice in order to discuss the basic concept of the planned volume. We will soon propose the publication to the publisher. (2) At first we organized an open workshop, which is a continuation of a series of symposia we have had organized annually during the tenure of the Grant-in-Aid Scientific Research, also this year on June 14 at Kanagawa Prefectural Hall. The workshop was very active, having more than 350 participants. Less

Report

(6 results)
  • 1999 Annual Research Report   Final Research Report Summary
  • 1998 Annual Research Report
  • 1997 Annual Research Report
  • 1996 Annual Research Report
  • 1995 Annual Research Report
  • Research Products

    (45 results)

All Other

All Publications (45 results)

  • [Publications] A. Kitao and N. Go: "Investigating protein dynamics in collective coordinate space"Current Opinion in Structural Biology. 9. 164-169 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] A. Matsumoto and N. Go: "Dynamical properties of double-standed DNA by normal mode analysis"J. Chem. Phys.. 110. 11070-11075 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] O. Miyashita and N. Go: "Dependence of protein electron transfer reaction theory and simulation"J. Phys. Chem.. 103. 562-571 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] K. Maki, T. Ikura, T. Hayano, N. Takahashi, K. Kuwajima: "Effects of proline mutations on the folding of staphylococcal nuclease"Biochemistry. 38. 2213-2223 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] T.K. Chavdhuri et al., K. Kuwajima, and T. Kumagai: "Effect of the extra N-terminal methionine residue on the stability and folding of recombinant alpha-lactibarium expressed in Escherichia coli"J. Mol. Biol.. 285. 1179-1194 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] K. Fujiwara, M. Arai, A. Shimizu, M. Ikeguchi, K. Kuwajima, S. Sugai: "Folding-unfolding equilibrium and kinetics of equine beta-lactoglobulin : Equivalence between quibrium molten globule state and a burst-phase folding intermediate"Biochemistry. 38. 4455-4463 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] A. Kitao and N. Go: "Investigating Protein Dynamics in Collective Coordinate Space"Current Opinion in Structural Biology. 9-2. 164-169 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] A. Matsumoto and N. Go: "Dynamical Properties of Double-Stranded DNA by Normal Mode Analysis"J. Chem. Phys. 110-22. 11070-11075 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] O. Miyashita and N. Go: "Pressure Dependence of Protein Electron Transfer Reaction Theory and Simulation"J. Phys. Chem. 103-3. 562-571 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] K. Maki, T. Ikura, T. Hayano, N. Takahashi, K. Kuwajima: "Effects of poline mutations on the folding of staphylococcal nuclease"Biochemistry. 28. 2213-2223 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] T.K.Chaudhuri et al., K. Kuwajima, and T. Kumagai: "Effect of the extra N-terminal methionine residue on the stability and folding of recombinant alpha-lactiburium expressed in Escherichia coli"J. Mol. Biol. 285. 1179-1194 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] K. Fujiwara, M. Arai, A. Shimizu, M. Ikeguchi, K. Kuwajima, S. Sugai: "Folding-unfolding equibrium and kinetics of equine beta-lactoblobulin : Equivalence between quibrium molten globule state and a burst-phase folding intermediate"Biochemistry. 38. 4455-4463 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] A. Kitao and N. Go: "Investigating protein dynamics in collective coordinate space"Current Opinion in Structural Biology. 9. 164-169 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] A. Matsumoto and N. Go: "Dynamical Properties of double-stonded DNA by normal mody analysis"J. Chem. Phys.. 110. 11070-11075 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] O. Miyashita and N. Go: "Dependence of protein electron transfer reaction theory and simulation"J. Phys. Chem.. 103. 562-571 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] K. Maki, T. Ikura, T. Hayano, N. Takahashi, and K. Kuwajima: "Effects of proline mutations on the folding of staphylococcal nuclease"Biochemistry. 38. 2213-2223 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] T. K. Chaudhuri et. al., K. Kuwajima, and I. Kumagai: "Effect of the extra N-terminal methionine residue on the stability and folding of recombinant alpha-lactiburium expressed in Escherichia coli"J. Mol. Biol.. 285. 1179-1194 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] K. Fujiwara, M. Arai, A.Shimizu, M. Ikeguchi, K. Kuwajima, S. Sugai: "Folding-unfolding equilibrium and kinetics of equine beta-lactoglobulin : Equivalence between equibrium molten globule state and a burst-phase folding intermediate"Biochemistry. 38. 4455-4463 (1999)

    • Related Report
      1999 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." J.Phys.Chem.12. 11-14 (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] T.H.Tahirov: "Crystal Structure of Methionine Aminopeptidase from Hyperthermophile, Pyrococcus furiosus." J.Mol.Biol.284. 101-124 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Y.Koga: "Thermostable glycerol kinase from a hyperthermophilic archaeon: gen cloning and characterization of the recombinant enzyme." Prot.Eng.11. 1219-1227 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] H.Wako: "Novel method to detect a motif of local structures in deifferent protein conformations." Prot.Eng.11. 981-990 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] K.Fujiwara: "Folding-unfolding equilibriumn and kinetics of equine beta-lactoglobulin: Equivalence between the equibrium molten globule state and a burst phase intermediate" Biochemistry. (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] K.Kinoshita: "Implication of symmetry of protein structures emerged from structure comparison study" Protein Science. (in press). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] 油谷 克英: "シリーズ分子生物学第6巻、構造生物学" 朝倉書店, 9 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] 油谷 克英: "タンパク質のアミノ酸置換と安定性、熱量測定・熱分析ハンドブック" 丸善株式会社, 1 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] N.Go: "ATP binding proteins with different folds share a common ATP-binding structure motif" Nature Structural Biology. 4. 6-7 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] K.Yutani: "Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability" J.Mol.Biol.274. 132-142 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] H.Nakamura: "Two-component multicanonical Monte Carlo method for effective conformation sampling" J.Comput.Chem.18. 2086-2092 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] S.Kidokoro: "Special folding pathway to tetramer only through the micelle state of the corticotropin-releasing factor" Biochemistry. 36. 15538-15545 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] A.Kitao: "Model-Free Methods of Analyzing Domain Motions in Proteins From Simulation : A Comparison of Normal Mode Analysis and Molecular Dynamics Simularion of Lysozyme" Proteins. 27. 425-437 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] M.Go: "Adaptive amino acid replacements accompanied by domain fusion in reverse transcript" J.Mol.Biol.44. (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] M.Go: "Adaptive amino acid replacements accompanied by domain fusion in reverse transcript" J.Mol.Biol.44. (1997)S115-S162

    • Related Report
      1997 Annual Research Report
  • [Publications] N.Go: "ATP binding proteins with different folds share a common ATP-binding structural motif." Nature Structural Biology. 4. 6-7 (1997)

    • Related Report
      1996 Annual Research Report
  • [Publications] N.Go: "Calculation of NMR Order Parameters in Proteins by Normal Mode Analysis 2 : Contribution from Localized High Frequency Motions." Journal of Chemical Physics. 105. 6560-6564 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] K.Yutani: "Equilibrium and kinetic Analyses of Unfolding and Refolding for the Conserved Proline Mutants of Tryptophan Synthase a Subunit." Biochemistry. 36. 932-940 (1997)

    • Related Report
      1996 Annual Research Report
  • [Publications] K.Yutani: "Contribution of Hydrophobic Effect to the Stability of Human Lysozyme : Calorimetric Studies and X-ray Structural Analyses of the Nine Valine to Alanine Mutants" Biochemistry. 36. 688-698 (1997)

    • Related Report
      1996 Annual Research Report
  • [Publications] M.Go: "Site-specific Mutagenesis of Rhodobacter capsulatus Ferredoxin I,FdxN,Taht Functions in Nitrogen Fixation : Role of Extra Residues." Journal of Biological Chemistry. 271. 31399-31406 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] K.Kuwajima: "Structural characterization of the molten globule of alpha-lactalbumin by solution X-ray Scattering" Protein Science. 6. 416-430 (1997)

    • Related Report
      1996 Annual Research Report
  • [Publications] K. Mizuguchi: "Seeking Significance in Three-Dimensional Protein Structure Comparison" Current Opinion in Structural Biology. 5. 377-382 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] S. Hayward: "Collectire Variable Description of Native Protein Dynamics" Annual Review of Physical Chemistry. 46. 223-250 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] K. Takano: "Contribution of Hydrophobic Residues to the Stability of Human Lysozy me: Calorimetric Studies and X-ray Structural Analysis of the Fire Isoleucine to Valine Mutants" J. Mol. Biol.254. 62-76 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] K. Yamazaki: "Folding Pathway of Escherichia coli Ribonuclease HI: A Ciraular Dichroism, Fluorescence, and NMR Study" Biochemistry. 34. 16552-16562 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] T. Noguti: "Insect Prothoracicotropic Hormone : A New Member of the Vertebrate Growth Factor Superfamily" FEBS Lett.376. 251-256 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] K. Kuwajima: "The Molten Globule State of Alpha-Lactalbumin" FASEB J.10. 102-109 (1996)

    • Related Report
      1995 Annual Research Report

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Published: 1995-04-01   Modified: 2019-02-15  

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