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Informatics on hydration structures of proteis

Research Project

Project/Area Number 13480214
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionKeio University (2002)
The University of Tokyo (2001)

Principal Investigator

NAKASAKO Masayoshi  Faculty of Science and Technology, Department of Physics, Associate Professor, 理工学部, 助教授 (30227764)

Project Period (FY) 2001 – 2002
Project Status Completed (Fiscal Year 2002)
Budget Amount *help
¥8,800,000 (Direct Cost: ¥8,800,000)
Fiscal Year 2002: ¥2,100,000 (Direct Cost: ¥2,100,000)
Fiscal Year 2001: ¥6,700,000 (Direct Cost: ¥6,700,000)
KeywordsProteins / protein hydrations / Cryogenic Crystallography / Molecular dynamics simulation / qlass transition / bio-informatics / バイオイオンフォマティクス / バイオインフォマティクス / 蛋白質 / 水和構造 / 低温結晶解析 / 蛋白質水和 / X線結晶構造解析
Research Abstract

Hydration of protein is one of the most important subjects to study the function, folding and dynamics of the protein. Among many techniques investigating hydration structures of proteins, cryogenic X-ray crystallography and molecular dynamics simulation have provided much information on protein hydration. In this project, I studied the static and dynamical characteristics of hydration structures of proteins. In particular, in the crystal structure analysis of glutamate dehydrogenase, I observed the dynamical coupling of hydration structural changes and the domain motion. This is the first experimental evidence to reveals such coupling in protein motion. In addition I investigated the glassy transition occurring around 160 K for human lysozyme. Through molecular dynamics simulations of proteins, we found the selective orientation of water dipoles on the surface of proteins. The results of the present research may provide new insights into the dynamics and folding of proteins in aqueous solution.

Report

(3 results)
  • 2002 Annual Research Report   Final Research Report Summary
  • 2001 Annual Research Report
  • Research Products

    (47 results)

All Other

All Publications (47 results)

  • [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 SectionD. 58. 1421-1432 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] J.Higo, M.Nakasako: "Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses"Journal of Computational Chemistry. 23. 1323-1336 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M.Nakasako: "Structural characteristics in protein hydration investigated by cryogenic X-ray crystal structure analyses"Journal of Biological Physics. 28. 129-137 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M.Nakasako, F.Tsuchiya, Y.Arata: "Roles of hydration water molecules in molecular packing of the killer toxin in its crystalline state investigated by cryogenic X-ray crystallography"Biophysical Chemistry. 95. 211-225 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M.Nakasako, M.Sawano, M.Kawamoto: "An open-flow helium cryostat for cryogenic X-ray diffraction experiments"Review of Scientific Instruments. 73. 1318-1320 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T.Motoyama, M.Nakasako, I.Yamaguchi: "Crystallization of scytalone dehydratase F162A mutant in the unligated state and a preliminary X-ray diffraction study at 37 K"Acta Crystallographica SectionD. 58. 148-150 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M.Nakasako: "Large-scale networks of hydration water molecules around proteins investigated by cryogenic X-ray crystallography"Cellular and Molecular Biology. 47. 767-790 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] I.Endo, M.Nojiri, M.Tsujimura, M.Nakasako, S.Nagashima, et al.: "Fe-type Nitrile Hydratase"Journal of Inorganic Biochemistry. 83. 247-253 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M.Nakasako, T.Fujisawa, S.Adachi, T.Kudo, S.Higuchi: "Large-scale domain movements and hydration structure changes in the active-site cleft in unligated glutamate dehydrogenase from Thermococcus profundus"Biochemistry. 40. 3069-3079 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M.Nakasako, H.Nomura, H.Ogawa, C.Toyoshima: "Crystal structure analyses of membrane proteins : a case study for calcium pump from sarcoplasmic reticulum"The Japanese Journal of Pharmacology. 85. Suppl.I, S1-1 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 中迫雅由, 肥後順一: "蛋白質の水和構造"現代化学. No.374. 24-30 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 中迫雅由, 澤野成民, 河本正秀: "低温ヘリウムガス吹き付け型結晶冷却装置の開発"放射光. 15. 163-166 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 豊島 近, 中迫雅由, 野村博美, 小川治夫: "筋小胞体カルシウムポンプの構造決定"蛋白質・核酸・酵素. 46. 1374-1380 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 豊島 近, 中迫雅由, 野村博美, 小川治夫: "筋小胞体カルシウムポンプの構造決定"放射光. 14. 204-210 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M.Nakasako, M.Sawano, M.Kawamoto: "Development of an open-flow cryostat utilizing helium gas"The Rigaku Journal. 18. 47-53 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 中迫雅由, 澤野成民, 河本正秀: "低温ヘリウムガス吹き付け型結晶冷却装置の開発"理学電機ジャーナル. 32. 8-15 (2001)

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

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] J. Higo and M. Nakasako: "Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between and crystal-water sites, solvent-density and solvent-dipole"Journal of Computational Chemisty. 23. 1323-1336 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M. Nakasako: "Structural characteristics in protein hydration investigated by cryogenic X-ray crystal structure analyses"Journal of Biological Physics. 28. 129-137 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M. Nakasako. F Tsuchiya and Y. Arata: "Roles of hydration water molecules in molecular packing of the killer toxin in its crystalline state investigated by cryogenic X-ray crystallography"Biophysical Chemistry. 95. 211-225 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M. Nakasako. M. Sawano and M. Kawamoto: "An open-flow helium cryostat for cryogenic X-ray diffraction experiments"Review of Scientific instruments. 73. 1318-1320 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T. Motoyama, M. Nakasako and I. Yamaguchi: "Crystallization of scytalone dehydratase F162A mutant in the unligated state and a preliminary X-ray diffraction study at 37 K"Acta Crystallographica Section D. 58. 148-150 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M. Nakasako: "Large-scale networks of hydration water molecules around proteins investigated by cryogenic X-ray crystallography"Cellular and Molecular Biology. 47. 767-790 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M. Nakasako. T. Fujisawa, S. Adachi, T. Kudo and S. Higuchi: "Large-scale domain movements and hydration structure changes in the active-site cleft in unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering"Biochemistry. 40. 3069-3079 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] I. Endo, M. Nojiri, M. Tsujimura, M. Nakasako, S. Nagashima, M. Yohda and M. Odaka: "Fe-type Nitrite Hydratase"Journal of Inorganic Biochemistry. 83. 247-253 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M. Nakasako, M. Sawano and M. Kawamoto: "Development of an open-flow cryostat utilizing helium gas"The Rigaku Journal. 18. 47-53 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] M. Nakasako. H. Nomura, H. Ogawa and C.Toyoshima: "Crystal structure analyses of membrane proteins: a case study for calcium pump from sarcoplasmic reticulum"The Japanese Journal of Pharmacology. 85 Suppl.1. S1-1 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [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 SectionD. 58. 1421-1432 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] J.Higo, M.Nakasako: "Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses"Journal of Computational Chemistry. 23. 1323-1336 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] M.Nakasako: "Structural characteristics in protein hydration investigated by cryogenic X-ray crystal structure analyses"Journal of Biological Physics. 28. 129-137 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] M.Nakasako, F.Tsuchiya, Y Arata: "Roles of hydration water molecules in molecular packing ofthe killer toxin in its crystalline state investigated by cryogenic X-ray crystallography"Biophysical Chemistry. 95. 211-225 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] M.Nakasako, M.Sawano, M.Kawamoto: "An open-flow helium crystat for cryogenic X-ray diffraction experiments"Review of Scientific Instruments. 73. 1318-1320 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] T.Motoyama, M.Nakasako, I.Yaniaguchi: "Crystallization of scytalone dehydratase F162A mutant in the unligated state and a preliminary X-ray diffraction study at 37 K"Acta Crystallographica SectionD. 58. 148-150 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 中迫雅由, 肥後順一: "蛋白質の水和構造"現代化学. No.374. 24-30 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 中迫雅由, 澤野成民, 河本正秀: "低温ヘリウムス吹き付け型結晶冷却装置の開発"放射光. 15. 163-166 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] M.Nakasako: "Structural characteristics in protein hydration investigated by cryogenic X-ray crystal structure analyses"Journal of Biological Physics. (in press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.Nakasako, M.Sawano, M.Kawamoto: "An open-flow helium cryostat for cryogenic X-ray diffraction experiments"Review of Scientific Instruments. (in press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] T.Motoyama, M.Nakasako, I.Yamaguchi: "Crystallization of scytalone dehydratase F162A mutant in the unligated state and a preliminary X-ray diffraction study at 37 K"Acta Crystallographica Sect. D. (in press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.Nakasako, F.Tsuchiya, Y.Arata: "Roles of hydration water molecules in molecular packing of the killer toxin in its crystalline state investigated by cryogenic X-ray crystallography"Biophysical Chemistry. (in press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] I.Endo, M.Noziri, M.Tsujimura, M.Nakasako, S.Nagashima, et al.: "Fe-type Nitrile Hydratase"Journal of Inorganic Biochemistry. 83. 247-253 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.Nakasako, T.Fujisawa, S.Adachi, T.Kudo, S.Higuchi: "Large-scale domain movements and hydration structure changes in the active-site cleft in unligated glutamate dehydrogenase from Thermococcus profundus"Biochemistry. 40. 3069-3079 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.Nakasako, H.Nomura, H.Ogawa, C.Toyoshima: "Crystal structure analyses of membrane proteins : a case study for calcium pump from sarcoplasmic reticulum"The Japanese Journal of Pharmacology. 85(Suppl. I, Sl-1). (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 豊島 近, 中迫雅由, 野村博美, 小川治夫: "筋小胞体カルシウムポンプの構造決定"蛋白質・核酸・酵素. 46. 1374-1380 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 豊島 近, 中迫雅由, 野村博美, 小川治夫: "筋小胞体カルシウムポンプの構造決定"放射光. 14. 204-210 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] N.Nakasako, M.Sawano, M.Kawamoto: "Development of an open-flow cryostat utilizing helium gas"The Rigaku Journal. 18. 47-53 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 中迫雅由, 澤野成民, 河本正秀: "低温ヘリウムガス吹き付け型結晶冷却装置の開発"理学電機ジャーナル. 32. 8-15 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.Nakasako: "Large-scale networks of hydration water molecules around proteins investigated by cryogenic X-ray crystallography"Cellular and Molecular Biology. 47. 767-790 (2001)

    • Related Report
      2001 Annual Research Report

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Published: 2001-04-01   Modified: 2016-04-21  

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