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Studies on Protein Folding by the High-Pressure Temperature-Jump Method and Computer Simulations

Research Project

Project/Area Number 12480197
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionThe University of Tokyo

Principal Investigator

KUWAJIMA Kunihiro  Graduate School of Science, Department of Physics, Professor, 大学院・理学系研究科, 教授 (70091444)

Co-Investigator(Kenkyū-buntansha) 新井 宗仁  東京大学, 大学院・理学系研究科, 助手 (90302801)
Project Period (FY) 2000 – 2002
Project Status Completed (Fiscal Year 2002)
Budget Amount *help
¥14,700,000 (Direct Cost: ¥14,700,000)
Fiscal Year 2002: ¥2,800,000 (Direct Cost: ¥2,800,000)
Fiscal Year 2001: ¥2,500,000 (Direct Cost: ¥2,500,000)
Fiscal Year 2000: ¥9,400,000 (Direct Cost: ¥9,400,000)
KeywordsFolding / Temperature jump / Molecular Dynamics / Staphylococcal nuclease / α-Lactalbumin / Ca^<2+>-binding lysozyme / Unfolding / Denaturation / 蛋白質フォールディング / 分子動力学シミュレーション / 高圧 / スタフィロコッカルヌクレアーゼ / リゾチーム
Research Abstract

To elucidate the folding mechanism of proteins, the present study has been carried out with two objectives. (1) For the purpose of monitoring refolding kinetics of globular proteins in a time regime of microsecond to millisecond, we have developed a high-pressure Joule heating temperature-jump apparatus, tested the apparatus and improved its capability. (2) For the purpose of describing the folding process of proteins at an atomic level, we have carried out unfolding simulations of a protein at a high temperature (400〜600 K), and compared the results with known experimental data.
The following results were obtained.
(1) The high-pressure temperature-jump apparatus developed in the present study allows us to monitor the reactions by both ultraviolet absorption and fluorescence spectroscopy, and the pressure achieved was 1,800 atm at 25℃ and 1,200 atm at -4℃. Because many proteins are in the cold denatured state at -4℃ and 1,200 atm, it will be possible to monitor the folding reaction of the proteins in a microsecond time regime by the temperature-jump method.
(2) We have studied the refolding reaction of proline-free pseudo wild-type staphylococcal nuclease, which will be used as a model protein in the temperature-jump measurements. As a result, this protein has been found to refold along multiple parallel reaction pathways from the denatured state although the protein does not have proline residues. This finding is the first case in which the presence of multiple parallel pathways in protein folding is clearly shown.
(3) It has been known experimentally that a recombinant form of goat α-lactalbumin unfolds 100-fold faster than its authentic form. Here, we have reproduced the experimental results by unfolding simulations by molecular dynamics. Because of the presence of an additional methione residue at the N terminus in the recombinant protein, the structure near the N-terminus has been found to show significantly large fluctuations even at room temperature.

Report

(4 results)
  • 2002 Annual Research Report   Final Research Report Summary
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (67 results)

All Other

All Publications (67 results)

  • [Publications] Arai, M.: "Effect of an alternative disulfide bond on the structure, Stability, and folding of human lysozyme"Biochemistry. 39. 3472-3479 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M.: "The role of the molten globule state in protein folding"Adv Protein Chem. 53. 209-282 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Chaudhuri, T.K.: "Equilibriun and kinetic studies on folding of the suthentic and recombimant Forms of human alpha_lactalbumin by circular dichroism spectroscopy"Biochemistry. 39. 15643-15651 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Fukuda, H.: "Folding of green fluorescent protein snd the cycle3 mutant"Biochemistry. 39. 12025-12032 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Ikura, T.: "Fast folding of Escherichia coli cyclophilim A : a hypothesis of a unique Hydrophobic core with a phenylalanine cluster"J Mol Biol. 297. 791-802 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kobashigawa, Y.: "Hydrogen exchange study of canine milk lysozyme : stabilization mechanism of the molten globule"Proteins. 40. 579-589 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kuwajima, K.: "The Role of the Molten Globule State in Protein Folding : The Search for a Universal View of Folding"Proc Indian Nat Sci Acad. 68. 333-340 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kuwajima, K.: "Chaperone-Affected Folding of Globular Proteins"J Biol Phys. 28. 77-93 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kuwajima, K.: "The use of the time-resolved X-ray solution scattering for studies of globular proteins"Spectroscopy--Int J. 16. 127-138 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M.: "Denaturation and reassembly of chaperonin GroEL studied by solution X-ray scattering"Protein Sci. 12. 672-680 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Inobe, T.: "Equilibrium and Kimetics of the Allostoric Transition of GroEL Studied By Solution X-ray Scattering and Fluorescence Spectroscopy"J Mol Biol. 327. 183-191 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Inobe, T.: "The Allosteric Transition of GroEL induced by Metal Fluoride-ADP Complexes"J Mol Biol. 329. 121-134 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Koshiba, T.: "Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme"Biochemistry. 39. 3248-3257 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Horii, K.: "Contribution of Thr29 to the thermodynamic stability of goat alpha laetalbumin as determined by experimental and theoretical approaches"Proteins. 45. 16-29 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Inobe, T.: "Nucleotide binding to the chaperonin GroEL. non-cooperative binding of ATP analogs and ADP, and cooperative effect of ATP"Biochim Biophys Acta. 1545. 160-173 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Makio, T.: "Nucleotide-induced transition of GroEL from the high-affinity to the low affinity state for a target protein : Effects of ATP and ADP on the GroEL-affected refolding of alpha-lactalbumin"J Mol Biol. 312. 555-567 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Yoda, T.: "Folding-unfolding of goat alpha-lactalbumin studied by stopped-flow circiular diehroism and molecular dynamics simulations"Proteins. 42. 49-65 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M.: "Fast Compaction of alpha-Lactalbumin During Folding Studied by Stopped-flow X-ray Scattering"J Mol Biol. 321. 121-132 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Nakao, M.: "Folding mechanism of canine milk lysozyme studied by circular dichroism and fluorescence spectroscopy"Spectroscopy--Int J. (印刷中). (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kamagata, K.: "Parallel folding pathway of prolimc-free staphylococcal nuclease studied by the stopped-flow double-jump method"Spectroscopy--Int J. (印刷中). (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M.: "Effeets of the Difference in the Unfoided-State Ensemble on the Folding of Escherichia coil Dihydrofolate Reductase"J Mol Biol. (印刷中). (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 桑島 邦博: "フォールディング:ゲノム科学と物理化学との接点"生物物理. 40. 310-311 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 後藤 祐児: "序論 ポストゲノム時代のフォールディング研究"蛋白質 核酸 酵素. 47. 653-655 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 桑島 邦博: "蛋白質フォールディングの2つの描像 普遍的描像は可能か?"蛋白質 核酸 酵素. 47. 657-662 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M., Hamel, P., Kanaya, E., Inaka, K., Miki, K., Kikuchi, M. & Kuwajima, K.: "Effect of an alternative disulfide bond on the structure, stability, and folding of human lysozyme"Biochemistry. 39. 3472-3479 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M. & Kuwajima, K: "The role of the molten globule state in protein folding"Adv Protein Chem. 53. 209-282 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Chaudhuri, T.K., Arai, M., Terada, T.P. Ikura, T. & Kuwajima, K.: "Equilibrium and kinetic studies on folding of the authentic and recombinant forms of human alpha-lactalbumin by circular dichroism spectroscopy"Biochemistry. 39. 15643-15651 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Fukuda, H., Arai, M. & Kuwajima, K.: "Folding of green fluorescent protein and the cycle3 mutant"Biochemistry. 39. 12025-12032 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Ikura, T., Hayano, T., Takahashi, N. & Kuwajima, K.: "Fast folding of Escherichia coli cyclophilin A : a hypothesis of a unique hydrophobic core with a phenylalanine cluster"J Mol Biol. 297. 791-802 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kobashigawa, Y., Demura, M., Koshiba, T., Kumaki, Y., Kuwajima, K. & Nitta, K.: "Hydrogen exchange study of canine milk lysozyme : stabilization mechanism of the molten globule"Proteins. 40. 579-589 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Koshiba, T., Yao, M., Kobashigawa, Y., Demura, M., Nakagawa, A., Tanaka, I., Kuwajima, K. & Nitta, K.: "Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme"Biochemistry. 39. 3248-3257 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Horii K., Saito, M., Yoda, T., Tsumoto, K., Matsushima, M., Kuwajima, K. & Kumagai, I.: "Contribution of Thr29 to the thermodynamic stability of goat alpha-lactalbumin as determined by experimental and theoretical approaches"Proteins. 45. 16-29 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Inobe, T., Makio, T., Takasu-Ishikawa, E., Terada, T.P. & Kuwajima, K.: "Nucleotide binding to the chaperonin GroEL : non-cooperative binding of ATP analogs and ADP, and cooperative effect of ATP"Biochim Biophys Ada. 1545. 160-173 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Makio, T., Takasu-Ishikawa, E. & Kuwajima, K.: "Nucleotide-induced transition of GroEL from the high-affinity to the low-affinity state for a target protein : Effects of ATP and ADP on the GroEL-affected refolding of alpha-lactalbumin"J Mol Biol. 312. 555-567 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Yoda, T., Saito, M., Arai, M., Horii, K., Tsumoto, K., Matsushima, M., Kumagai, I. & Kuwajima, K.: "Folding-unfolding of goat alpha-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations"Proteins. 42. 49-65 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M., Ito, K., Inobe, T., Nakao, M., Maki, K., Kamagata, K., Kihara, H., Amemiya, Y. & Kuwajima, K.: "Fast Compaction of alpha-Lactalbumin During Folding Studied by Stopped-flow X-ray Scattering"J Mol Biol. 321. 121-132 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kuwajima, K.: "The Role of the Molten Globule State in Protein Folding : The Search for a Universal View of Folding"Proc Indian Nat Sci Acad. 68. 333-340 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kuwajima, K., Makio, T. & T. Inobe: "Chaperone-Affected Folding of Globular Proteins"J Biol Phys. 28. 77-93 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kuwajima, K, Arai, M., Inobe, T., Ito, K., Nakao, M., Maki, K., Kamagata, K., Kihara, H. & Amemiya Y.: "The use of the time-resolved X-ray solutions scattering for studies of globular proteins"Spectroscopy-Int J. 16. 127-138 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M., Inobe, T., Maki, K., Ikura, T., Kihara, H., Amemiya, Y. & Kuwajima, K.: "Denaturation and reassembly of chaperonin GroEL studied by solution X-ray scatterihg"Protein Sci. 12. 672-680 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Inobe, T., Arai, M., Nakao, M., Ito, K., Kamagata, K., Makio, T., Amemiya, Y., Kihara, H. & Kuwajima, K.: "Equilibrium and Kinetics of the Allosteric Transition of GroEL Studied by Solution X-ray Scattering and Fluorescence Spectroscopy"J Mol Biol. 327. 183-191 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Inobe, T., Kikushima, K., Makio, T., Arai, M. & Kuwajima, K.: "The Allosteric Transition of GroEL induced by Metal Fluoride-ADP Complexes"J Mol Biol. 329. 121-134 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Nakao, M., Arai, M., Koshiba, T., Nitta, K; & Kuwajima, K.: "Folding mechanism of canine milk lysozyme studied by circular dichroism and fluorescence spectroscopy"Spectroscopy-lnt J. in press. (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Kamagata, K. & Kuwajima, K.: "Parallel folding pathway of proline-free staphylococcal nuclease studied by the stopped-flow double-jump method"Spectrascopy-Int J. in press. (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Arai, M., Kataoka, M., Kuwajima, K., Matthews, C.R. & Iwakura, M.: "Effects of the Difference in the Unfolded-State Ensemble on the Folding of Escherichia coli Dihydrofolate Reductase"J Mol Biol. in press. (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] K.Kuwajima: "Chaperone-Affected Folding of Globular Proteins"J. Biol. Phys.. 28. 77-93 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 桑島 邦博: "蛋白質フォールディングの2つの描像:普遍的描像は可能か?"蛋白質 核酸 酵素. 47・6. 657-662 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] K.Kuwajima: "The Role of the Molten Globule State in Protein Folding : The Search for a Universal View of Folding"Proc. Indian Nat. Sci. Acad.. 68. 333-240 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] K.Kuwajima: "The use of the time-resolved X-ray solution scattering for studies of globular proteins"Spectroscopy : an international J.. 16. 127-138 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] M.Arai: "Fast Compaction of alpha-lactalbumin During Folding Studied by Stopoed-Flow X-rav Scattering"J. Mol. Biol.. 321. 121-132 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] T.Inobe: "Equilibrium and Kinetics of the Allosteric Transition of GroEL Studied by Solution X-ray Scattering and Fluorescence Spectroscopy"J. Mol. Biol.. 327. 183-191 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] K.Horii: "Contribution of Thr29 to the thermodynamic stability of goat alpha-lactalbumin as determined by experimental and theoretical approaches"Proteins. 45. 16-29 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] T.Makio: "Nucleotide-Induced Transition of GroEL from the High-affinity to the Low-affinity State for a Target Protein : Effect of ATP and ADP on the GroEL-Affected Refolding of alpha-Lactalbumin"J.Mol.Biol.. 312. 555-567 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] T.Inobe: "Nucleotide binding to the chaperonin GroEL : Noncooperative binding of ATP analogs and ADP, and cooperative effect of ATP"Biochimica et Biophysica Acta. 1545. 160-173 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] K.Kuwajima: "Chaperonin-Affected Folding of Globular Proteins"J.Biol.Phys.. 28(印刷中). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] 桑島 邦博: "蛋白質フォールディングの2つの描像:普遍的描像は可能か?"蛋白質 核酸 酵素. (印刷中).

    • Related Report
      2001 Annual Research Report
  • [Publications] Inobe,T.,Makio,T.,Takasu-Ishikawa,E.,Terada,T.P.and Kuwajima,K.: "Nucleotide binding to the chaperonin GroEL : Noncooperative binding of ATP analogs and ADP, and cooperative effect of ATP"Biochim.Biophys.Acta. (印刷中). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Yoda.T.,Saito,M.,Arai,M.;Horii,K.,Tsumoto,K.,Matsushima,M.,Kumagai,I.and Kuwajima,K.: "Folding-unfolding of goat alpha-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations."Proteins. 42. 49-65 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Arai,M.,Hamel,P.,Kanaya,E.,Inaka,K.,Miki,K.,Kikuchi,M.and Kuwajima,K.: "Effect of an alternative disulfide bond on the structure, stability, and folding of human lysozyme."Biochemistry. 39. 3472-3479 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Arai,M.and Kuwajima,K.: "Role of the molten globule state in protein folding."Adv.Protein Chem.. 53. 209-282 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Chaudhuri,T.K.,Arai,M.,Terada,T.P.,Ikura,T. and Kuwajima,K.: "Equilibrium and kinetic studies on folding of the authentic and recombinant forms of human alpha-lactalbumin by circular dichroism spectroscopy."Biochemistry. 39. 15643-15651 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Forge,V.,Hoshino,M.,Kuwata,K.,Arai,M.,Kuwajima,K.,Batt,C.A.and Goto,Y.: "Is folding of beta-Lactoglobulin non-hierarchic?Intermediate with native-like beta-sheet and non-native alpha-helix."J.Mol.Biol.. 296. 1039-1051 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Fukuda,H.,Arai,M.and Kuwajima,K.: "Folding of green fluorescent protein and the cycle3 mutant."Biochemistry. 39. 12025-12032 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Ikura,T.,Hayano,T.,Takahashi,N.and Kuwajima,K.: "Fast folding of Escherichia coli cyclophilin A : a hypothesis of a unique hydrophobic core with a phenylalanine cluster."J.Mol.Biol.. 297. 791-802 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Kobashigawa,Y.,Demura,M.,Koshiba,T.,Kumaki,Y.,Kuwajima,K.and Nitta,K.: "Hydrogen exchange study of canine milk lysozyme : stabilization mechanism of the molten globule."Proteins. 40. 579-589 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Koshiba,T.,Yao,M.,Kobashigawa,Y.,Demura,M.,Nakagawa,A.,Tanaka,I.,Kuwajima,K.and Nitta,K.: "Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme."Biochemistry. 39. 3248-3257 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] 桑島邦博: "-タンパク質フォールディング-ゲノム科学と物理化学との接点"生物物理. 40(5). 310-311 (2000)

    • Related Report
      2000 Annual Research Report

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Published: 2000-04-01   Modified: 2016-04-21  

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