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Thermodynamic Analysis of Protein Stability

Research Project

Project/Area Number 09044222
Research Category

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

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionOsaka University

Principal Investigator

YUTANI Katsuhide  Inst. Protein Res., Osaka Univ., Associate Prof., 蛋白質研究所, 助教授 (90089889)

Co-Investigator(Kenkyū-buntansha) NISHIKAWA Ken  National Inst. Genetics, Professor, 教授 (10093288)
MAKHATADZE G  テキサス, テック大学, 助教授
Project Period (FY) 1997 – 1999
Project Status Completed (Fiscal Year 1999)
Budget Amount *help
¥3,400,000 (Direct Cost: ¥3,400,000)
Fiscal Year 1999: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 1998: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 1997: ¥1,200,000 (Direct Cost: ¥1,200,000)
Keywordsstability of proteins / lysozyme / DSC / hydrogen bond / hydrophobic interaction / X-ray analysis / prediction of tertiary structure / stabilization factors of proteins
Research Abstract

Understanding how tertiary structures of proteins are coded for in their amino acid sequences is one of the main targets in modern life science research. However, this goal has not yet been achieved. One of the reasons is that a protein structure is prescribed not only by a part of the amino acid sequence but also by an extensive interaction. In fact, the same kinds of substitutions give different changes in conformational stability. These results show that the effect of a single amino acid substitution on protein stability depends on the location of the mutation site and its environment in the protein structure. In order to estimate the contribution of each factor to protein stability, the data of structure and stability changes must be expanded by studying many mutant proteins with systematic and comprehensive substitutions. In this project, we tried to estimate some factors that contribute to conformational stability of a protein using data base of stability/structure, which are obtained from a series of mutant human lysozymes. Then, we constructed more than 100 mutant human lysozymes. Changes in stabilities and structures due to mutations were evaluated by DSC and X-ray analysis, respectively. Using database of structure and stability changes due to mutations, which are obtained in this project, the magnitude of hydrophobicity of carbon atom (C), and the hydrophobicity of nitrogen and neutral oxygen atoms (N/O) could be estimated to be 0.178 kJ/mol/ÅィイD12ィエD1, and -0.013 kJ/mol/ÅィイD12ィエD1, respectively. The net contribution of an intramolecular hydrogen bond, an intermolecular one between protein and ordered water molecules, and an intermolecular one between ordered water molecules was estimated to be 8.5, 5.2, and 5.0 kJ/mol, respectively, for a hydrogen bond with 3 Å length. The entropic cost due to the introduction of a water molecule could be also estimated to be about 8 kJ/mol.

Report

(4 results)
  • 1999 Annual Research Report   Final Research Report Summary
  • 1998 Annual Research Report
  • 1997 Annual Research Report
  • Research Products

    (40 results)

All Other

All Publications (40 results)

  • [Publications] Takano, K. et al.: "Contribution of Intra- and Intermolecular Hygrogen Bonds to the Conformational Stability of Human Lysozyme"Biochemistry. 38. 12698-12708 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Funahashi, J. et al.: "Contribution of Amino Acid Substitutions at Two Different Interior Positions to the Stability of Human Lysozyme"Protein Engineering. 12. 841-850 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Lopez, M.M. et al.: "Interactions of the Major Cold Shock Protein of Bacillus subtilis CspB with Singlestranded DNA Templates of Different Base Composition"J. Biol. Chem.. 247. 33601-33608 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Takano, K. et al.: "Effect of Forign N-terminal Residues on the Conformational Stability of Human Lysozyme"Eur. Jap. Biochem.. 266. 675-682 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Takano, K. et al.: "Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme : Calorimetry and X-ray Analysis of Six Ser -> Ala Mutants"Biochemistry. 38. 6623-6629 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Takano, K. et al.: "Experimental verification of the "stability profile of mutant protein" (SPMP) data using mutant human lysozyme"Protein Engineering. 12. 663-672 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kaori Hiraga and Katsuhide Yutani: "Roles of Hydrogen Bonding Residues in the Interaction between the a and b Subunits in the Tryptophan Synthase Complex : Asn104 of the a Subunit is Especially Important."J.Biol. Chem.. 272. 4935-4940 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kazufumi Takano, Yuriko Yamagata, Satoshi Fujii, and Katsuhide Yutani: "Contribution of the 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)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kyoko Ogasahara and Katsuhide Yutani: "Equilibrium and Kinetic Analyses of Unfolding and Refolding for the Conserved Proline Mutants of Tryptophan Synthase a Subunit."Biochemistry. 36. 932-940 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Chieko Kobayashi, Yasuichiro Suga, Keizo Yamamoto, Tetsuya Yomo, Kyoko Ogasahara, Katsuhide Yutani, and Itaru Urabe: "Thermal Conversion from Low-to High-Activity Forms of Catalase I from Bacillus stearothermophilus."J. Biol. Chem.. 272. 23011-23016 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kazufumi Takano, Jun Funahashi, Yuriko Yamagata, Satoshi Fugii, and Katsuhide Yutani: "Contribution of Water Molecules in the Interior of a Protein to the Conforamtional Stability."J.Mol.Biol.. 274. 132-142 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Katsuhiko Aoki, Hideki Taguchi, Yoshitaka Shindo, Masasuke Yoshida, Kyoko Ogasahara, Katsuhide Yutani, and Naoko Tanaka: "Calorimetric Observation of a GroEL-Protein Binding Reaction with Little Contribution of Hydrohobic Interaction."J.Biol.Chem.. 272. 32158-32164 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kyoko Ogasahara, Elena A. Lapshina, Yukiko Izu, Susumu Tsunasawa, Ikunoshin Kato, and Katsuhide Yutani: "Electrostatic Stabilization in Methionine Aminopeptidase from Hyperthermophile."Biochemistry. 37. 5939-5946 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Yuriko Yamagata, Masahiro Kubota, Yohei Sumikawa, Jun Funahashi, Kazufumi Takano, Satoshi Fujii, and Katsuhide Yutani: "Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme : Calorimetry and X-ray Analysis of Six Tyr-> Phe Mutants."Biochemistry. 37. 9355-9362 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kazufumi Takano, Yuriko Yamagata, and Katsuhide Yutani: "A General Rule for the Relationship between hlydrophobic Effect and Conformational Stability of a Protein : Stability and Structure of a Series of Hydrophobic Mutants of Human Lysozymes."J.Mol.Biol.. 280. 749-761 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Tahir H. Tahirov, Hideyuki Oki, Tomitake Tsukihara, Kyoko Ogasahara, Katsuhide Yutani, Kazuhiro Ogata, Yukiko, Izu, Susumu Tsunasawa, and Ikunoshin Kato: "Crystal Structure of Methionine Aminopeptidase from Hyperthermophile, Pyrococcus furiosus."J.Mol.Biol.. 284. 101-124 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kyoko Ogasahara, Mamoru Nakamura, Satomi, Nakura, Susumu Tsunasawa, Ikunoshinn Kato, Tadashi Yoshi Yoshimoto, and Katsuhide Yutani: "Unusual Slow Unfolding Rate Causes the High Stability of Pyrrolidone Carboxyl Peptidase from a Hyperthermophile, Pyrococcus furiosus : Equilibrium and Kinetic Studies of Guanidine Hydrochloride-Induced Unfolding and Refolding."Biochemistry. 37. 17535-17544 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Ryota Kuroki and Katsuhide Yutani: "Structural and Thermodynamic Responses of Mutations at a Ca2+ Binding Site Engineered into Human Lysozyme"J Biol Chem. 273. 34310-34315 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kazufumi Takano, Yuriko Yamagata, Masahiro Kubota, Jun Funahashi, Satoshi Fujii, and Katsuhide Yutani: "Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme : Calorimetry and X-ray Analysis of Six Ser-> Ala Mutants"Biochemistry. 38. 6623-6629 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kazufumi Takano, Motonori Ota, Kyoko Ogasahara, Yuriko Yamagata, Ken Nishikawa, and Katsuhide Yutani: "Experimental verification of the "stability profile of mutant protein" (SPMP) data using mutant human lysozymes"Protein Engineering. 12. 663-672 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Kazufumi Takano, Yuriko Yamagata, Jun Funahashi, Yusaku Hioki, Seiki Kuramitsu, and Katsuhide Yutani: "Contribution of Intra-and Intermolecular Hydrogen Bonds to the Conformational Stability of Human Lysozyme"Boichemistry. 38. 12698-12708 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Maria M. Lopez, Katsuhide Yutani, and George I. Makhatadze: "Interactions of the Major Cold Shock Protein of Bacillus subtilis CspB with S"J.Biol.Chem.. 247. 33601-3608 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1999 Final Research Report Summary
  • [Publications] Takano,K. et al.: "Contribution of Intra-and Intermolecular Hydorgen Bonds to the Conformational Stability of Human Lysozyme"Biochemistry. 38. 12698-12708 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Funahashi,J. et al.: "Contribution of Amino Acid Substitutions at Two Different Interior Positions to the Stablity of Human Lysozyme"Protein Engineering. 12. 841-850 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Lopez,M.M. et al.: "Interactions of the Major Cold Shock Protein of Bacillus subtilis CspB with Single-stranded DNA Templates of Different Base composition"J.Biol.Chem.. 247. 33601-33608 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Takano,K. et al.: "Effect of Foreign N-terminal Residues on the Conformational Stability of Human Lysozyme"Eur.J.Biochem.. 266. 675-682 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Takano,K. et al.: "Contribution of Hydrogen Bond to the Conformational Stability of Human Lysozyme : Calorimetry and X-ray Analysis of Six Ser -> Ala Mutants"Biochemistry. 38. 6623-6629 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Takano,K. et al.: "Experimental verification of the ''stability profile of mutant protein''(SPMP) data using mutant human lysozymes"Protein Engineering. 12. 663-672 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] K.Ogasahara et al.: "Electrostatic Stabilization in Methionine Aminopeptidasc from Hyperthermophile." Biochemistry. 37. 5939-5946 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Y.Yamagata et al.: "Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme : Calorimetry and X-ray Analysis of Six Tyr->Phe Mutants." Biochemistry. 37. 9355-9362 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] K.Takano: "A General Rule for the Relationship between hydrophobic Effect and Conformational Stability of a Protein : Stability and Structure of a Series of Hydrophobic Mutants of Human Lysozymes." J.Mol.Biol.280. 749-761 (1998)

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

    • Related Report
      1998 Annual Research Report
  • [Publications] K.Ogasawara et al.: "Unsual Slow Unfolding Rate Causes the High Stability of Pyrrolidone Carboxyl Peptidase from a Hyperthermophile, Pyrococcus furiosus" Biochemistry. 37. 17535-17544 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] R.Kuroki & K.Yutani: "Structural and Thermodynamic Responses of Mutations at a Ca Binding Site Engineered into Human Lysozyme" J.Mol.Biol.273. 34310-34315 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Hiraga, K.& Yutani, K.: "Roles of Hydrogen Bonding Residues in the Interaction between the α and β Subunits in the Tryptophan Synthase Complex:Asn104 of the α Subunit is Especially Important" J.Biol.Chem.272. 4935-4940 (1997)

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

    • Related Report
      1997 Annual Research Report
  • [Publications] Takano, K.et al.,: "Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme:Calorimetric Studies and X-ray Structural Analyses of the Nine Val to Ala Mutants" Biochemistry. 36. 688-698 (1997)

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

    • Related Report
      1997 Annual Research Report
  • [Publications] Ota, M.& Nishikawa, K.,: "Assessment of the pseudo-energy potential by the best-five test:a new use of the three-dimensional profiles of proteins" Protein Engineering. 10. 339-351 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Ota, M.et al.,: "Structural requirement of highly-conserved residues in globins" FEBS Lett.,. 415. 129-133 (1997)

    • Related Report
      1997 Annual Research Report

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

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