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Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme.

Funahashi J, Takano K, Yamagata Y, Yutani K
Protein Eng 12 841-50 (1999)
Related entries: 2mea, 2meb, 2mec, 2med, 2mee, 2mef, 2meg, 2mei

Cited: 29 times
EuropePMC logo PMID: 10556244

Abstract

To elucidate correlative relationships between structural change and thermodynamic stability in proteins, a series of mutant human lysozymes modified at two buried positions (Ile56 and Ile59) were examined. Their thermodynamic parameters of denaturation and crystal structures were studied by calorimetry and X-ray crystallography. The mutants at positions 56 and 59 exhibited different responses to a series of amino acid substitutions. The changes in stability due to substitutions showed a linear correlation with changes in hydrophobicity of substituted residues, having different slopes at each mutation site. However, the stability of each mutant was found to be represented by a unique equation involving physical properties calculated from mutant structures. By fitting present and previous stability data for mutant human lysozymes substituted at various positions to the equation, the magnitudes of the hydrophobicity of a carbon atom and the hydrophobicity of nitrogen and neutral oxygen atoms were found to be 0.178 and -0.013 kJ/mol.A(2), respectively. It was also found that the contribution of a hydrogen bond with a length of 3.0 A to protein stability was 5.1 kJ/mol and the entropy loss of newly introduction of a water molecules was 7.8 kJ/mol.

Articles - 2meh mentioned but not cited (1)

  1. Effect of dC → d(m5C) substitutions on the folding of intramolecular triplexes with mixed TAT and C+GC base triplets. Carr CE, Ganugula R, Shikiya R, Soto AM, Marky LA. Biochimie 146 156-165 (2018)


Articles citing this publication (28)

  1. Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes. Gianese G, Bossa F, Pascarella S. Proteins 47 236-249 (2002)
  2. Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior. Loladze VV, Ermolenko DN, Makhatadze GI. J Mol Biol 320 343-357 (2002)
  3. Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs. Wohlkönig A, Huet J, Looze Y, Wintjens R. PLoS One 5 e15388 (2010)
  4. Stability scale and atomic solvation parameters extracted from 1023 mutation experiments. Zhou H, Zhou Y. Proteins 49 483-492 (2002)
  5. Buried water molecules contribute to the conformational stability of a protein. Takano K, Yamagata Y, Yutani K. Protein Eng 16 5-9 (2003)
  6. Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins? Funahashi J, Takano K, Yutani K. Protein Eng 14 127-134 (2001)
  7. Impact of the native-state stability of human lysozyme variants on protein secretion by Pichia pastoris. Kumita JR, Johnson RJ, Alcocer MJ, Dumoulin M, Holmqvist F, McCammon MG, Robinson CV, Archer DB, Dobson CM. FEBS J 273 711-720 (2006)
  8. Effect of foreign N-terminal residues on the conformational stability of human lysozyme. Takano K, Tsuchimori K, Yamagata Y, Yutani K. Eur J Biochem 266 675-682 (1999)
  9. Effect of extra N-terminal residues on the stability and folding of human lysozyme expressed in Pichia pastoris. Goda S, Takano K, Yamagata Y, Katakura Y, Yutani K. Protein Eng 13 299-307 (2000)
  10. Interatomic potentials and solvation parameters from protein engineering data for buried residues. Lomize AL, Reibarkh MY, Pogozheva ID. Protein Sci 11 1984-2000 (2002)
  11. Knowledge-based potential defined for a rotamer library to design protein sequences. Ota M, Isogai Y, Nishikawa K. Protein Eng 14 557-564 (2001)
  12. Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: gene V protein mutants. Fernández L, Caballero J, Abreu JI, Fernández M. Proteins 67 834-852 (2007)
  13. Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. Verma D, Jacobs DJ, Livesay DR. PLoS Comput Biol 8 e1002409 (2012)
  14. Hydrophobic effect on the stability and folding of a hyperthermophilic protein. Dong H, Mukaiyama A, Tadokoro T, Koga Y, Takano K, Kanaya S. J Mol Biol 378 264-272 (2008)
  15. Tolerance of point substitution of methionine for isoleucine in hen egg white lysozyme. Ohmura T, Ueda T, Hashimoto Y, Imoto T. Protein Eng 14 421-425 (2001)
  16. Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes. Saraboji K, Gromiha MM, Ponnuswamy MN. Comput Biol Chem 29 25-35 (2005)
  17. A non-natural variant of human lysozyme (I59T) mimics the in vitro behaviour of the I56T variant that is responsible for a form of familial amyloidosis. Hagan CL, Johnson RJ, Dhulesia A, Dumoulin M, Dumont J, De Genst E, Christodoulou J, Robinson CV, Dobson CM, Kumita JR. Protein Eng Des Sel 23 499-506 (2010)
  18. Predicting the melting point of human C-type lysozyme mutants. Verma D, Jacobs DJ, Livesay DR. Curr Protein Pept Sci 11 562-572 (2010)
  19. Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme. Takano K, Yamagata Y, Yutani K. Proteins 44 233-243 (2001)
  20. The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors. Hioki Y, Ogasahara K, Lee SJ, Ma J, Ishida M, Yamagata Y, Matsuura Y, Ota M, Ikeguchi M, Kuramitsu S, Yutani K. Eur J Biochem 271 2624-2635 (2004)
  21. The Significance of the Location of Mutations for the Native-State Dynamics of Human Lysozyme. Ahn M, Hagan CL, Bernardo-Gancedo A, De Genst E, Newby FN, Christodoulou J, Dhulesia A, Dumoulin M, Robinson CV, Dobson CM, Kumita JR. Biophys J 111 2358-2367 (2016)
  22. Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein. Takano K, Yamagata Y, Yutani K. Proteins 45 274-280 (2001)
  23. Protein Evolution is Potentially Governed by Protein Stability: Directed Evolution of an Esterase from the Hyperthermophilic Archaeon Sulfolobus tokodaii. Kurahashi R, Sano S, Takano K. J Mol Evol 86 283-292 (2018)
  24. Crystal structure of glucose-6-phosphate isomerase from Thermus thermophilus HB8 showing a snapshot of active dimeric state. Yamamoto H, Miwa H, Kunishima N. J Mol Biol 382 747-762 (2008)
  25. Molecular dynamics study of naturally existing cavity couplings in proteins. Barbany M, Meyer T, Hospital A, Faustino I, D'Abramo M, Morata J, Orozco M, de la Cruz X. PLoS One 10 e0119978 (2015)
  26. Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry. Asada Y, Sawano M, Ogasahara K, Nakamura J, Ota M, Kuroishi C, Sugahara M, Yutani K, Kunishima N. J Biochem 138 343-353 (2005)
  27. Dimeric crystal structure of rabbit L-gulonate 3-dehydrogenase/lambda-crystallin: insights into the catalytic mechanism. Asada Y, Kuroishi C, Ukita Y, Sumii R, Endo S, Matsunaga T, Hara A, Kunishima N. J Mol Biol 401 906-920 (2010)
  28. The mutational effect of Ile58 at subsite C in hen egg-white lysozyme on substrate binding, enzymatic activity, and protein stability. Kawamura S, Chijiiwa Y, Torikata T, Araki T. Biosci Biotechnol Biochem 77 560-565 (2013)


Related citations provided by authors (5)

  1. Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyr-->Phe Mutants. Yamagata Y, Kubota M, Sumikawa Y, Funahashi J, Takano K, Fujii S, Yutani K To be published -
  2. 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. Takano K, Yamagata Y, Fujii S, Yutani K Biochemistry 36 688- (1997)
  3. Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability. Takano K, Funahashi J, Yamagata Y, Fujii S, Yutani K J. Mol. Biol. 274 132- (1997)
  4. The Structure, Stability, and Folding Process of Amyloidogenic Mutant Human Lysozyme. Funahashi J, Takano K, Ogasahara K, Yamagata Y, Yutani K J. Biochem. 120 1216- (1996)
  5. Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants. Takano K, Ogasahara K, Kaneda H, Yamagata Y, Fujii S, Kanaya E, Kikuchi M, Oobatake M, Yutani K J. Mol. Biol. 254 62- (1995)

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