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Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six tyrosine --> phenylalanine mutants.

Yamagata Y, Kubota M, Sumikawa Y, Funahashi J, Takano K, Fujii S, Yutani K
Biochemistry 37 9355-62 (1998)
Related entries: 1wqm, 1wqn, 1wqo, 1wqp, 1wqr

Cited: 32 times
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Abstract

The contribution of hydrogen bonds to the conformational stability of human lysozyme was investigated by the combination of calorimetric and X-ray analyses of six Tyr --> Phe mutants. Unfolding Delta G and unfolding Delta H values of the Tyr --> Phe mutant proteins were changed by from +0.3 to -4.0 kJ/mol and from 0 to -16 kJ/mol, respectively, compared to those of the wild-type protein. The net contribution of a hydrogen bond at a specific site to stability (Delta Gwild/HB), considering factors affected by substitutions, was evaluated on the basis of X-ray structures of the mutant proteins. In the present study, one of six mutant proteins was suitable for evaluating the strength of the hydrogen bond. Delta Gwild/HB for the intramolecular hydrogen bond at Tyr124 was evaluated to be 7.5 kJ/mol. Results of the analysis of other mutants also suggest that hydrogen bonds of the hydroxyl group of Tyr, including the hydrogen bond with a water molecule, contribute to the stabilization of the human lysozyme.

Articles - 1wqq mentioned but not cited (1)

  1. Predicting the melting point of human C-type lysozyme mutants. Verma D, Jacobs DJ, Livesay DR. Curr Protein Pept Sci 11 562-572 (2010)


Articles citing this publication (31)

  1. Contribution of hydrogen bonds to protein stability. Pace CN, Fu H, Lee Fryar K, Landua J, Trevino SR, Schell D, Thurlkill RL, Imura S, Scholtz JM, Gajiwala K, Sevcik J, Urbanikova L, Myers JK, Takano K, Hebert EJ, Shirley BA, Grimsley GR. Protein Sci 23 652-661 (2014)
  2. Heat capacity changes upon burial of polar and nonpolar groups in proteins. Loladze VV, Ermolenko DN, Makhatadze GI. Protein Sci 10 1343-1352 (2001)
  3. Tyrosine hydrogen bonds make a large contribution to protein stability. Pace CN, Horn G, Hebert EJ, Bechert J, Shaw K, Urbanikova L, Scholtz JM, Sevcik J. J Mol Biol 312 393-404 (2001)
  4. Evaluation of direct and cooperative contributions towards the strength of buried hydrogen bonds and salt bridges. Albeck S, Unger R, Schreiber G. J Mol Biol 298 503-520 (2000)
  5. 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)
  6. Buried water molecules contribute to the conformational stability of a protein. Takano K, Yamagata Y, Yutani K. Protein Eng 16 5-9 (2003)
  7. 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)
  8. Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease. Baran KL, Chimenti MS, Schlessman JL, Fitch CA, Herbst KJ, Garcia-Moreno BE. J Mol Biol 379 1045-1062 (2008)
  9. Energetics of a hydrogen bond (charged and neutral) and of a cation-pi interaction in apoflavodoxin. Fernández-Recio J, Romero A, Sancho J. J Mol Biol 290 319-330 (1999)
  10. 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 12 841-850 (1999)
  11. Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes. Takano K, Ota M, Ogasahara K, Yamagata Y, Nishikawa K, Yutani K. Protein Eng 12 663-672 (1999)
  12. 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)
  13. 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)
  14. Hydrogen bonding increases packing density in the protein interior. Schell D, Tsai J, Scholtz JM, Pace CN. Proteins 63 278-282 (2006)
  15. Prudent modeling of core polar residues in computational protein design. Bolon DN, Marcus JS, Ross SA, Mayo SL. J Mol Biol 329 611-622 (2003)
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  17. Knowledge-based potential defined for a rotamer library to design protein sequences. Ota M, Isogai Y, Nishikawa K. Protein Eng 14 557-564 (2001)
  18. 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)
  19. Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. Verma D, Jacobs DJ, Livesay DR. PLoS Comput Biol 8 e1002409 (2012)
  20. Molecular dynamics simulations of the Bcl-2 protein to predict the structure of its unordered flexible loop domain. Raghav PK, Verma YK, Verma YK, Gangenahalli GU. J Mol Model 18 1885-1906 (2012)
  21. The stability and folding process of amyloidogenic mutant human lysozymes. Takano K, Funahashi J, Yutani K. Eur J Biochem 268 155-159 (2001)
  22. Role of charged residues in stabilization of Pyrococcus horikoshii CutA1, which has a denaturation temperature of nearly 150 °C. Matsuura Y, Takehira M, Sawano M, Ogasahara K, Tanaka T, Yamamoto H, Kunishima N, Katoh E, Yutani K. FEBS J 279 78-90 (2012)
  23. 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)
  24. 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)
  25. 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)
  26. Underexposed polar residues and protein stabilization. Ayuso-Tejedor S, Abián O, Sancho J. Protein Eng Des Sel 24 171-177 (2011)
  27. Mutational analysis of hydrogen bonding residues in the BPTI folding pathway. Bulaj G, Goldenberg DP. J Mol Biol 313 639-656 (2001)
  28. Structure and effective charge characterization of proteins by a mobility capillary electrophoresis based method. Zhang W, Wu H, Zhang R, Fang X, Xu W. Chem Sci 10 7779-7787 (2019)
  29. Hydrogen-bond disruption probability in proteins by a modified self-consistent harmonic approach. Cao ZW, Chen YZ. Biopolymers 58 319-328 (2001)
  30. Titania Nanosheet Generates Peroxynitrite-Dependent S-Nitrosylation and Enhances p53 Function in Lung Cancer Cells. Soonnarong R, Tungsukruthai S, Nutho B, Rungrotmongkol T, Vinayanuwattikun C, Maluangnont T, Chanvorachote P. Pharmaceutics 13 1233 (2021)
  31. Nickel(II) complexes based on L-amino-acid-derived ligands: synthesis, characterization and study of the role of the supramolecular structure in carbon dioxide capture. Rivas Marquina A, Movilla F, Sánchez Montilva OC, Rentschler E, Carrella L, Albores P, Di Salvo F. Acta Crystallogr B Struct Sci Cryst Eng Mater 76 825-838 (2020)


Related citations provided by authors (3)

  1. 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)
  2. 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)
  3. 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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