Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect

Proteins: Structure, Function and Genetics

Volumn 31, Issue 2, 1998, Pages 107-115

  Zou, Qin ^a   Habermann Rottinghaus, Susan M ^a,b   Murphy, Kenneth P ^a  

^a UNIVERSITY OF IOWA   (United States)

^b ABBOTT LABORATORIES   (United States)

Author keywords

Binding; Calorimetry; Denaturation; Desolvation; Linear extrapolation model

Indexed keywords

UREA;

AQUEOUS SOLUTION; ARTICLE; CALORIMETRY; HYDROGEN BOND; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; SOLUBILITY; SOLVATION; THERMODYNAMICS;

AMIDES; CHEMISTRY, PHYSICAL; HYDROGEN BONDING; MODELS, CHEMICAL; PEPTIDES, CYCLIC; PROTEIN DENATURATION; THERMODYNAMICS; UREA; WATER;

EID: 0032080534     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980501)31:2<107::AID-PROT1>3.0.CO;2-J     Document Type: Article

References (58)

1. Pace, C.N. Determination and analysis of urea and guanidine hydrocholride denaturation curves. Methods Enzymol. 131:266-280, 1986.
2. Robinson, D.R., Jencks, W.P. The effect of compounds of the urea-guanidinium class on the activity coefficient of acetyltetraglycine ethyl ester and related compounds. J. Am. Chem. Soc. 87:2462-2470, 1965.
3. Nandi, P.K., Robinson, D.R. Effects of urea and guanidine hydrochloride on peptide and nonpolar groups. Biochemistry 23:6661-6668, 1984.
4. Gill, S.J., Hutson, J., Clopton, J.R., Downing, M. Solubility of diketopiperazine in aqueous solutions of urea. J. Phys. Chem. 65:1432-1435, 1961.
5. Wetlaufer, D.B., Malik, S.K., Stoller, L., Coffin, R.L. Nonpolar group participation in the denaturation of proteins by urea and guanidinium salts: Model compound studies. J. Am. Chem. Soc. 86:508-514, 1964.
6. Schönert, H., Stroth, L. Thermodynamic interaction between urea and the peptide group in aqueous solutions at 25°C. Biopolymers 20:817-831, 1981.
7. Kresheck, G.C., Benjamin, L. Calorimetric studies of the hydrophobic nature of several protein constituents and ovalbumin in water and in aqueous urea. J. Phys. Chem. 68:2476-2486, 1964.
8. Savage, J.J., Wood, R.H. Enthalpy of dilution of aqueous mixtures of amides, sugars, urea, ethylene glycol, and pentaerythritol at 25°C: Enthalpy of interaction of the hydrocarbon, amide, and hydroxyl functional groups in dilute aqueous solutions. J. Solution Chem. 5:733-750, 1976.
9. Sijpkes, A.H., Somsen, G., Lilley, T.H. Enthalpies of interacton of some N-acetyl amino acid amides in aqueous urea solutions at 298.15 K. J. Chem. Soc. Farady Trans. 86:2943-2949, 1990.
10. Brandts, J.F., Linda, H. The thermodynamics of protein denaturation. III. The denaturation of ribonuclease in water and in aqueous urea and aqueous ethanol mixtures. J. Amer. Chem. Soc. 89:4826-4838, 1967.
11. Johnson, C.M., Fersht, A.R. Protein stability as a function of denaturant concentration: The thermal stability of barnase in the presence of urea. Biochemistry 34:6795-6804, 1995.
12. Makhatadze, G.I., Privalov, P.L. Protein interactions with urea and guanidinium chloride: A calorimetric study. J. Mol. Biol. 226:491-505, 1992.
13. Neri, D., Billeter, M., Wider, G., Wüthrich, K. NMR determination of residual structure in a urea-denatured protein, the 434 repressor. Science 257:1559-1563, 1992.
14. Pace, C.N., Laurents, D.V., Thomson, J.A. pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1. Biochemistry 29:2564-2572, 1990.
15. Pace, C.N., Laurents, D.V., Erickson, R.E. Urea denaturation of barnase: pH dependence and characterization of the unfolded state. Biochemistry 31:2728-2734, 1992.
16. Paz-Andrade, M.I., Jones, M.N., Skinner, H.A. The enthalpy of interaction of urea with some globular proteins. Eur. J. Biochem. 66:127-131, 1976.
17. Schellman, J.A., Gassner, N.C. The enthalpy of transfer of unfolded protiens into solutions of urea and quanidinium chloride. Biophys. Chem. 59:259-275, 1996.
18. DeKoster, G.T., Robertson, A.D. Calorimetrically derived parameters for protein interactions with urea and guanidine-HCl are not consistent with denaturant m-values. Biophys. Chem. 64:59-68, 1997.
19. Sijpkes, A.H., van de Kleut, G., Gill, S.C. The solubilities of five cyclic dipeptides in water and in aqueous urea at 298.15 K: A quantitative model for the denaturation of proteins in aqueous urea solutions. Biophys. Chem. 52:75-82, 1994.
20. Stokes, R.H. Thermodynamics of aqueous urea solutions. Aust. J. Chem. 20:2087-2100, 1967.
21. Murphy, K.P., Gill, S.J. Group additivity thermodynamics for dissolution of solid cyclic dipeptides into water. Thermochim. Acta 172:11-20, 1990.
22. Murphy, K.P., Gill, S.J. Calorimetric measurement of the enthalpy of dissolution of diketopiperazine in water as a function of temperature. Thermochim. Acta 139:279-290, 1989.
23. Roseman, M., Jencks, W.P. Interactions of urea and other polar compounds in water. J. Am. Chem. Soc. 97:631-640, 1975.
24. Frank, H.S., Evans, M.W. Free volume and entropy in condensed systems. III. Entropy in binary liquid mixtures, partial molal entropy in dilute solutions, structure and thermodynamics in aqueous electrolytes'. J. Chem. Phys. 13:507-532, 1945.
25. Swenson, C.A. Effects of protein denaturants of the urea-guanidinium class on bulk water structure. Arch. Biochem. Biophys. 117:494-498, 1966.
26. Kuharski, R.A., Rossky, P.J. Molecular dynamics study of solvation in urea-water solution. J. Am. Chem. Soc. 106: 5786-5793, 1984.
27. Tsai, J., Gerstein, M., Levitt, M. Keeping the shape but changing the charges: A simulation of urea and its isosteric analogs. J. Chem. Phys. 104:9417-9430, 1996.
28. Kuharski, R.A., Rossky, P.J. Solvation of hydrophobic species in aqueous urea solution: A molecular dynamics study. J. Am. Chem. Soc. 106:5794-5800, 1984.
29. Muller, N. A model for the partial reversal of hydrophobic hydration by addition of a urea-like cosolvent. J. Phys. Chem. 94:3856-3859, 1990.
30. Baldwin, R.L. Temperature dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. U.S.A. 83:8069-8072, 1986.
31. Habermann, S.M., Murphy, K.P. Energetics of hydrogen bonding in proteins: A model compound study. Protein Sci. 5:1229-1239, 1996.
32. Spolar, R.S., Livingstone, J.R., Record, M.T., Jr. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry 31:3947-3955, 1992.
33. Barone, G., Del Vecchio, P., Giancola, C., Graziano, G. The liquid amide transfer model and the unfolding thermodynamics of small globular proteins. Int. J. Biol. Macromol. 17:2-51257, 1995.
34. Gill, S.J., Nichols, N.F., Wadsö, I. Calorimetric determination of enthalpies of solution of slightly soluble liquids. II. Enthalpy of solution of some hydrocarbons in water and their use in establishing the temperature dependence of their solubilities. J. Chem. Thermo. 8:445-452, 1976.
35. Gill, S.J., Wadsö, I. An equation of state describing hydrophobic interactions. Proc. Natl. Acad. Sci. U.S.A. 73:2955-2958, 1976.
36. Makhatadze, G.I., Privalov, P.L. Energetics of interactions of aromatic hydrocarbons with water. Biophys. Chem. 50:285-291, 1994.
37. Thayer, M.M., Haltiwanger, R.C., Allured, V.S., Gill, S.C., Gill, S.J. Peptide-urea interactions as observed in diketopiperazine-urea cocrystal. Biophys. Chem. 46:165-169, 1993.
38. Dunbar, J., Yennawar, H.P., Banerjee, S., Luo, J., Farber, G.K. The effect of denaturants on protein structure. Protein. Sci. 6:1727-1733, 1997.
39. Tirado-Rivas, J., Orozco, M., Jorgensen, W.L. Molecular dynamics simulations of the unfolding of barnase in water and 8-M aqueous urea. Biochemistry 36:7313-7329, 1997.
40. Schellman, J.A. Macromolecular binding. Biopolymers 14: 999-1018, 1975.
41. Sijpkes, A.H., van de Kleut, G.J., Gill, S.C. Urea-diketopiperazine interactions: A model for urea-induced denaturation of proteins. Biophys. Chem. 46:171-177, 1993.
42. Murphy, K.P., Gill, S.J. Thermodynamics of dissolution of cyclic dipeptide solids containing hydrophobic side groups. J. Chem. Thermodynamics 21:903-913, 1989.
43. Némethy, G., Scheraga, H.A. The structure of water and hydrophobic bonding in proteins. III. The thermodynamic properties of hydrophobic bonds in proteins. J. Phys. Chem. 66:1773-1789, 1962.
44. Klotz, I.M., Franzen, J.S. Hydrogen bonds between model peptide groups in solution. J. Am. Chem. Soc. 84:3461-3466, 1962.
45. Schellman, J.A. A simple model for solvation in mixed solvents: Application to the stabilization and destabilization of macromolecular structures. Biophys. Chem. 37:121-140, 1990.
46. Yang, A.-S., Sharp, K.A., Honig, B. Analysis of the heat capacity dependence of protein folding. J. Mol. Biol. 227: 889-900, 1992.
47. Makhatadze, G.I., Privalov, P.L. Energetics of protein structure. Adv. Protein Chem. 47:307-425, 1995.
48. Makhatadze, G.I., Privalov, P.L. Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration. J. Mol. Biol. 232:639-659, 1993.
49. Honig, B., Yang, A.-S. Free Energy balance in protein folding. Adv. Prot. Chem. 46:27-58, 1995.
50. Brady, G.P., Sharp, K.A. Energetics of cyclic dipeptide crystal packing and solvation. Biophys. J. 72:913-927, 1997.
51. Tanford, C. Protein denaturation. Adv. Protein Chem. 24:1-95, 1970.
52. Santoro, M.M., Bolen, D.W. A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concenration range. Biochemistry 31:4901-4907, 1992.
53. Myers, J.K., Pace, C.N., Scholtz, J M. Denaturant m-values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding. Protein. Sci. 4:2138-2148, 1995.
54. Dill, K.A., Shortle, D. Denatured states of proteins. Annu. Rev. Biochem. 60:795-825, 1991.
55. Shortle, D. The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J. 10:27-34, 1996.
56. Bai, Y., Sosnick, T.R., Mayne, L., Englander, S.W. Protein folding intermediates: Native-state hydrogen exchange. Science 269:192-197, 1995.
57. Chamberlain, A.K., Handel, T.M., Marqusee, S. Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nature Struct. Biol. 3:782-787, 1996.
58. Scholtz, J.M., Barrick, D., York, E.J., Stewart, J.M., Baldwin, R.L. Urea unfolding of peptide helices as a model for interpreting protein unfolding. Proc. Natl. Acad. Sci. U.S.A. 92:185-189, 1995.