Protein stability in mixed solvents: A balance of contact interaction and excluded volume

Biophysical Journal

Volumn 85, Issue 1, 2003, Pages 108-125

  Schellman, John A ^a,b  

^a UNIVERSITY OF OREGON   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANIDINE; NUCLEASE; RIBONUCLEASE; SOLVENT; SUCROSE; TRIMETHYLAMINE OXIDE; UREA;

ARTICLE; CALCULATION; CONCENTRATION RESPONSE; ENERGY; MOLECULAR MODEL; NONHUMAN; PARAMETER; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SOLVATION; SOLVENT EFFECT; STRUCTURE ANALYSIS; SURFACE PROPERTY; THEORY;

STAPHYLOCOCCUS;

EID: 0038311869     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74459-2     Document Type: Article

References (78)

1. Ahmad, F., and C. Bigelow. 1982. Estimation of the free energy of stabilization of ribonuclease A, lysozyme, α-lactalbumin, and myoglobin. J. Biol. Chem. 257:12935-12938.
2. Arakawa, T., and S. N. Timasheff. 1982. Stabilization of protein structure by sugars. Biochemistry. 21:6536-6544.
3. Aune, K. C., A. Salahuddin, M. H. Zarlengo, and C. Tanford. 1967. Evidence for residual structure in acid- and heat-denatured proteins. J. Biol. Chem. 242:4486-4489.
4. Averbuch-Pouchot, M.-T., and A. Durif. 1993. Synthèse et structure cristalline d'un composé d'addition entre le monophosphate et le chlorure de guanidinium. C. R. Acad. Sci. Paris 317. Ser. II:1179-1184.
5. Baldwin, R. L. 1996. How Hofmeister ion interactions affect protein stability. Biophys. J. 71:2056-2063.
6. Baskakov, I., and D. W. Bolen, 1998. Forcing thermodynamically unfolded proteins to fold. J. Biol. Chem. 273:4831-4834.
7. Baskakov, I. V., and D. W. Bolen. 1999. The paradox between m values and deltaCp's for denaturation of ribonuclease T1 with disulfide bonds intact and broken. Protein Sci. 8:1314-1319.
8. Beychok, B., and R. C. Warner. 1959. Denaturation and electrophoretic behavior of lysozyme. J. Am. Chem. Soc. 81:1892-1897.
9. Bolen, D. W., and I. V. Baskakov. 2001. The osmophobic effect: natural selection of a thermodynamic force in protein folding. J. Mol. Biol. 310:955-963.
10. Casassa, E. F., and H. Eisenberg. 1964. Thermodynamic analysis of multicomponent systems. Adv. Protein Chem. 19:287-395.
11. Chothia, C. 1975. Structural invariants in protein folding. Nature. 254:304-308.
12. Colonna-Cesan, F., and C. Sander. 1990. Excluded volume approximation to protein solvent interaction. Biophys. J. 57:1103-1107.
13. Connolly, M. L. 1983. Analytical molecular surface calculation. J. App. Cryst. 16:548-558.
14. Connolly, M. L. 1993. The molecular surface package. J. Mol. Graph. 11:139-141.
15. Courtenay, E. S., M. W. Capp, and M. T. Record, Jr. 2001. Thermodynamics of interactions of urea and guanidinium salts with protein surface: Relationship between solute effects on protein processes and changes in water-accessible surface area. Protein Sci. 10:2485-2497.
16. Courtenay, E. S., M. W. Capp, R. M. Saecker, and M. T. Record, Jr. 2000. Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model. Proteins. Suppl. 4:72-85.
17. CRC Handbook of Chemistry and Physics. 1965. R. C. Weast, S. M. Selby, and C. D. Hodgman, editors. Chemical Rubber Co, Cleveland.
18. Creamer, T. P., R. Srinivasan, and G. D. Rose. 1997. Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility. Biochemistry. 36:2832-2835.
19. Davis-Searles, P. R., A. J. Saunders, D. A. Erie, D. J. Winzor. and G. J. Pielak. 2001. Interpreting the effects of small uncharged solutes on protein-folding equilibria. Annu. Rev. Biophys. Biomol. Struct. 30:271-306.
20. Ebel, C., H. Eisenberg, and R. Ghirlando. 2000. Probing protein sugar interactions. Biophys. J. 78:385-393.
21. Eisenberg, H. 1976. Biological Macromolecules and Polyelectrolytes in Solution. Clarendon Press, Oxford.
22. Flory, P. J. 1953. Principles of Polymer Chemistry. Comell University Press, Ithaca.
23. Garrod, J. E., and T. M. Herrington. 1969. Dilute solution of two nonelectrolytes in a solvent. J. Phys. Chem. 73:1877-1884.
24. Garrod, J. E., and T. M. Herrington. 1970. Apparent molar volumes and temperatures of maximum density of dilute aqueous sucrose solutions. J. Phys. Chem. 74:363-370.
25. Green, S. M., A. K. Meeker, and D. Shortle. 1992. Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: evidence for mutational effects on the free energy of the denatured state. Biochemistry. 31:5717-5728.
26. Greene, R. F. J., and C. N. Pace. 1974. Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, α-chymotrypsin, and β-lactoglobulin. J. Biol. Chem. 249:5388-5393.
27. Harned, H. S., and B. B. Owen. 1950. The Physical Chemistry of Electrolyte Solutions. Reinhold, New York.
28. Hill, T. L. 1957. Theory of solutions I. J. Am. Chem. Soc. 79:4885-4890.
29. Hill, T. L. 1959. Theory of solutions II. Osmotic pressure virial expansion and light scattering in two component systems. J. Chem. Phys. 30:93-97.
30. Hill, T. L. 1960. Introduction to Statistical Thermodynamics. Addison-Wesley, Reading, MA.
31. Isihara, A., and T. Hayashida. 1951a. Theory of high polymer solutions. 1. Second virial coefficient for ovaloids model. Bull. Phys. Soc. Japan. 6:40-45.
32. Isihara, A., and T. Hayashida. 1951b. Theory of high polymer solutions. 2. Special form of second osmotic coefficient. Bull. Phys. Soc. Japan. 6:46-50.
33. Kawahara, K., and C. Tanford. 1966. Viscosity and density of aqueous solutions of urea and guanidine hydrochloride. J. Biol. Chem. 241:3228-3232.
34. Kirkwood, J. G., and F. P. Buff. 1951. The statistical mechanical theory of solutions. J. Chem. Phys. 19:774-777.
35. Kita, Y., T. Arakawa, T.-Y. Lin, and S. N. Timasheff. 1994. Contribution of the surface free energy perturbation to protein-solvent interactions. Biochemistry. 33:15178-15189.
36. Kuhn, L. A., M. A. Siani, M. E. Pique, C. L. Fisher, E. D. Getzoff, and J. A. Tainer. 1992. The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J. Mol. Biol. 228:13-22.
37. Lee, B., and F. M. Richards. 1971. Interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
38. Lee, J. C., and S. N. Timasheff. 1974. Partial specific volumes and interactions with solvent components of proteins in guanidine hydrochloride. Biochemistry. 13:257-265.
39. Lee, J. C., and S. N. Timasheff. 1981. The stabilization of proteins by sucrose. J. Biol. Chem. 256:7193-7201.
40. Li, A.-J., and R. Nussinov. 1998. A set of van der Waals and Coulombic radii of protein atoms for molecular and solvent accessibility surface calculation, packing evaluation, and docking. Proteins. 32:111-127.
41. Lin, T.-Y., and S. N. Timasheff. 1994. Why do some organisms use a ureamethylamine mixture as osmolyte? Thermodynamic compensation of urea and trimethylamine N-oxide interactions with protein. Biochemistry. 33:12695-12701.
42. Mak, T. C. W. 1988. Crystal structure of TMAO dihydrate. J. Mol. Struct. 178:169-175.
43. McCammon, J. A., P. G. Wolynes, and M. Karplus. 1979. Picosecond dynamics of tyrosine side chains in proteins. Biochemistry. 18:927-942.
44. Meeker, A. K., B. Garcia-Moreno, and D. Shortle. 1996. Contributions of the ionizable amino acids to the stability of staphylococcal nuclease. Biochemistry. 35:6443-6449.
45. Minton, A. P. 1998. Molecular crowding. In Methods in Enzymology. G. K. Ackers and M. J. Johnson, editors. Academic Press, New York. 127-149.
46. Mukerjee, P. 1961. Ion-solvent interactions. I. Partial molal volumes of ions in aqueous solutions. II. Internal pressure and electrostriction of aqueous solutions of electrolytes. J. Phys. Chem. 65:740-744, 744-746.
47. Mukerjee, P. 1966. Ionic partial molal volumes and electrostrictions in aqueous solution. J. Phys. Chem. 70:2708.
48. Myers, J. K., C. N. Pace, and J. M. Scholtz. 1995. Denaturant m values and heat capacity changes: relation to changes in accessible surface area of protein unfolding. Protein Sci. 4:2138-2148.
49. Nozaki, Y., and C. Tanford. 1963. The solubility of amino acids and related compounds in aqueous urea solutions. J. Biol. Chem. 238:4074-4080.
50. Pace, C. N. 2001. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry. 40:310-313.
51. Pace, C. N., D. V. Laurents, and J. A. Thomson. 1990. pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1. Biochemistry. 29:2564-2572.
52. Qu, Y., C. L. Bolen, and D. W. Bolen. 1998. Osmolyte-driven contraction of a random coil protein. Proc. Natl. Acad. Sci. USA. 95:9268-9273.
53. Quillan, M. L., and B. W. Matthews. 2000. Accurate calculation of the density of proteins. Acta Crystallogr. 56:791-794.
54. Record, M. T., Jr., and C. F. Anderson. 1995. Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model. Biophys. J. 68:786-794.
55. Saito, Y., and A. Wada. 1983. Comparative study of GuHCI denaturation of globular proteins II A phenomenological classification of denaturation profiles of 17 proteins. Biopolymers. 22:2123-2132.
56. Saunders, A. J., P. R. Davis-Searles, D. L. Allen, G. J. Pielak, and D. A. Erie. 2000. Osmolyte-induced changes in protein conformational equilibria. Biopolymers. 53:293-307.
57. Schellman, J. A. 1958. Optical rotatory properties of proteins and polypeptides. V. Rotatory properties of clupein, the oxidized A-chain of insulin, and oxidized ribonuclease. Compt. rend. lab. Carlsberg, Ser. chim. 30:439-449.
58. Schellman, J. A. 1975. Macromolecular binding. Biopolymers. 14:999-1018.
59. Schellman, J. A. 1978. Solvent denaturation. Biopolymers. 17:1305-1322.
60. Schellman, J. A. 1987. Selective binding and solvent denaturation. Biopolymers. 26:549-559.
61. Schellman, J. A. 1990. A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures. Biophys. Chem. 37:121-140.
62. Schellman, J. A., and N. C. Gassner. 1996. The enthalpy of transfer of unfolded proteins into solutions of urea and guanidinium chloride. Biophys. Chem. 59:259-275.
63. Shirley, B. A., P. Stanssens, U. Hahn, and C. N. Pace. 1992. Contribution of hydrogen bonding to the conformational stability of ribonuclease T1. Biochemistry. 31:725-732.
64. Shortle, D., H. S. Chan, and K. A. Dill. 1992. Modeling the effects of mutations on the denatured states of proteins. Protein Sci. 1:201-215.
65. Shortle, D., and A. K. Meeker. 1986. Mutant forms of staphylococcal nuclease with altered patterns of guanidinium chloride and urea denaturatin. Proteins. 1:81-89.
66. Shortle, D., W. E. Stites, and A. K. Meeker. 1990. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry. 29:8033-8041.
67. Tanford, C. 1961. Physical Chemistry of Macromolecules. Wiley, New York.
68. Tanford, C. 1970. Protein denaturation. C. Theoretical models for the mechanism of denaturation. Advan. Protein Chem. 24:1-95.
69. Tanford, C., K. Kawahara, and S. Lapanje. 1966. Proteins in 6M guanidine hydrochloride. Demonstration of random coil behavior. J. Biol. Chem. 241:1921-1923.
70. Timasheff, S. N. 1998. Control of protein stability and reactions by weakly interacting cosolvents: the simplicity of the complicated. Adv. Protein. Chem. 51:355-432.
71. von Hippel, P. H., and K.-Y. Wong. 1964. Neutral salts. The generality of their effects on the stability of macromolecular conformations. Science. 145:577-580.
72. von Hippel, P. H., and K. Y. Wong. 1965. The conformational stability of globular proteins. The effects of various electrolytes and nonelectrolytes on the thermal ribonuclease transition. J. Biol. Chem. 240:3909-3923.
73. Wang, A., and D. W. Bolen. 1997. A naturally occurring protective system in urea-rich cells: mechanism of osmolyte protection of proteins against urea denaturation. Biochemistry. 36:9101-9108.
74. Wills, P. R., W. D. Comper, and D. J. Winzor. 1993. Thermodynamic nonideality in macromolecular solutions: interpretation of virial coefficients. Arch. Biochem. Biophys. 300:206-212.
75. Wills, P. R., D. R. Hall, and D. J. Winzor. 2000. Interpretation of thermodynamic non-ideality in sedimentation equilibrium experiments on proteins. Biophys. Chem. 84:217-225.
76. Wills, P. R., and D. J. Winzor. 1993. Thermodynamic analysis of preferential solvation in protein solutions. Biopolymers. 33:1627-1629.
77. Wu, H. 1931. Studies on denaturation of proteins XIII. A theory of denaturation. Clin. J. Physiol. 5:321-344.
78. Zhang, T., E. Bertelsen, D. Benvegnu, and T. Alber. 1993. Circular permutation of T4 lysozyme. Biochemistry. 32:12311-12318.