Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface

Biochemistry

Volumn 43, Issue 28, 2004, Pages 9276-9288

  Felitsky, Daniel J ^a   Record Jr , M Thomas ^a,b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEINS; UREA;

PROTEIN SURFACE; PROTEIN UNFOLDING;

BIOCHEMISTRY;

BETAINE; BIOPOLYMER; PROTEIN; UREA;

ARTICLE; CONCENTRATION (PARAMETERS); ISOTHERM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; REACTION ANALYSIS; SURFACE PROPERTY; THERMODYNAMICS; THERMOSTABILITY;

BETAINE; BINDING, COMPETITIVE; MODELS, CHEMICAL; PROTEIN BINDING; PROTEINS; SOLUTIONS; SOLVENTS; THERMODYNAMICS; UREA;

EID: 3142655877     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049862t     Document Type: Article

References (53)

1. Record, M. T., Jr., Zhang, W., and Anderson, C. F. (1998) Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv. Protein Chem. 51, 281-353.
2. Timasheff, S. N. (1998) Control of protein stability and reactions by weakly interacting cosolvents: The simplicity of the complicated. Adv. Protein Chem. 51 51, 355-432.
3. Davis-Searles, P. R., Saunders, A. J., Erie, D. A., Winzor, D. J., and Pielak, G. J. (2001) Interpreting the effects of small uncharged solutes on protein-folding equilibria. Annu. Rev. Biophys. Biomolec. Struct. 30, 271-306.
4. Parsegian, V. A., Rand, R. P., and Rau, D. C. (2000) Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives. Proc. Natl. Acad. Sci. U. S. A. 97, 3987-3992.
5. Timasheff, S. N. (2002) Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components. Proc. Natl. Acad. Sci. U. S. A. 99, 9721-9726.
6. Timasheff, S. N. (1998) In disperse solution, "osmotic stress" is a restricted case of preferential interactions. Proc. Natl. Acad. Sci. U. S. A. 95, 7363-7367.
7. Yancey, P. H., Clark, M. E., Hand, S. C., Bowlus, R. D., and Somero, G. N. (1982) Living with Water-Stress - Evolution of Osmolyte Systems. Science 217, 1214-1222.
8. Record, M. T., Courtenay, E. S., Cayley, D. S., and Guttman, H. J. (1998) Responses of E-coli to osmotic stress: Large changes in amounts of cytoplasmic solutes and water. Trends Biochem. Sci. 23, 143-148.
9. Record, M. T., Courtenay, E. S., Cayley, S., and Guttman, H. J. (1998) Biophysical compensation mechanisms buffering E-coli protein-nucleic acid interactions against changing environments. Trends Biochem. Sci. 23, 190-194.
10. Timasheff, S. N. (1993) The Control of Protein Stability and Association by Weak-Interactions with Water - How Do Solvents Affect These Processes. Annual Rev. Biophys. Biomolec. Struct. 22, 67-97.
11. Courtenay, E. S., Capp, M. W., Anderson, C. F., and Record, M. T. (2000) Vapor pressure osmometry studies of osmolyte-protein interactions: Implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro. Biochemistry 39, 4455-4471.
12. Schellman, J. A. (1994) The Thermodynamics of Solvent Exchange. Biopolymers 34, 1015-1026.
13. 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.
14. Schellman, J. A. (1987) Selective Binding and Solvent Denaturation. Biopolymers 26, 549-559.
15. Courtenay, E. S., Capp, M. W., Saecker, R. M., and Record, M. T. (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: Struct., Funct., Genet. 72-85.
16. Record, M. T., Zhang, W. T., and Anderson, C. F. (1998) Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: A practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv. Protein Chem. 51, 281-353.
17. Record, M. T., and Anderson, C. F. (1995) Interpretation of Preferential Interaction Coefficients of Nonelectrolytes and of Electrolyte Ions in Terms of a 2-Domain Model. Biophys. J. 68, 786-794.
18. Schellman, J. A., and Gassner, N. C. (1996) The enthalpy of transfer of unfolded proteins into solutions of urea and guanidinium chloride. Biophys. Chem. 59, 259-275.
19. Scholtz, J. M., Barrick, D., York, E. J., Stewart, J. M., and Baldwin, R. L. (1995) Urea Unfolding of Peptide Helices as a Model for Interpreting Protein Unfolding. Proc. Natl Acad. Sci. U. S. A. 92, 185-189.
20. Schellman, J. A. (2003) Protein stability in mixed solvents: A balance of contact interaction and excluded volume. Biophys. J. 85, 108-125.
21. Felitsky, D. J., and Record, M. T. (2003) Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: A model system for analysis of solute effects on protein processes. Biochemistry 42, 2202-2217.
22. Courtenay, E. S., Capp, M. W., and Record, M. T. (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.
23. Kirkwood, J. G., and Buff, F. P. (1951) Statistical mechanical theory of solutions. I. J. Chem. Phys. 19, 774-777.
24. Ben-Naim, A. (1992) Statistical Thermodynamics for Chemists and Biochemists, Plenum Press, New York.
25. Chitra, R., and Smith, P. E. (2001) Preferential interactions of cosolvents with hydrophobic solutes. J. Phys. Chem. B 105, 11513-11522.
26. Yin, M., Palmer, H. R., Fyfe-Johnson, A. L., Bedford, J. J., Smith, R. A. J., and Yancey, P. H. (2000) Hypotaurine, N-methyltaurine, taurine, and glycine betaine as dominant osmolytes of vestimentiferan tubeworms from hydrothermal vents and cold seeps. Physiol. Biochem. Zool. 73, 629-637.
27. Yancey, P. H. (2001) Water stress, osmolytes, and proteins. Am. Zool. 41, 699-709.
28. Bedford, J. J., Schofield, J., Yancey, P. H., and Leader, J. P. (2002) The effects of hypoosmotic infusion on the composition of renal tissue of the Australian brush-tailed possum Trichosurus vulpecula. Comp. Biochem. Physiol., Part B: Biochem. Mol. Biol. 132, 645-652.
29. Bedford, J. J., Harper, J. L., Leader, J. P., Yancey, P. H., and Smith, R. A. J. (1998) Betaine is the principal counteracting osmolyte in tissues of the elephant fish, Callorhincus millii (Elasmobranchii, Holocephali). Comp. Biochem. Physiol., Part B: Biochem. Mol. Biol. 119, 521-526.
30. Edmands, S. D., Hughs, K. S., Lee, S. Y., Meyer, S. D., Saari, E., and Yancey, P. H. (1995) Time-Dependent Aspects of Osmolyte Changes in Rat-Kidney, Urine, Blood, and Lens with Sorbinil and Galactose Feeding. Kidney Int. 48, 344-353.
31. Lewis, B. A., Cayley, S., Padmanabhan, S., Kolb, V. M., Brushaber, V., Anderson, C. F., and Record, M. T. (1990) Natural Abundance N-14 and C-13 NMR of Glycine Betaine and Trehalose as Probes of the Cytoplasm of Escherichia-Coli-K12. J. Magn. Reson. 90, 612-617.
32. Arakawa, T., and Timasheff, S. N. (1983) Preferential Interactions of Proteins with Solvent Components in Aqueous Amino-Acid Solutions. Arch. Biochem. Biophys. 224, 169-177.
33. Santoro, M. M., Liu, Y. F., Khan, S. M. A., Hou, L. X., and Bolen, D. W. (1992) Increased Thermal-Stability of Proteins in the Presence of Naturally-Occurring Osmolytes. Biochemistry 31, 5278-5283.
34. Anjum, F., Rishi, V., and Ahmad, F. (2000) Compatibility of osmolytes with Gibbs energy of stabilization of proteins. Biochim. Biophys. Acta 1476, 75-84.
35. Yancey, P. H., and Somero, G. N. (1979) Counteraction of urea destabilization of protein structure by methylamine osmoregulatory compounds of elasmobranch fishes. Biochem. J. 183, 317-323.
36. Anderson, C. F., Felitsky, D. J., Hong, J., and Record, M. T. (2002) Generalized derivation of an exact relationship linking different coefficients that characterize thermodynamic effects of preferential interactions. Biophys. Chem. 101, 497-511.
37. Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Denaturant m-values and heat capacity changes - Relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4, 2138-2148.
38. Schellman, J. A. (2002) Fifty years of solvent denaturation. Biophys. Chem. 96, 91-101.
39. Smith, P. K., and Smith, E. R. B. (1940) Thermodynamic properties of solutions of animo acids and related substances. V. The activities of some hydroxy- and N-methylanimo acids and proline in aqueous solution at twenty-five degrees. Journal of Biological Chemistry 132, 57-64.
40. Klotz, I. M., and Rosenberg, R. M. (2000) Chemical Thermodynamics, 6th ed., John Wiley & Sons, New York.
41. Tsodikov, O. V., Record, M. T., Jr., and Sergeev, Y. V. (2002) Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem. 23, 600-609.
42. Livingstone, J. R., Spolar, R. S., and Record, M. T. (1991) Contribution to the Thermodynamics of Protein Folding from the Reduction in Water-Accessible Nonpolar Surface-Area. Biochemistry 30, 4237-4244.
43. Weatherly, G. T., and Pielak, G. J. (2001) Second virial coefficients as a measure of protein-osmolyte interactions. Protein Sci. 10, 12-16.
44. Edward, J. T. (1970) Molecular volumes and the Stokes-Einstein equation. J. Chem. Educ. 47, 261-270.
45. Bevington, P. R., and Robinson, D. K. (1992) Data Reduction and Error Analysis for the Physical Sciences, 2nd ed., WCB McGraw-Hill, Boston.
46. Santoro, M. M., and Bolen, D. W. (1992) A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concentration range. Biochemistry 31, 4901-4907.
47. Johnson, C. M., and Fersht, A. R. (1995) Protein stability as a function of denaturant concentration: ther thermal stability of barnase in the presence of urea. Biochemistry 34, 6795-804.
48. Nicholson, E. M., and Scholtz, J. M. (1996) Conformational stability of the Escherichia coli HPr protein: Test of the linear extrapolation method and a thermodynamic characterization of cold denaturation. Biochemistry 35, 11369-11378.
49. Arakawa, T., and Timasheff, S. N. (1983) Preferential interactions of proteins with solvent components in aqueous amino acid solutions. Arch. Biochem. Biophys. 224, 169-177.
50. Spolar, R. S., Livingstone, J. R., and Record, M. T., Jr. (1992) 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.
51. Spolar, R. S., and Record, M. T., Jr. (1994) Coupling of local folding to site-specific binding of proteins to DNA. Science 263, 777-784.
52. Creamer, T. P., Srinivasan, R., and Rose, G. D. (1997) Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility. Biochemistry 36, 2832-2835.
53. Cayley, S., and Record, M. T., Jr. (2003) Roles of Cytoplasmic Osmolytes, Water, and Crowding in the Response of Escherichia coli to Osmotic Stress: Biophysical Basis of Osmoprotection by Glycine Betaine. Biochemistry 42, 12596-12609.