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

Volumn 42, Issue 7, 2003, Pages 2202-2217

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

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN DENATURATION;

DNA; ENTHALPY; EXTRAPOLATION; PROTEINS;

UREA;

BOVINE SERUM ALBUMIN; DNA BINDING PROTEIN; UREA;

ARTICLE; CIRCULAR DICHROISM; ENTHALPY; NONHUMAN; PARTITION COEFFICIENT; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN DNA BINDING; PROTEIN FOLDING; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

BACTERIAL PROTEINS; DNA-BINDING PROTEINS; DOSE-RESPONSE RELATIONSHIP, DRUG; ENTROPY; ESCHERICHIA COLI PROTEINS; HELIX-TURN-HELIX MOTIFS; LACTOSE; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PEPTIDE FRAGMENTS; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; TEMPERATURE; THERMODYNAMICS; UREA;

BOVINAE;

EID: 0037465426     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0270992     Document Type: Article

References (72)

1. Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A., Brennan, R. G., and Lu, P. Z. (1996) Science 271, 1247-1254.
2. Levandoski, M. M., Tsodikov, O. V., Frank, D. E., Melcher, S. E., Saecker, R. M., and Record, M. T. (1996) J. Mol. Biol. 260, 697-717.
3. Tsodikov, O. V., Saecker, R. M., Melcher, S. E., Levandoski, M. M., Frank, D. E., Capp, M. W., and Record, M. T. (1999) J. Mol. Biol. 294, 639-655.
4. Law, S. M., Bellomy, G. R., Schlax, P. J., and Record, M. T. (1993) J. Mol. Biol. 230, 161-173.
5. Muller, J., Oehler, S., and MullerHill, B. (1996) J. Mol. Biol. 257, 21-29.
6. Spolar, R. S., and Record, M. T. (1994) Science 263, 777-784.
7. Spronk, C. A. E. M., Slijper, M., vanBoom, J. H., Kaptein, R., and Boelens, R. (1996) Nat. Struct. Biol. 3, 916-919.
8. Mossing, M. C., and Record, M. T. (1985) J. Mol. Biol. 186, 295-305.
9. Kalodimos, C. G., Bonvin, A. M. J. J., Salinas, R. K., Wechselberger, R., Boelens, R., and Kaptein, R. (2002) EMBO J. 21, 2866-2876.
10. Frank, D. E., Saecker, R. M., Bond, J. P., Capp, M. W., Tsodikov, O. V., Melcher, S. E., Levandoski, M. M., and Record, M. T. (1997) J. Mol. Biol. 267, 1186-1206.
11. Spronk, C. A., Bonvin, A. M., Radha, P. K., Melacini, G., Boelens, R., and Kaptein, R. (1999) Struct. Fold Des. 7, 1483-1492.
12. Kalodimos, C. G., Folkers, G. E., Boelens, R., and Kaptein, R. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 6039-6044.
13. Spronk, C. A., Folkers, G. E., Noordman, A. M., Wechselberger, R., van den Brink, N., Boelens, R., and Kaptein, R. (1999) EMBO J. 18, 6472-6480.
14. Kalodimos, C. G., Boelens, R., and Kaptein, R. (2002) Nat. Struct. Biol. 9, 193-197.
15. Kalodimos, C. G., Folkers, G. E., Boelens, R., and Kaptein, R. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 6039-6044.
16. Pace, C. N., and Shaw, K. L. (2000) Proteins, 1-7.
17. Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Protein Sci. 4, 2138-2148.
18. Dalby, P. A., Oliveberg, M., and Fersht, A. R. (1998) J. Mol. Biol. 276, 625-646.
19. Wrabl, J., and Shortle, D. (1999) Nat. Struct. Biol. 6, 876-883.
20. Shortle, D., and Meeker, A. K. (1986) Proteins 1, 81-89.
21. Pace, C. N., Laurents, D. V., and Erickson, R. E. (1992) Biochemistry 31, 2728-2734.
22. Greene, R. F., and Pace, C. N. (1974) J. Biol. Chem. 249, 5388-5393.
23. Santoro, M. M., and Bolen, D. W. (1992) Biochemistry 31, 4901-4907.
24. Nicholson, E. M., and Scholtz, J. M. (1996) Biochemistry 35, 11369-11378.
25. Johnson, C. M., and Fersht, A. R. (1995) Biochemistry 34, 6795-6804.
26. Wu, J. W., and Wang, Z. X. (1999) Protein Sci. 8, 2090-2097.
27. Wyman, J. (1964) Adv. Protein Chem. 19, 223-286.
28. Schellman, J. A. (1994) Biopolymers 34, 1015-1026.
29. Timasheff, S. N. (1998) Adv. Protein Chem. 51, 355-432.
30. Record, M. T., Zhang, W. T., and Anderson, C. F. (1998) Adv. Protein Chem. 51, 281-353.
31. Courtenay, E. S., Capp, M. W., Saecker, R. M., and Record, M. T. (2000) Proteins 41, 72-85.
32. Aune, K. C., and Tanford, C. (1969) Biochemistry 8, 4586-4590.
33. Schellman, J. A. (1990) Biophys. Chem. 37, 121-140.
34. Scholtz, J. M., Barrick, D., York, E. J., Stewart, J. M., and Baldwin, R. L. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 185-189.
35. Stokes, R. H. (1967) Aust. J. Chem. 20, 2087-2100.
36. Pace, C. N. (1975) CRC Crit. Rev. Biochem. 3, 1-43.
37. Record, M. T., and Anderson, C. F. (1995) Biophys. J. 68, 786-794.
38. Courtenay, E. S., Capp, M. W., Anderson, C. F., and Record, M. T. (2000) Biochemistry 39, 4455-4471.
39. Courtenay, E. S., Capp, M. W., and Record, M. T. (2001) Protein Sci. 10, 2485-2497.
40. Slijper, M., Boelens, R., Davis, A. L., Konings, R. N., van der Marel, G. A., van Boom, J. H., and Kaptein, R. (1997) Biochemistry 36, 249-54.
41. Woody, R. W. (1995) Methods Enzymol. 246, 34-71.
42. Spronk, C. A., Slijper, M., van Boom, J. H., Kaptein, R., and Boelens, R. (1996) Nat. Struct. Biol. 3, 916-9.
43. Klotz, I. M., and Rosenberg, R. M. (1994) Chemical Thermodynamics, 5th ed., John Wiley & Sons, Inc., New York.
44. Richmond, T. J. (1984) J. Mol. Biol. 178, 63-89.
45. Livingstone, J. R., Spolar, R. S., and Record, M. T. (1991) Biochemistry 30, 4237-4244.
46. Knapp, S., Mattson, P. T., Christova, P., Berndt, K. D., Karshikoff, A., Vihinen, M., Smith, C. I. E., and Ladenstein, R. (1998) Proteins 31, 309-319.
47. Viguera, A. R., Martinez, J. C., Filimonov, V. V., Mateo, P. L., and Serrano, L. (1994) Biochemistry 33, 2142-2150.
48. Alexander, P., Fahnestock, S., Lee, T., Orban, J., and Bryan, P. (1992) Biochemistry 31, 3597-3603.
49. Jackson, S. E., and Fersht, A. R. (1991) Biochemistry 30, 10428-10435.
50. Gonzalez, M., Weiler, S., Ferretti, J. A., and Ginsburg, A. (2001) Biochemistry 40, 4923-4931.
51. Carra, J. H., and Privalov, P. L. (1997) Biochemistry 36, 526-535.
52. Damante, G., Tell, G., Leonardi, A., Fogolari, F., Bortolotti, N., Dilauro, R., and Formisano, S. (1994) FEBS Lett. 354, 293-296.
53. Huang, G. W. S., and Oas, T. G. (1996) Biochemistry 35, 6173-6180.
54. Padmanabhan, S., Laurents, D. V., Fernandez, A. M., Elias-Arnanz, M., Ruiz-Sanz, J., Mateo, P. L., Rico, M., and Filimonov, V. V. (1999) Biochemistry 38, 15536-15547.
55. Agashe, V. R., and Udgaonkar, J. B. (1995) Biochemistry 34, 3286-3299.
56. Ibarra-Molero, B., Makhatadze, G. I., and Sanchez-Ruiz, J. M. (1999) Biochim. Biophys. Acta 1429, 384-390.
57. Pace, C. N., and Vanderburg, K. E. (1979) Biochemistry 18, 288-292.
58. Schellman, J. A., and Gassner, N. C. (1996) Biophys. Chem. 59, 259-275.
59. Makhatadze, G. I., and Privalov, P. L. (1992) J. Mol. Biol. 226, 491-505.
60. Zolkiewski, M., Nosworthy, N. J., and Ginsburg, A. (1995) Protein Sci. 4, 1544-1552.
61. Sijpkes, A. H., Vandekleut, G. J., and Gill, S. C. (1993) Biophys. Chem. 46, 171-177.
62. Sijpkes, A. H., Vandekleut, G. J., and Gill, S. C. (1994) Biophys. Chem. 52, 75-82.
63. Nozaki, Y., and Tanford, C. (1963) J. Biol. Chem. 238, 4074-4081.
64. Nandi, P. K., and Robinson, D. R. (1984) Biochemistry 23, 6661-6668.
65. Schonert, H., and Stroth, L. (1981) Biopolymers 20, 817-831.
66. Robinson, D. R., and Jencks, W. P. (1965) J. Am. Chem. Soc. 87, 2462-2470.
67. Zou, Q., Habermann-Rottinghaus, S. M., and Murphy, K. P. (1998) Proteins Struct. Funct. Genet. 31, 107-115.
68. Pace, C. N., Laurents, D. V., and Thomson, J. A. (1990) Biochemistry 29, 2564-2572.
69. Pace, C. N., Laurents, D. V., and Erickson, R. E. (1992) Biochemistry 31, 2728-2734.
70. Privalov, P. L. (1979) Adv. Protein Chem. 33, 167-241.
71. Del Pino, I. M. P., and Sanchez-Ruiz, J. M. (1995) Biochemistry 34, 8621-8630.
72. Padmanabhan, S., Laurents, D. V., Fernandez, A. M., Elias-Amanz, M., Ruiz-Sanz, J., Mateo, P. L., Rico, M., and Filimonov, V. V. (1999) Biochemistry 38, 15536-47.