Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea

Biochemistry

Volumn 36, Issue 24, 1997, Pages 7313-7329

  Tirado Rives, Julian ^a   Orozco, Modesto ^b   Jorgensen, William L ^a  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; SOLVENT; UREA; WATER;

AQUEOUS SOLUTION; ARTICLE; CRYSTAL STRUCTURE; ENZYME STABILITY; ENZYME STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SIMULATION; SITE DIRECTED MUTAGENESIS;

COMPUTER SIMULATION; HEAT; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RIBONUCLEASES; UREA; WATER;

EID: 0030939289     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi970096i     Document Type: Article

References (77)

1. Allen, T. J. (1993) Ph.D. Thesis, Massachusetts Institute of Technology.
2. Åqvist, J., Medina, C., & Samuelsson, J. E. (1994) Protein Eng. 7, 385.
3. Arcus, V. L., Vuilleumier, S., Freund, S. M. V., Bycroft, M., & Fersht, A. R. (1995) J. Mol. Biol. 254, 305.
4. Auer, H. E., & Doty, P. (1966) Biochemistry 5, 1716.
5. Baldwin, R. L. (1989) Trends Biochem. Sci. 14, 291.
6. Baudet, S., & Janin, J. (1991) J. Mol. Biol. 219, 123.
7. Baum, J., Dobson, C. M., Evans, P. A., & Hanley, C. (1989) Biochemistry 28, 7.
8. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) J. Mol. Biol. 112, 535.
9. Braxenthaler, M., Avbelj, F., & Moult, J. (1995) J. Mol. Biol. 250, 239.
10. Breslow, R., & Guo, T. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 167.
11. Bycroft, M., Matouscheck, A., Kellis, J. T., Serrano, L., & Fersht, A. R. (1990a) Nature 346, 488.
12. Bycroft, M., Sheppard, R. N., Lau, F. T.-K., & Fersht, A. R. (1990b) Biochemistry 29, 7425.
13. Bycroft, M., Ludvigsen, S., Fersht, A. R., & Poulsen, F. M. (1991) Biochemistry 30, 8697.
14. Caflish, A., & Karplus, M. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 1746.
15. Caflish, A., & Karplus, M. (1995) J. Mol. Biol. 252, 672.
16. Carlson, H. A., & Jorgensen, W. L. (1995) J. Phys. Chem. 99, 10667.
17. Creighton, T. E. (1985) J. Phys. Chem. 89, 2452.
18. Daggett, V., & Levitt, M. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 5142.
19. Duffy, E. M., Kowalczyk, P. J., & Jorgensen, W. L. (1993a) J. Am. Chem. Soc. 115, 9271.
20. Duffy, E. M., Severance, D. L., & Jorgensen, W. L. (1993b) Isr. J. Chem. 33, 323.
21. Fersht, A. R. (1993) FEBS Lett. 325, 5.
22. Fersht, A. R., Matouscheck, A., & Serrano, L. (1992) J. Mol. Biol. 224, 771.
23. Gratzer, W. B., & Doty, P. (1963) J. Am. Chem. Soc. 85, 1193.
24. Hermans, J., Jr. (1966) J. Am. Chem. Soc. 88, 2418.
25. Horovitz, A., & Fersht, A. R. (1992) J. Mol. Biol. 224, 733.
26. Horovitz, A., Serrano, L., & Fersht, A. R. (1991) J. Mol. Biol. 219, 5.
27. Hughson, F. M., Wright, P. E., & Baldwin, R. L. (1990) Science 249, 1544.
28. Hünenberger, P. H., Mark, A. E., & van Gunsteren, W. (1995) Proteins 21, 196.
29. Jaenicke, R. (1987) Prog. Biophys. Mol. Biol. 49, 117.
30. Jorgensen, W. L., & Tirado-Rives, J. (1988) J. Am. Chem. Soc. 110, 1657.
31. Jorgensen, W. L., & Severance, D. L. (1990) J. Am. Chem. Soc. 112, 4768.
32. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983) J. Chem. Phys. 79, 926.
33. Kabsch, W., & Sander, C. (1983) Biopolymers 22, 2757.
34. Kim, P. S., & Baldwin, R. L. (1990) Annu. Rev. Biochem. 59, 631.
35. King, J (1989) Chem. Eng. News 67, 32.
36. Kraulis, P. (1991) J. Appl. Crystallogr. 24, 946.
37. Kumar, T. K. S., Jayaraman, G., Lin, W.-Y., & Yu, C. (1996) Biochim. Biophys. Acta 1294, 103.
38. Kuwajima, K. (1989) Proteins: Struct., Funct., Genet. 56, 87.
39. Li, A. J., & Daggett, V. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 10430.
40. Li, A. J., & Daggett, V. (1996) J. Mol. Biol. 257, 412.
41. Liepinsh, E., & Otting, G. (1994) J. Am. Chem. Soc. 116, 9670.
42. Lu, J., & Dahlquist, F. W. (1992) Biochemistry 31, 4749.
43. Makhatadze, G. I., & Privalov, P. L (1992) J. Mol. Biol. 224, 491.
44. Mark, A. E., & van Gunsteren, W. F. (1992) Biochemistry 31, 7745.
45. Matouschek, A., & Fersht, A. R. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 7814.
46. Matouschek, A., Kellis, J. T., Jr., Serrano, L., Bycroft, M., & Fersht, A. R. (1990) Nature 346, 440.
47. Matouschek, A., Serrano, L., Meiering, E. M., Bycroft, M., & Fersht, A. R. (1992) J. Mol. Biol. 224, 837.
48. Mauguen, Y., Hartley, R. W., Dodson, E. J., Dodson, G. G., Bricogne, G., Chothia, C., & Jack, A. (1982) Nature 297, 162.
49. Miranker, A., Radford, S. E., Karplus, M., & Dobson, C. M. (1991) Nature 349, 633.
50. Nishimura, S., & Nomura, M. (1958) Biochim. Biophys. Acta 30, 430.
51. Otzen, D. E., Itzhaki, L. S., ElMasry, N. F., Jackson, S. E., & Fersht, A. R, (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 10422.
52. Pace, C. N., Laurents, D. V., & Erickson, R. E. (1992) Biochemistry 31, 2728.
53. Pearlman, D. A., Case, D. A., Caldwell, J. C., Seibel, G. L., Singh, U. C., Weiner, P., & Kollman, P. A. (1991) AMBER 4.0, University of California, San Francisco.
54. Perrett, S., Clarke, J., Hounslow, A. M., & Fersht, A. R. (1995) Biochemistry 34, 9288.
55. Prévost, M. (1996) J. Mol. Biol. 260, 99.
56. Prévost, M., Wodak, S. J., Tidor, B., & Karplus, M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 10880.
57. Privalov, P. L. (1979) Adv. Protein Chem. 33, 167.
58. Ptitsyn, O. B. (1987) J. Protein Chem. 6, 273.
59. Pugliese, L., Prévost, M., & Wodak, S. J. (1995) J. Mol. Biol. 251, 432.
60. Radford, S. E., Dobson, C. M., & Evans, P. A. (1992) Nature 358, 302.
61. Richardson, J. S. (1981) Adv. Protein Chem. 34, 167.
62. Roder, H., Elöve, G. A., & Englander, S. W. (1988) Nature 335, 700.
63. Roseman, M., & Jencks, W. P. (1975) J. Am. Chem. Soc. 97, 631.
64. Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977) J. Comput. Phys. 23, 327.
65. Sali, D., Bycroft, M., & Fersht, A. R. (1988) Nature 335, 740.
66. Smythe, M. L., Huston, S. E., & Marshall, G. R. (1993) J. Am. Chem. Soc. 115, 11594.
67. Soman, K. V., Karimi, A., & Case, D. A. (1991) Biopolymers 31, 1351.
68. Sun, Y.-C., Veenstra, D. L., & Kollman, P. A. (1996) Protein Eng. 9, 273.
69. Tanford, C. (1968) Adv. Protein Chem. 23, 121.
70. Tiffany, M. L., & Krimm, S. (1973) Biopolymers 32, 575.
71. Tirado-Rives, J., & Jorgensen, W. L. (1991) Biochemistry 30, 3864.
72. Tirado-Rives, J., & Jorgensen, W. L. (1993) Biochemistry 32, 4175.
73. Tirado-Rives, J., Maxwell, D. S., & Jorgensen, W. L. (1993) J. Am. Chem. Soc. 115, 11590.
74. Udgaonkar, J. B., & Baldwin, R. L. (1988) Nature 335, 694.
75. Vijayakumar, S., Vishveshwara, S., Ravishanker, G., & Beveridge, D. L. (1993) Biophys. J. 65, 2304.
76. Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ohio, C., Alagona, G., Profeta, S., & Weiner, P. J. (1984) J. Am. Chem. Soc. 106, 765.
77. White, F. H., Jr., & Anfinsen, C. B (1959) Ann. N.Y. Acad. Sci. 81, 515.