Folding funnels and binding mechanisms

Protein Engineering

Volumn 12, Issue 9, 1999, Pages 713-720

  Ma, Buyong ^a   Kumar, Sandeep ^b   Tsai, Chung Jung ^b   Nussinov, Ruth ^b,c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

Binding; Conformational ensembles; Energy landscape; Folding; Funnels; Lock and key vs induced fit; Misfolding

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ISOMER; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; SOLUTION AND SOLUBILITY; STATISTICAL ANALYSIS;

EID: 0032824805     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/12.9.713     Document Type: Article

References (75)

1. Abad-Zapatero, C., Rydel, T.J. and Erickson, J. (1990) Proteins, 8, 62-81.
2. Amit, A.G., Mariuzza, R.A., Phillips, S.E.V. and Poljak, R.J. (1986) Science, 233, 747-753.
3. Arrowsmith, C.H., Carey, J., Treat-Clemons, L. and Jardetzky, O. (1989) Biochemistry ,28, 3875-3879.
4. Baldwin, R.L. (1994) Nature, 369, 183-184.
5. Baldwin, R.L. (1995) J. Biomol. NMR, 5, 103-109.
6. Barford, D. and Johnson, L.N. (1989) Nature, 340, 609-616.
7. Bennett, M.J., Choe, S. and Eisenberg, D. (1994) Proc. Natl Acad. Sci. USA, 91, 3127-3131.
8. Bennett, M.J., Schlunegger, M.P. and Eisenberg, D. (1995) Protein Sci., 4, 2455-2468.
9. Bhat, T.N., Bentley, G.A., Fischmann, T.O., Boulot, G. and Poljak, R.J. (1990) Nature, 347, 483-485.
10. Boczko, E.M. and Brooks, C.L. III (1995) Science, 269, 393-396.
11. Braden B.C., Fields B.A., Ysern X., Goldbaum F.A., Dall'Acqua W., Schwarz F.P., Poljak R.J. and Mariuzza R.A. (1996) J. Mol. Biol., 257, 889-894.
12. Bryngelson, J.D. and Wolynes, P.G. (1989) J. Phys. Chem., 93, 6902-6915.
13. Carey, J. (1989) J. Biol. Chem., 264, 1941-1945.
14. D'Alessio, G. (1995) Nature Struct. Biol., 2, 11-13.
15. DebBurman, S.K., Raymond, G.J., Caughey, B. and Lindquist, S. (1997) Proc. Natl Acad. Sci. USA, 94, 13938-13943.
16. Dill, K.A. (1999) Protein Sci., 6, 1166-1180.
17. Dill, K.A. and Chan, H.S. (1995) Protein Sci., 4, 561-602.
18. Dill, K.A. and Chan, H.S. (1997) Nature Struct. Biol 4, 10-19.
19. Ditzel, H.J., Itoh, K. and Burton, D.R. (1996) J. Immunol., 157, 739-749.
20. Erickson, J.W., Baldwin, E.T., Bhat, T.N. and Gulik, S. (1995) In Takahashi, K. (ed.), Aspartic Proteinases: Structure, Function, Biology and Biomedical Implications. Plenum Press, New York.
21. Feller, G., Payan, F., Theys, F., Qian, M., Haser, R. and Gerday, C. (1994) Eur. J. Biochem., 222, 441-447.
22. Fischer, E. (1894) Ber. Dtsch. Chem. Ges., 27, 2985-2991.
23. Foote, J. and Milstein, C. (1994) Proc. Natl Acad. Sci. USA, 91, 10370-10374.
24. Frauenfelder, H. and Leeson, D.T. (1998) Nature Struct. Biol., 5, 757-759.
25. Frauenfelder, H., Sligar, S.G. and Wolynes, P.G. (1991) Science, 254, 1598-1603.
26. Gruebele, M. and Wolynes, P. (1998) Nature Struct. Biol., 5, 662-665.
27. Gryk, M.R., Jardetzky, O., Klig, L.S. and Yanofsky, C. (1996) Protein Sci., 5, 1195-1197.
28. Herron, J.N., He, X.M., Ballard, D.W., Blier, P.R., Pace, P.E., Bothwell, A.L., Voss, E.,Jr and Edmundson, A.B. (1991) Proteins, 11, 159-175.
29. Huang, M., Syed, R., Stura, E.A., Stone, M.J., Stefano, R.S., Ruf, W., Edgington, T.S. and Wilson, I. (1998) J. Mol. Biol., 275, 873-894.
30. Ichiyoshi, Y. and Casali, P. (1994) J. Exp. Med., 180, 885-895.
31. James, M.N.G., Sielecki, A., Salituro, F., Rich, D.H. and Hofmann, T. (1982) Proc. Natl Acad. Sci. USA, 79, 6137-6141.
32. Jarrett, J.T. and Lansbury, P.T., Jr (1993) Cell, 73, 1055-1058.
33. Karplus, M. (1997) Folding Des., 2, S69-S75.
34. Karplus, M. and Shakhnovitch, E. (1992) In Creighton, T. (ed.), Protein Folding. Freeman, New York, pp. 127-195.
35. Karplus, M., Sali, A. and Shakhnovitch, E. (1995) Nature, 373, 664-665.
36. Ke H.M., Liang J.Y., Zhang Y.P. and Lipscomb W.N. (1991) Biochemistry, 30, 4412-4420.
37. Koshland, D.E., Jr (1958) Proc. Natl Acad. Sci. USA, 44, 98-123.
38. Lazaridis, T. and Karplus, M. (1997) Science 278, 1928-1931.
39. Lawson, C.L., Zhang, R.G., Schevitz, R.W., Otwinowski, Z., Joachimiak, A. and Sigler, P.B. (1988) Proteins, 3, 18-31,.
40. Lee, A.Y., Gulnik, S.V. and Erickson, J.W. (1998) Nature Struct. Biol., 5, 866-871.
41. Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace H.C., Schumacher M.A., Brennan, R.G. and Lu P. (1996) Science, 271, 1247-1254.
42. Marmorstein, R. and Harrison, S.C. (1994) Genes Dev., 8, 2404-2412.
43. Martinez, J.C., Pisabarro, M.T. and Serrano, L. (1998) Nature Struct. Biol., 5, 721-729.
44. Milburn, M.V., Prive, G.G., Milligan, D.L., Scott, W.G., Yeh, J., Jancarik, J, Koshland, D.E., Jr and Kim, S.H. (1991) Science, 254, 1342-1347.
45. Muller, Y., Ultch, M.H. and De Vos, A.M. (1996) J. Mol. Biol., 256, 144-159.
46. Muller, Y., Kelley, R.F. and De Vos, A.M. (1998) Protein Sci., 7, 1106-1115.
47. Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I. and Aggarwal, A.K. (1995) Science, 269, 656-663.
48. Ogata, K. et al. (1996) Nature Struct. Biol., 3, 178-187.
49. Onuchic, J.N., Wolynes, P.G., Luthey-Schulten, Z. and Socci, N.D. (1995) Proc. Natl Acad. Sci. USA, 92, 3626-3630.
50. Perutz, M.F., Wilkinson, A,J., Paoli, M. and Dodson, G.G. (1998) Annu. Rev. Biophys. Biomol. Struct., 27, 1-34.
51. Piccoli, R., Tamburrini, M., Piccialli, G., Di Donato, A., Parente, A. and D'Alessio, G. (1992) Proc. Natl Acad. Sci. USA, 89, 1870-1874.
52. Pieper, U., Hayakawa, K., Li, Z. and Herzberg, O. (1997) Biochemistry, 36, 8767-8774.
53. Prusiner, S.B. (1991) Science, 252, 1515-1522.
54. Rini, J.M., Stanfield, R.L., Stura, E.A., Salinas, P.A., Profy, A.T. and Wilson, I.A. (1993) Proc Natl Acad Sci USA, 90, 6325-6329.
55. Rose, R.B., Craik, C.S. and Stroud, R.M. (1998) Biochemistry, 37, 2607-2621.
56. Sali, A., Cooper, J.B., Foundling, S.I., Hoover, D.J. and Blundell, T.L. (1989) EMBO J., 8, 2179-2188.
57. Schirmer, T. and Evans, P.R. (1990) Nature, 343, 140-145.
58. Shaknovich, E.T. and Gutin, A.M. (1993) Protein Engng, 6, 793-800.
59. Shoichet, B.K., Baase, W.A., Kuroki, R. and Matthews, B.W. (1995) Proc. Natl Acad. Sci. USA, 92, 452-456.
60. Silva, A.M. et al. (1996) Proc. Natl Acad. Sci. USA, 93, 10034-10039.
61. Stanfield, R.L., Takimoto-Kanimura, M., Rini, J.M., Profy, A.T. and Wilson, I.A. (1993) Structure, 1, 83-93.
62. Stevens, R.C. and Lipscomb, W.N. (1992) Proc. Natl Acad. Sci. USA, 89, 5281-5285.
63. Sun, J. and Sampson, N.S. (1998) Protein Sci., 7, 1495-1505.
64. Tsai, C.J. and Nussinov, R. (1997a) Protein Sci. 6, 24-42.
65. Tsai, C.J. and Nussinov, R. (1997b) Protein Sci., 6, 1426-1437.
66. Tsai, C.J., Xu, D. and Nussinov, R. (1998) Folding Des., 3, R71-R80.
67. Tsai, C.J., Kumar, S., Ma, B. and Nussinov, R. (1999) Protein Sci., 6, 1181-1190.
68. Waldburger, C.D., Jonsson, T. and Sauer, R.T. (1996) Proc. Natl Acad. Sci. USA, 93, 2629-2634.
69. Wallon, G., Lovett, S.T., Magyar, C., Svingor, A., Szilagyi, A., Zavodszky, P., Ringe, D., Patsko, G.A. (1997) Protein Engng, 10, 665-672.
70. Wang, Y. and Shortle, D. (1996) Protein Sci., 5, 1898-1906.
71. Wedemayer, G.J., Patten, P.A., Wang, L.H., Schultz, P.G. and Stevens R.C. (1997) Nature Struct. Biol., 276, 1665-1669.
72. Wilderspin, A.F. and Sugrue, R.J. (1994) J. Mol. Biol., 239, 97-103.
73. Wolynes, P.G., Onuchic, J.N. and Thirumalai, D. (1995) Science, 267, 1619-1620.
74. Yip, K.S.P. et al. (1995) Structure, 3, 1147-1158.
75. Zavodszky, P., Kardos, J., Svingor, A. and Petsko, G.A. (1998) Proc. Natl Acad. Sci. USA, 95, 7406-7411.