Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance

Advances in Protein Chemistry

Volumn 62, Issue , 2002, Pages 311-340

  Dyson, H Jane ^a   Wright, Peter E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOMYOGLOBIN;

DIFFUSION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; REVIEW; STRUCTURE ANALYSIS;

EID: 0036400715     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3233(02)62012-1     Document Type: Review

References (117)

1. Alexandrescu, A. T., Abeygunawardana, C., and Shortle, D. (1994). Biochemistry 33, 1063-1072.
2. Alexandrescu, A. T., and Shortle, D. (1994). J. Mol. Biol. 242, 527-546.
3. Altieri, A. S., Hinton, D. P., and Byrd, R. A. (1995). J. Am. Chem. Soc. 117, 7566-7567.
4. Arcus, V. L., Vuilleumier, S., Freund, S. M. V., Bycroft, M., and Fersht, A. R. (1995). J. Mol. Biol. 254, 305-321.
5. Ayed, A., Mulder, F. A., Yi, G. S., Lu, Y., Kay, L. E., and Arrowsmith, C. H. (2001). Nat. Struct. Biol. 8, 756-760.
6. Bai, Y., Chung, J., Dyson, H. J., and Wright, P. E. (2001). Protein Sci. 10, 1056-1066.
7. Barrick, D., and Baldwin, R. L. (1993). Biochemistry 32, 3790-3796.
8. Baum, J., Dobson, C. M., Evans, P. A., and Hanley, C. (1989). Biochemistry 28, 7-13.
9. Bax, A., and Grzesiek, S. (1993). Acc. Chem. Res. 26, 131-138.
10. Billeter, M., Braun, W., and Wüthrich, K. (1982). J. Mol. Biol. 155, 321-346.
11. Botuyan, M. V., Koth, C. M., Mer, G., Chakrabartty, A., Conaway, J. W., Conaway, R. C., Edwards, A. M., Arrowsmith, C. H., and Chazin, W. J. (1999). Proc. Natl. Acad. Sci. USA 96, 9033-9038.
12. Botuyan, M. V., Mer, G., Yi, G. S., Koth, C. M., Case, D. A., Edwards, A. M., Chazin, W. J., and Arrowsmith, C. H. (2001). J. Mol. Biol. 312, 177-186.
13. Brant, D. A., Miller, W. G., and Flory, P. J. (1967). J. Mol. Biol. 23, 47-65.
14. Braun, D., Wider, G., and Wüthrich, K. (1994). J. Am. Chem. Soc. 116, 8466-8469.
15. Brutscher, B., Brüschweiler, R., and Ernst, R. R. (1997). Biochemistry 36, 13043-13053.
16. Buchberger, A., Howard, M. J., Freund, S. M., Proctor, M., Butler, P. J., Fersht, A. R., and Bycroft, M. (2000). Biochemistry 39, 12512.
17. Buck, M., Radford, S. E., and Dobson, C. M. (1994). J. Mol. Biol. 237, 247-254.
18. Buck, M., Schwalbe, H., and Dobson, C. M. (1996). J. Mol. Biol. 257, 669-683.
19. Buevich, A. V., and Baum, J. (1999). J. Am. Chem. Soc. 121, 8671-8672.
20. Buevich, A. V., Shinde, U. P., Inouye, M., and Baum, J. (2001). J. Biomol. NMR 20, 233-249.
21. Choy, W. Y., and Forman-Kay, J. D. (2001). J. Mol. Biol. 308, 1011-1032.
22. Choy, W. Y., Mulder, F. A., Crowhurst, K. A., Muhandiram, D. R., Millett, I. S., Doniach, S., Forman-Kay, J. D., and Kay, L. E. (2002). J. Mol. Biol. 316, 101-112.
23. Constantine, K. L., Mueller, L., Andersen, N. H., Tong, H., Wandler, C. F., Friedrichs, M. S., and Bruccoleri, R. E. (1995). J. Am. Chon. Soc. 117, 10841-10854.
24. de Dios, A. C., Pearson, J. G., and Oldfield, E. (1993). Science 260, 1491-1496.
25. Demarest, S. J., Martinez-Yamout, M., Chung, J., Chen, H., Xu, W., Dyson, H. J., Evans, R. M., and Wright, P. E. (2002). Nature 415, 549-553.
26. Dunker, A. K., and Obradovic, Z. (2001). Nat. Biotechnol. 19, 805-806.
27. Dyson, H. J., and Wright, P. E. (1991). Annu. Rev. Biophys. Biophys. Chem. 20, 519-538.
28. Dyson, H. J., and Wright, P. E. (1996). Annu. Rev. Phys. Chem. 47, 369-395.
29. Dyson, H. J., and Wright, P. E. (1998). Nat. Struct. Biol. 5, 499-503.
30. Dyson, H. J., and Wright, P. E. (2002). Curr. Opin. Struct. Biol. 12, 54-60.
31. Eliezer, D., Chung, J., Dyson, H. J., and Wright, P. E. (2000). Biochemistry 39, 2894-2901.
32. Eliezer, D., Jennings, P. A., Wright, P. E., Doniach, S., Hodgson, K. O., and Tsuruta, H. (1995). Science 270, 487-488.
33. Eliezer, D., and Wright, P. E. (1996). J. Mol. Biol. 263, 531-538.
34. Eliezer, D., Yao, J., Dyson, H. J., and Wright, P. E. (1998). Nat. Struct. Biol. 5, 148-155.
35. Epand, R. M., and Scheraga, H. A. (1968). Biochemistry 7, 2864-2872.
36. Evans, P. A., Topping, K. D., Woolfson, D. N., and Dobson, C. M. (1991). Proteins 9, 248-266.
37. Farrow, N. A., Muhandiram, R., Singer, A. U., Pascal, S. M., Kay, C. M., Gish, G., Shoelson, S. E., Pawson, T., Forman-Kay, J. D., and Kay, L. E. (1994). Biochemistry 33, 5984-6003.
38. Farrow, N. A., Zhang, O., Forman-Kay, J. D., and Kay, L. E. (1995a). Biochemistry 34, 868-878.
39. Farrow, N. A., Zhang, O., Forman-Kay, J. D., and Kay, L. E. (1997). Biochemistry 36, 2390-2402.
40. Farrow, N. A., Zhang, O., Szabo, A., Torchia, D. A., and Kay, L. E. (1995b). J. Biomol. NMR 6, 153-162.
41. Frank, M. K., Clore, G. M., and Gronenborn, A. M. (1995). Protein Sci. 4, 2605-2615.
42. Frenkiel, T., Bauer, C., Carr, M. D., Birdsall, B., and Feeney, J. (1990). J. Magn. Reson. 90, 420-425.
43. Gast, K., Damaschun, H., Misselwitz, R., Müller-Frohne, M., Zirwer, D., and Damaschun, G. (1994). Eur. Biophys. J. 23, 297-305.
44. Gillespie, J. R., and Shortle, D. (1997a). J. Mol. Biol. 268, 158-169.
45. Gillespie, J. R., and Shortle, D. (1997a). J. Mol. Biol. 268, 170-184.
46. Gilmanshin, R., Gulotta, M., Dyer, R. B., and Callender, R. H. (2001). Biochemistry 40, 5127-5136.
47. Gilmanshin, R., Williams, S., Callender, R. H., Woodruff, W. H., and Dyer, R. B. (1997). Proc. Natl. Acad. Sci. USA 94, 3709-3713.
48. Griko, Y. V., and Privalov, P. L. (1994). J. Mol. Biol. 235, 1318-1325.
49. Griko, Y. V., Privalov, P. L., Venyaminov, S. Y., and Kutyshenko, V. P. (1988). J. Mol. Biol. 202, 127-138.
50. Grossmann, J. G., Sharff, A. J., O'Hare, P., and Luisi, B. (2001). Biochemistry 40, 6267-6274.
51. Gulotta, M., Gilmanshin, R., Buscher, T. C., Callender, R. H., and Dyer, R. B. (2001). Biochemistry 40, 5137-5143.
52. Hermans, J., Puett, D., and Acampora, G. (1969). Biochemistry 8, 22-30.
53. Hua, Q. X., Jia, W. H., Bullock, B. P., Habener, J. F., and Weiss, M. A. (1998). Biochemistry 37, 5858-5866.
54. Hughson, F. M., Wright, P. E., and Baldwin, R. L. (1990). Science 249, 1544-1548.
55. Ikura, M., Bax, A., Clore, G. M., and Gronenborn, A. M. (1990). J. Am. Chem. Soc. 112, 9020-9022.
56. Ishima, R., and Nagayama, K. (1995). J. Magn. Reson. Ser. B 108, 73-76.
57. Jamin, M., and Baldwin, R. L. (1998). J. Mol. Biol. 276, 491-504.
58. Jennings, P. A., and Wright, P. E. (1993). Science 262, 892-896.
59. Jones, J. A., Wilkins, D. K., Smith, L. J., and Dobson, C. M. (1997). J. Biomol. NMR 10, 199-203.
60. Kay, L. E. (1995). Prog. Biophys. Mol. Biol. 63, 277-299.
61. Kim, S., Bracken, C., and Baum, J. (1999). J. Mol. Biol. 294, 551-560.
62. Kuriyan, J., Wilz, S., Karplus, M., and Petsko, G. A. (1986). J. Mol. Biol. 192, 133-154.
63. Kussie, P. H., Gorina, S., Marechal, V., Elenbaas, B., Moreau J., Levine, A. J., and Pavletich, N. P. (1996). Science 274, 948-953.
64. Lecomte, J. T., Sukits, S. F., Bhattacharjya, S., and Falzone, C. J. (1999). Protein Sci. 8, 1484-1491.
65. Lipari, G., and Szabo, A. (1982a). J. Am. Chem. Soc. 104, 4546-4559.
66. Lipari, G., and Szabo, A. (1982b). J. Am. Chem. Soc. 104, 4559-4570.
67. Liu, A., Riek, R., Wider, G., Von Schroetter, C., Zahn, R., and Wüthrich, K. (2000). J. Biomol. NMR 16, 127-138.
68. Logan, T. M., Thériault, Y., and Fesik, S. W. (1994). J. Mol. Biol. 236, 637-648.
69. Lumb, K. J., and Kim, P. S. (1994). J. Mol. Biol. 236, 412-420.
70. McDonald, C. A., and Phillips, D. C. (1969). J. Am. Chem. Soc. 91, 1513.
71. Meekhof, A. E., and Freund, S. M. V. (1999). J. Mol. Biol. 286, 579-592.
72. Meirovitch, E., and Meirovitch, H. (1996). Biopolymers 38, 69-88.
73. Merutka, G., Dyson, H. J., and Wright, P. E. (1995). J. Biomol. NMR 5, 14-24.
74. Mok, Y. K., Kay, C. M., Kay, L. E., and Forman-Kay, J. (1999). J. Mol. Biol. 289, 619-638.
75. Neri, D., Billeter, M., Wider, G., and Wüthrich, K. (1992a). Science 257, 1559-1563.
76. Neri, D., Wider, G., and Wüthrich, K. (1992b). Proc. Natl. Acad. Sci. USA 89, 4397-4401.
77. Nishii, I., Kataoka, M., and Goto, Y. (1995). J. Mol. Biol. 250, 223-238.
78. Nishii, I., Kataoka, M., Tokunaga, F., and Goto, Y. (1994). Biochemistry 33, 4903-4909.
79. Nishimura, C., Prytulla, S., Dyson, H. J., and Wright, P. E. (2000). Nat. Struct. Biol. 7, 679-686.
80. Palmer, A. G., Cavanagh, J., Wright, P. E., and Rance, M. (1991). J. Magn. Reson. 93, 151-170.
81. Peng, J. W., and Wagner, G. (1992). J. Magn. Reson. 98, 308-332.
82. Penkett, C. J., Redfleid, C., Jones, J. A., Dodd, I., Hubbard, J., Smith, R. A. G., Smith, L. J., and Dobson, C. M. (1998). Biochemistry 37, 17054-17067.
83. Radhakrishnan, I., Pérez-Alvarado, G. C., Dyson, H. J., and Wright, P. E. (1998). FEBS Lett. 430, 317-322.
84. Radhakrishnan, I., Pérez-Alvarado, G. C., Parker, D., Dyson, H. J., Montminy, M. R., and Wright, P. E. (1999). J. Mol. Biol. 287, 859-865.
85. Ramachandran, G. N., Ramakrishnan, C., and Sasisekharan, V. (1963). J. Mol. Biol. 7, 95-99.
86. Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H., and Zehfus, M. H. (1985). Science 229, 834-838.
87. Sari, N., Alexander, P., Bryan, P. N., and Orban, J. (2000). Biochemistry 39, 965-977.
88. Schwalbe, H., Fiebig, K. M., Buck, M., Jones, J. A., Grimshaw, S. B., Spencer, A., Glaser, S. J., Smith, L. J., and Dobson, C. M. (1997). Biochemistry 36, 8977-8991.
89. Schwarzinger, S., Kroon, G. J. A., Foss, T. R., Chung, J., Wright, P. E., and Dyson, H. J. (2001). J. Am. Chem. Soc. 123, 2970-2978.
90. Schwarzinger, S., Wright, P. E., and Dyson, H. J. (2002). Biochemistry (in press).
91. Smith, L. J., Bolin, K. A., Schwalbe, H., MacArthur, M. W., Thornton, J. M., and Dobson, C. M. (1996a). J. Mol. Biol. 255, 494-506.
92. Smith, L. J., Fiebig, K. M., Schwalbe, H., and Dobson, C. M. (1996b). Fold. Design 1, R95-R106.
93. Spera, S., and Bax, A. (1991). J. Am. Chem. Soc. 113, 5490-5492.
94. Taniuchi, H., and Anfinsen, C. B. (1969). J. Biol. Chem. 244, 3864-3875.
95. Tsui, V., Garcia, C., Cavagnero, S., Siuzdak, G., Dyson, H. J., and Wright, P. E. (1999). Protein Sci. 8, 45-49.
96. Uesugi, M., Nyanguile, O., Lu, H., Levine, A. J., and Verdine, G. L. (1997). Science 277, 1310-1313.
97. Waltho, J. P., Feher, V. A., Merutka, G., Dyson, H. J., and Wright, P. E. (1993). Biochemistry 32, 6337-6347.
98. Wang, J. J., Hodges, R. S., and Sykes, B. D. (1995). J. Am. Chem. Soc. 117, 8627-8634.
99. Wijesinha-Bettoni, R., Dobson, C. M., and Redfield, C. (2001). J. Mol. Biol. 307, 885-898.
100. Wilkins, D. K., Grimshaw, S. B., Receveur, V., Dobson, C. M., Jones, J. A., and Smith, L. J. (1999). Biochemistry 38, 16424-16431.
101. Williamson, M. P. (1990). Biopolymers 29, 1423-1431.
102. Wishart, D. S., Bigam, C. G., Holm, A., Hodges, R. S., and Sykes, B. D. (1995). J. Biomol. NMR 5, 67-81.
103. Wishart, D. S., and Nip, A. M. (1998). Biochem. Cell Biol. 76, 153-163.
104. Wishart, D. S., and Sykes, B. D. (1994). Methods Enzymol. 239, 363-392.
105. Wong, K. B., Clarke, J., Bond, C. J., Neira, J. L., Freund, S. M. V., Fersht, A. R., and Daggett, V. (2000). J. Mol. Biol. 296, 1257-1282.
106. Wright, P. E., and Dyson, H. J. (1999). J. Mol. Biol. 293, 321-331.
107. Wright, P. E., Dyson, H. J., and Lerner, R. A. (1988). Biochemistry 27, 7167-7175.
108. Yang, D. W., Mok, Y. K., Muhandiram, D. R., Forman-Kay, J. D., and Kay, L. E. (1999). J. Am. Chem. Soc. 121, 3555-3556.
109. Yao, J., Chung, J., Eliezer, D., Wright, P. E., and Dyson, H. J. (2001). Biochemistry 40, 3561-3571.
110. Yao, J., Dyson, H. J., and Wright, P. E. (1994). J. Mol. Biol. 243, 754-766.
111. Yao, J., Dyson, H. J., and Wright, P. E. (1997). FEBS Lett. 419, 285-289.
112. Zhang, O., and Forman-Kay, J. D. (1995). Biochemistry 34, 6784-6794.
113. Zhang, O., and Forman-Kay, J. D. (1997). Biochemistry 36, 3959-3970.
114. Zhang, O., Forman-Kay, J. D., Shortle, D., and Kay, L. E. (1997a). J. Biomol. NMR 9, 181-200.
115. Zhang, O., Kay, L. E., Olivier, J. P., and Forman-Kay, J. D. (1994). J. Biomol. NMR 4, 845-858.
116. Zhang, O., Kay, L. E., Shortle, D., and Forman-Kay, J. D. (1997b). J. Mol. Biol. 272, 9-20.
117. Zimm, B. H., and Bragg, K. J. (1959). J. Chem. Phys. 31, 526-535.