Relation between native ensembles and experimental structures of proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 29, 2006, Pages 10901-10906

  Best, Robert B ^a,d   Lindorff Larsen, Kresten ^b   DePristo, Mark A ^c   Vendruscolo, Michele ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c HARVARD UNIVERSITY   (United States)

^d NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

NMR order parameters; Protein dynamics; Residual dipolar couplings

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ANIMALS; CHICKENS; DATABASES, PROTEIN; METHYLATION; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 33746652529     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0511156103     Document Type: Article

References (52)

1. Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., et al. (2002) Acta Crystallogr. D 58, 899-907.
2. Karplus, M. & McCammon, J. A. (2002) Nat. Struct. Biol. 9, 646-652.
3. Wand, A. J. (2001) Nat. Struct. Biol. 8, 926-931.
4. Palmer, A. G., III (2004) Chem. Rev. 104, 3623-3640.
5. Eisenmesser, E. Z., Millet, O., Labeikovsky, W., Korzhnev, D. M., Wolf-Watz, M., Bosco, D. A., Skalicky, J. J., Kay, L. E. & Kern, D. (2005) Nature 438, 117-121.
6. Kay, L. E. (2005) J. Magn. Reson. 173, 193-207.
7. Mittermaier, A. & Kay, L. E. (2004) Protein Sci. 13, 1088-1099.
8. Kay, L. E., Muhandiram, D. R., Wolf, G., Shoelson, S. E. & Forman-Kay, J. D. (1998) Nat. Struct. Biol. 5, 156-163.
9. Chaykovski, M. M., Bae, L. C., Cheng, M.-C., Murray, J. H., Tortolani, K. E., Zhang, R., Seshadri, K., Findlay, J. H. B. C., Hsieh, S.-Y., Kalverda, A. P., et al. (2003) J. Am. Chem. Soc. 125, 15767-15771.
10. Best, R. B., Rutherford, T. J., Freund, S. M. V. & Clarke, J. (2004) Biochemistry 43, 1145-1155.
11. Klein-Seetharaman, J., Oikawa, M., Grimshaw, S. B., Wirmer, J., Duchardt, E., Ueda, T., Imoto, T., Smith, L. J., Dobson, C. M. & Schwalbe, H. (2002) Science 295, 1719-1722.
12. Halle, B. (2002) Proc. Natl. Acad. Sci. USA 99, 1274-1279.
13. Zhang, F. & Brüschweiler, R. (2002) J. Am. Chem. Soc. 124, 12654-12655.
14. Chou, J. J., Case, D. A. & Bax, A. (2003) J. Am. Chem. Soc. 125, 8959-8966.
15. Best, R. B., Clarke, J. & Karplus, M. (2004) J. Mol. Biol. 349, 185-203.
16. Mittermaier, A., Kay, L. E. & Forman-Kay, J. D. (1999) J. Biomol. NMR 13, 181-185.
17. Ming, D. & Brüschweiler, R. (2004) J. Biomol. NMR 29, 363-368.
18. Zoete, V., Michielin, O. & Karplus, M. (2002) J. Mol. Biol. 315, 21-52.
19. Zhang, X. J., Wozniak, J. A. & Matthews, B. W. (1995) J. Mol. Biol. 250, 527-552.
20. Lipari, G. & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559.
21. Lipari, G., Szabo, A. & Levy, R. M. (1982) Nature 300, 197-198.
22. Chandler, D. (1987) Introduction to Modern Statistical Mechanics (Oxford Univ. Press, New York).
23. Levy, R., Sheridan, R., Keepers, J., Dubey, G., Swaminathan, S. & Karplus, M. (1985) Biophys. J. 48, 509-518.
24. Chothia, C. & Lesk, A. M. (1986) EMBO J. 5, 823-826.
25. Best, R. B., Clarke, J. & Karplus, M. (2004) J. Am. Chem. Soc. 126, 7734-7735.
26. Mittermaier, A., Davidson, A. R. & Kay, L. E. (2003) J. Am. Chem. Soc. 125, 9004-9005.
27. DePristo, M. A., de Bakker, P. I. W. & Blundell, T. L. (2004) Structure (London) 12, 831-838.
28. Bonvin, A. M. J. J. & Brünger, A. T. (1995) J. Mol. Biol. 250, 80-93.
29. Lindorff-Larsen, K., Best, R. B. & Vendruscolo, M. (2005) J. Biomol. NMR 32, 273-280.
30. Lindorff-Larsen, K., Best, R. B., DePristo, M. A., Dobson, C. M. & Vendruscolo, M. (2005) Nature 433, 128-132.
31. Schwalbe, H., Grimshaw, S. B., Spencer, A., Buck, M., Boyd, J., Dobson, C. M., Redfield, C. & Smith, L. J. (2001) Protein Sci. 10, 677-688.
32. Cornilescu, G., Marquardt, J. L., Ottiger, M. & Bax, A. (1998) J. Am. Chem. Soc. 120, 6836-6837.
33. Bax, A., Kontaxis, G. & Tjandra, N. (2001) Methods Enzymol. 339, 127-174.
34. Lazaridis, T. & Karplus, M. (1999) Proteins 35, 133-152.
35. Prabhu, N. V., Lee, A. L., Wand, A. J. & Sharp, K. A. (2003) Biochemistry 42, 562-570.
36. Ohlendorf, D. H. (1994) Acta Crystallogr. D 50, 808-812.
37. Hodel, A. Kim, S. H. & Brunger, A. T. (1992) Acta Crystallogr. A 48, 851-858.
38. Clarkson, M. W. & Lee, A. L. (2004) Biochemistry 43, 12448-12458.
39. Clore, G. M. & Schwieters, C. D. (2004) J. Am. Chem. Soc. 126, 2923-2938.
40. Clore, G. M. & Schwieters, C. D. (2004) Biochemistry 43, 10678-10691.
41. Clore, G. M. & Schwieters, C. D. (2006) J. Mol. Biol. 355, 879-886.
42. Buck, M. & Karplus, M. (1999) J. Am. Chem. Soc. 121, 9645-9658.
43. Prestegard, J. H., Bougault, C. M. & Kishore, A. L. (2004) Chem. Rev. 104, 3519-3540.
44. Lukin, J. A., Kontaxis, G., Simplaceanu, V., Yuan, Y., Bax, A. & Ho, C. (2003) Proc. Natl. Acad. Sci. USA 100, 517-520.
45. Perutz, M. F., Wilkinson, A. J., Paoli, M. & Dodson, G. G. (1998) Annu. Rev. Biophys. Biomol. Struct. 27, 1-34.
46. Meiler, J., Prompers, J. J., Peti, W., Griesinger, C. & Brüschweiler, R. (2001) J. Am. Chem. Soc. 123, 6098-6107.
47. Ma, B., Shatsky, M., Wolfson, H. J. & Nussinov, R. (2002) Protein Sci. 11, 184-197.
48. Carlson, H. A., Masukawa, K. M., Rubins, K., Bushman, F. D., Jorgensen, W. L., Lins, R. D., Briggs, J. M. & McCammon, J. A. (2000) J. Med. Chem. 43, 2100-2114.
49. Carlson, H. A., Masukawa, K. M. & McCammon, J. A. (1999) J. Phys. Chem. A 103, 10213-10219.
50. Shindyalov, I. N. & Bourne, P. E. (1998) Protein Eng. 11, 739-747.
51. Vondrasek, J. & Wlodawer, A. (2002) Proteins 49, 29-31.
52. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) J. Comp. Chem. 4, 187-217.