Rapid protein fold determination using unassigned NMR data

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

Volumn 100, Issue 26, 2003, Pages 15404-15409

  Meiler, Jens ^a   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Chemical shift atom assignment; De novo fold prediction; Nuclear magnetic resonance; ROSETTA Monte Carlo optimization

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; UBIQUITIN;

EID: 0346103679     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.2434121100     Document Type: Article

References (45)

1. Tolman, J. R., Flanagan, J. M., Kennedy, M. A. & Prestegard, J. H. (1995) Proc. Natl. Acad. Sci. USA 92, 9279-9283.
2. Tjandra, N. & Bax, A. (1997) Science 278, 1111-1113.
3. Sattler, M., Schleucher, J. & Griesinger, C. (1999) Prog. Nucl. Magn. Reason. Spectrosc. 34, 93-158.
4. Reif, B., Hennig, M. & Griesinger, C. (1997) Science 276, 1230-1233.
5. Prestegard, J. H., Valafar, H., Glushka, J. & Tian, F. (2001) Biochemistry 40, 8677-8685.
6. Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225.
7. Bonneau, R., Strauss, C. E. M., Rohl, C., Chivian, D., Bradley, P., Malmström, L., Robertson, T. & Baker, D. (2002) J. Mol. Biol. 322, 65-78.
8. Bonneau, R., Tsai, J., Ruczinski, I., Chivian, D., Rohl, C., Strauss, C. E. M. & Baker, D. (2001) Proteins 45, Suppl., 119-126.
9. Bradley, P., Chivian, D., Meiler, J., Misura, K., Wedemeyer, W., Rohl, C., Schief, B. & Baker, D. (2003) Proteins Struct. Funct. Genet. 53, 457-468.
10. Jones, D. T. (1999) J. Mol. Biol. 292, 195-202.
11. Rost, B. & Sander, C. (1993) Proc. Natl. Acad. Sci. USA 90, 7558-7562.
12. Meiler, J., Müller, M., Zeidler, A. & Schmäschke, F. (2001) J. Mol. Model. 7, 360-369.
13. Oschkinat, H. & Croft, D. (1994) Methods Enzymol. 239, 308-318.
14. Zimmerman, D. E., Kulikowski, C. A., Huang, Y. P., Feng, W. Q., Tashiro, M., Shimotakahara, S., Chien, C. Y., Powers, R. & Montelione, G. T. (1997) J. Mol. Biol. 269, 592-610.
15. Moseley, H. N. B. & Montelione, G. T. (1999) Struct. Biol. 9, 635-642.
16. Gronwald, W., Kirchhöfer, R., Görler, A., Kremer, W., Ganslmeier, B., Neidig, K.-P. & Kalbitzer, H. R. (2000) J. Biomol. NMR 17, 137-151.
17. Wishart, D. S., Sykes, B. D. & Richards, F. M. (1992) Biochemistry 31, 1647-1651.
18. Wishart, D. S. & Sykes, B. D. (1994) J. Biomol. NMR 4, 171-180.
19. Grishaev, A. & Llinas, M. (2002) Proc. Natl. Acad. Sci. USA 99, 6707-6712.
20. Grishaev, A. & Llinas, M. (2002) Proc. Natl. Acad. Sci. USA 99, 6713-6718.
21. Hus, J.-C., Marion, D. & Blackledge, M. (2000) J. Mol. Biol. 298, 927-936.
22. Meiler, J., Blomberg, N., Nilges, M. & Griesinger, C. (2000) J. Biomol. NMR 16, 245-252.
23. Delaglio, F., Kontaxis, G. & Bax, A. (2000) J. Am. Chem. Soc. 122, 2142-2143.
24. Meiler, J., Peti, W. & Griesinger, C. (2000) J. Biomol. NMR 17, 283-294.
25. Clore, G. M., Gronenborn, A. M. & Bax, A. (1998). J. Magn. Reson. 133, 216-221.
26. Meiler, J. (2003) J. Biomol. NMR 26, 25-37.
27. Losonczi, J. A., Andrec, M., Fischer, M. W. F. & Prestegard, J. H. (1999) J. Magn. Reson. 138, 334-342.
28. Bowers, P. M., Strauss, C. E. M. & Baker, D. (2000) J. Biomol. NMR 18, 311-318.
29. Rohl, C. & Baker, D. (2002) J. Am. Chem Soc. 124, 2723-2729.
30. Drohat, A. C., Tjandra, N., Baldisseri, D. M. & Weber, D. J. (1999) Protein Sci. 8, 800-809.
31. de Alba, E., de Vries, L., Farquhar, M. G. & Tjandra, N. (1999) J. Mol. Biol. 291, 927-939.
32. Gronenborn, A. M., Filpula, D. R., Essig, N. Z., Achari, A., Whitlow, M., Wingfield, P. T. & Clore, G. M. (1991) Science 253, 657-661.
33. Clore, G. M., Starich, M. R. & Gronenborn, A. M. (1998) J. Am. Chem. Soc. 120, 10571-10572.
34. Kuszewski, J., Gronenborn, A. M. & Clore, G. M. (1999) J. Am. Chem. Soc. 121, 2337-2338.
35. Ramirez, B. E., Voloshin, O. N., Camerini-Otero, R. D. & Bax, A. (2000) Protein Sci. 9, 2161-2169.
36. Baber, J. L., Libutti, D., Levens, D. & Tjandra, N. (1999) J. Mol. Biol. 289, 949-962.
37. Cornileseu, G., Marquardt, J. L., Ottiger, M. & Bax, A. (1998) J. Am. Chem. Soc. 120, 6836-6837.
38. Bewley, C.A., Gustafson, K. R., Boyd, M. R., Covell, D. G., Bax, A., Clore, G. M. & Gronenborn, A. M. (1998) Nat. Struct. Biol. 5, 571-578.
39. Cai, M., Huang, Y., Zheng, R., Wei, S.-Q., Ghirlando, R., Lee, M. S., Craigie, R., Gronenborn, A. M. & Clore, G. M. (1998) Nat. Struct. Biol. 5, 903-909.
40. Bruenger, A. T. (1992) X-PLOR: A System for X-Ray Crystallography and NMR (Yale Univ. Press, New Haven, CT).
41. Bruenger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kuntsleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1990) Acta Crystallogr. D 54, 905-921.
42. Linge, J. P., O'Donoghue, S. I. & Nilges, M. (2001) Methods Enzymol 339, 71-90.
43. Hus, J.-C., Prompers, J. & Brueschweiler, R. (2002) J. Magn. Reson. 157, 119-123.
44. Pappalardo, L., Janausch, I. G., Vijayan, V., Zientz, E., Junker, J., Peti, W., Zweckstetter, M., Unden, G. & Griesinger, C. (2003) J. Biol. Chem. 278, 39185-39188.
45. Ho, Y. S., Burden. L. M. & Hurley, J. H. (2000) EMBO J. 19, 5288-5299.