Deuterated protein folds obtained directly from unassigned nuclear overhauser effect data

Journal of the American Chemical Society

Volumn 130, Issue 12, 2008, Pages 3797-3805

  Bermejo, Guíllermo A ^a   Llinás, Míguel ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DATA REDUCTION; DATABASE SYSTEMS; GRAPH THEORY; NUCLEAR MAGNETIC RESONANCE;

BIPARTITE GRAPH MATCHING; DEUTERATED PROTEIN; NUCLEAR OVERHAUSER EFFECT (NOE); SIDE-CHAIN PROTONS;

PROTEINS;

PEPTIDE; PROTEIN; PROTON; STAPHYLOCOCCUS PROTEIN A;

ANALYTIC METHOD; ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; FEASIBILITY STUDY; NITROGEN NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE;

COMPUTER SIMULATION; DATABASES, PROTEIN; DEUTERIUM; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTONS; REFERENCE STANDARDS; SOFTWARE; STAPHYLOCOCCAL PROTEIN A;

EID: 41149166656     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja074836e     Document Type: Article

References (49)

1. Gronwald, W.; Kalbitzer, H. R. Prog. Nucl. Magn. Reson. Spectrosc. 2004, 44 (1-2), 33-96.
2. Wüthrich, K. NMR of Proteins and Nucleic Acids; Wiley: New York, 1986; p 292.
3. Goto, N. K.; Kay, L. E. Curr. Opin. Struct. Biol. 2000, 10 (5), 585-592.
4. Gardner, K. H.; Rosen, M. K.; Kay, L. E. Biochemistry 1997, 36 (6), 1389-1401.
5. Berardi, M. J.; Sun, C. H.; Zehr, M.; Abildgaard, F.; Peng, J.; Speck, N. A.; Bushweller, J. H. Struct. Fold Des. 1999, 7 (10), 1247-1256.
6. Mueller, G. A.; Choy, W. Y.; Yang, D. W.; Forman-Kay, J. D.; Venters, R. A.; Kay, L. E. J. Mol. Biol. 2000, 300 (1), 197-212.
7. Zheng, D. Y.; Huang, Y. P. J.; Moseley, H. N. B.; Xiao, R.; Aramini, J.; Swapna, G. V. T.; Montelione, G. T. Protein Sci. 2003, 12 (6), 1232-1246.
8. Tugarinov, V.; Choy, W. Y.; Orekhov, V. Y.; Kay, L. E. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (3), 622-627.
9. Grishaev, A.; Llinás, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (10), 6707-6712.
10. Grishaev, A.; Llinás, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (10), 6713-6718.
11. Atkinson, R. A.; Saudek, V., The Direct Determination of Protein Structure from Multidimensional NMR Spectra Without Assignment. In Dynamics and the Problem of Recognition in Biological Macromolecules; Jardetzky, O., Lefèvre, J. F., Eds.; Plenum Press: New York, 1996; Vol. 288, pp 49-55.
12. Atkinson, R. A.; Saudek, V. J. Chem. Soc., Faraday Trans. 1997, 93 (18), 3319-3323.
13. Kraulis, P. J. J. Mol. Biol. 1994, 243 (4), 696-718.
14. Malliavin, T. E.; Rouh, A.; Delsuc, M. A.; Lallemand, J. Y. C. R. Acad. Sci. Paris, Ser.. 11 1992, 315 (6), 653-659.
15. Tashiro, M.; Tejero, R.; Zimmerman, D. E.; Celda, B.; Nilsson, B.; Montelione, G. T. J. Mol. Biol. 1997, 272 (4), 573-590.
16. Tugarinov, V.; Hwang, P. M.; Kay, L. E., Annu. Rev. Biochem. 2004, 73, 107-146.
17. Goto, N. K.; Gardner, K. H.; Mueller, G. A.; Willis, R. C.; Kay, L. E. J. Biomol. NMR 1999, 13 (4), 369-374.
18. Malliavin, T. E.; Barthe, P.; Delsuc, M. A. Theor. Chem. Acc. 2001, 106 (1-2), 91-97.
19. Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. J. Mol. Biol. 1999, 285 (4), 1735-1747.
20. Tropp, J. J. Chem. Phys. 1980, 72 (11), 6035-6043.
21. Zhu, L. M.; Dyson, H. J.; Wright, P. E. J. Biomol. NMR 1998, 11 (1), 17-29.
22. Russell, S. J.; Norvig, P. Artificial Intelligence: a Modern Approach, 2nd ed.; Prentice Hall/Pearson Education: Upper Saddle River, NJ, 2003; pp xxviii, 1080.
23. Asratian, A. S.; Denley, T. M. J.; Hèaggkvist, R. Bipartite Graphs and their Applications; Cambridge University Press: Cambridge, U. K., and New York, 1998; pp xi, 259.
24. Hus, J. C.; Prompers, J. J.; Brüschweiler, R. J. Magn. Reson. 2002, 157 (1), 119-123.
25. Xu, Y.; Xu, D.; Kim, D.; Olman, V.; Razumovskaya, J.; Jiang, T. Comput. Sci. Eng. 2002, 4 (1), 50-62.
26. Langmead, C. J.; Donald, B. R. J. Biomol. NMR 2004, 29 (2), 111-138.
27. Langmead, C. J.; Yan, A.; Lilien, R.; Wang, L. C.; Donald, B. R. J. Comput. Biol. 2004, 11 (2-3), 277-298.
28. Constantine, K. L.; Davis, M. E.; Metzler, W. J.; Mueller, L.; Claus, B. L. J. Am. Chem. Soc. 2006, 128 (22), 7252-7263.
29. Wishart, D. S.; Sykes, B. D. J. Biomol. NMR 1994, 4 (2), 171-180.
30. Cornilescu, G.; Delaglio, F.; Bax, A. J. Biomol. NMR 1999, 13 (3), 289-302.
31. Simons, K. T.; Kooperberg, C.; Huang, E.; Baker, D. J. Mol. Biol. 1997, 268 (1), 209-225.
32. Bowers, P. M.; Strauss, C. E. M.; Baker, D. J. Biomol. NMR 2000, 18 (4), 311-318.
33. AB, E.; Pugh, D. J. R.; Kaptein, R.; Boelens, R.; Bonvin, A. M. J. J. J. Am. Chem. Soc. 2006, 128 (23), 7566-7571.
34. Clore, G. M.; Kuszewski, J. J. Am. Chem. Soc. 2002, 124 (12), 2866-2867.
35. Schwieters, C. D.; Kuszewski, J. J.; Clore, G. M. Prog. Nucl. Magn. Reson. Spectrosc. 2006, 48 (1), 47-62.
36. Schwieters, C. D.; Kuszewski, J. J.; Tjandra, N.; Clore, G. M. J. Magn. Reson. 2003, 160 (1), 65-73.
37. Koradi, R.; Billeter, M.; Wüthrich, K. J. Mol. Graphics 1996, 14 (1), 51-55.
38. Nilges, M.; Clore, G. M.; Gronenborn, A. M. FEBS Lett. 1988, 239 (1), 129-136.
39. Morris, R. J.; Perrakis, A.; Lamzin, V. S. Acta. Crystallogr. D 2002, 58, 968-975.
40. Linge, J. P.; Habeck, M.; Rieping, W.; Nilges, M. Bioinfcrmatics 2003, 19 (2), 315-316.
41. Herrmann, T.; Güntert, P.; Wüthrich, K. J. Mol. Biol. 2002, 319 (1), 209-227.
42. Grishaev, A.; Llinás, M. J. Biomol. NMR 2004, 28 (1), 1-10.
43. Grishaev, A.; Llinás, M. J. Biomol. NMR 2002, 24 (3), 203-213.
44. Grishaev, A.; Llinás, M. Methods Enzymol. 2005, 394, 261-295.
45. Jung, Y. S.; Sharma, M.; Zweckstetter, M. Angew. Chem., Int. Ed. 2004, 43 (26), 3479-3481.
46. Meiler, J.; Baker, D. J. Magn. Reson. 2005, 173 (2), 310-316.
47. Meiler, J.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (26), 15404-15409.
48. Folmer, R. H. A.; Hilbers, C. W.; Konings, R. N. H.; Nilges, M. J. Biomol. NMR 1997, 9 (3), 245-258.
49. Rohl, C. A. Methods Enzymol. 2005, 394, 244-260.