Model-free analysis of protein dynamics: Assessment of accuracy and model selection protocols based on molecular dynamics simulation

Journal of Biomolecular NMR

Volumn 29, Issue 3, 2004, Pages 243-257

  Chen, Jianhan ^a   Brooks III, Charles L ^a   Wright, Peter E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

AIC; BIC; Hypothesis testing; Model selection; NMR relaxation

Indexed keywords

AMIDE; DIHYDROFOLATE REDUCTASE; WATER;

ACCURACY; ARTICLE; BAYES THEOREM; CLINICAL PROTOCOL; CONTROLLED STUDY; DATA ANALYSIS; HYPOTHESIS; MEASUREMENT; MOLECULAR DYNAMICS; MOTION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; SIMULATION; STATISTICAL MODEL; VARIANCE;

ANISOTROPY; BAYES THEOREM; ESCHERICHIA COLI; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, STATISTICAL; MODELS, THEORETICAL; NITROGEN; PROTEIN FOLDING; PROTEINS; SOFTWARE; TETRAHYDROFOLATE DEHYDROGENASE; TIME FACTORS;

EID: 3042846786     PISSN: 09252738     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:JNMR.0000032504.70912.58     Document Type: Article

References (55)

1. Abragam, A. (1961) The Principles of Nuclear Magnetism, Clarendon Press, Oxford.
2. Akaike, H. (1974) IEEE Trans. Automat. Contr., AC-19, 716-723.
3. Akke, M., Skelton, N.J., Kordel, J., Palmer. A.G., III and Chazin, W.J. (1993) Biochemistry, 32, 9832-9844.
4. Andrec, M., Montelione, G.T., and Levy, R.M. (1999) J. Magn. Reson., 139, 408-421.
5. Andrec, M., Montelione, G.T. and Levy, R.M. (2000) J. Biomol. NMR, 18, 83-100.
6. Bertini, I, Bryant, D.A., Ciurli, S., Dikiy, A., Fernandez, C.O., Luchinat, C., Safarov, N., Vila, A.J. and Zhao, J. (2001) J. Biol. Chem., 276, 47217-47226.
7. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M. (1983) J. Comput. Chem., 4, 187-217.
8. Brooks, III, C.L., Karplus, M. and Pettitt, B.M. (1988) Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics, John Wiley and Sons, New York.
9. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, N., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and Warren, G.L. (1998) Acta. Cryst., D54, 905-921.
10. Brüschweiler, R., Roux, B., Blackledge, M., Griesinger, C., Kalpus, M. and Ernst, R.R. (1992) J. Am. Chem. Soc., 114, 2289-2302.
11. Burnham, K.P. and Anderson, D.R. (1998) Model Selection and Inference: A Practical Information-Theoretic Approach, Springer-Verlag, New York.
12. Case, D.A. (2002) Acc. Chem. Res., 35, 325-331.
13. Cavanagh, J., Faribrother, W.J., Palmer, III, A.G. and Skelton, M.J. (1996) Protein NMR Spectroscopy: Principles and Practice, Academic Press, San Diego.
14. Clore, G.M., Szabo, A., Bax, A., Kay, L.E., Driscoll, P.C. and Gronenborn, A.M. (1990) J. Am. Chem. Soc., 112, 4989-4991.
15. Cole, R. and Loria, J.R. (2002) Biochemistry, 41, 6072-6081.
16. Dangi. B., Dobrodumov, A.V., Louis, J.M. and Gronenborn, A.M. (2002) Biochemistry 41, 9376-9388.
17. d'Auvergne, E.J. and Gooley, P.R. (2003) J. Biomol. NMR, 25, 25-39.
18. Deep, S., Walker, III, K.P., Shu, Z. and Hinck, A.P. (2003) Biochemistry, 42, 10126-10139
19. Farrow, N.A., Zhang, O., Szabo, A., Torchia, D.A. and Kay, L.E. (1995) J. Biomol. NMR, 6, 153-162.
20. Ishima, R. and Torchia, D.A. (2000) Nat. Struct. Biol., 7, 740-743.
21. Jin, D., Andrec, M., Montelione, G.T. and Levy, R.M. (1998) J. Biomol. NMR, 12, 471-492.
22. Joregensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L. (1983) J. Chem. Phys., 79, 926-35.
23. Karplus, M. and McCammon, J.A. (2002) Nat. Struct. Biol., 9, 646-652.
24. Kelley, III, J.J., Caputo, T.M., Eaton, S.F., Laue, T.M. and Bushweller, J.H. (1997) Biochemistry, 36, 5029-5044.
25. Koehl, P. (1999) Prog. NMR. Spec., 34, 257-299.
26. Kroenke, C.D., Loria, J.P., Lee, L.K., Rance, M. and Palmer, III, A.G. (1998) J. Am. Chem. Soc., 120, 7905-7915.
27. Kullback, S. and Leibler, R.A. (1951) Ann. Math. Stat., 22, 79-86.
28. Levy, R. M., Karplus, M. and Wolynes, P.G. (1981) J. Am. Chem. Soc., 103, 5998-6011.
29. Lipari, G. and Szabo. A. (1982) J. Am. Chem. Soc., 104, 4546-4559.
30. Ma, L., Hass, M.A.S., Vierick, N., Kristensen, S.M., Ulstrup, J. and Led, J.J. (2003) Biochemistry, 42, 320-330.
31. MacKerell, Jr., A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Gun, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, III, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D. and Karplus, M. (1998) J. Phys. Chem. B, 102, 3586-3616.
32. Mandel, A.M., Akke, M. and Palmer, III, A.G. (1995) J. Mol. Biol., 246, 144-163.
33. Osborne, M.J. and Wright, P.E. (2001) J. Biomol. NMR, 19, 209-230.
34. Osborne, M.J., Schnell, J., Benkovic, S.J., Dyson, H.J. and Wright, P.E. (2001) Biochemistry, 40, 9846-9859.
35. Palmer, III, A.G. (2001) Annu. Rev. Biophys. Biomol. Struct., 30, 129-155.
36. Palmer, A.G., Rance, M. and Wright, P.E. (1991) J. Am. Chem. Soc., 113, 4371-4380.
37. Pavelites, J.J., Gao, J., Bash, P.A., Alexander, D. and Mackerell, J. (1997) J. Comput. Chem., 18, 221-229.
38. Pawley, N.H., Wang, C., Koide, S. and Nicholson, L.K. (2001) J. Biomol. NMR, 20, 149-165.
39. Peng, J.W. and Wagner, G. (1992) J. Magn. Reson., 98, 308-332.
40. Pfeiffer, S., Fushman, D. and Cowburn, D. (2001) J. Am. Chem. Soc., 123, 3021-3036.
41. Prompers, J.J. and Brüschweiler, R. (2002) J. Am. Chem. Soc., 124, 4522-4534.
42. Radkiewicz, J.L. and Brooks, III, C.L. (2000) J. Am. Chem. Soc., 122, 225-231.
43. Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) J. Comput. Phys., 23, 327-341.
44. Schwarz, G. (1978) Ann. Stat., 6, 461-464.
45. Song, J. and Markley, J.L. (2003) Biochemistry, 42, 5194-5196.
46. Tjandra, N., Feller, S.E., Pastor, R.W. and Bax, A. (1995) J. Am. Chem. Soc., 117, 12562-12566.
47. Tugarinov, V., Liang, Z., Shapiro, Y.E., Freed, J.H. and Meirovitch, E. (2001) J. Am. Chem. Soc., 123, 3055-3063.
48. Tugarinov, V., Shapiro, Y.E., Liang, Z., Freed, J.H. and Meirovitch, E. (2002) J. Mol. Biol., 315, 155-170.
49. Wallach, D.J. (1967) J. Chem. Phys., 47, 5258.
50. Wand, A.J. (2001) Nat. Struct. Biol., 8, 926-931.
51. Wax, M. and Ziskind, I. (1989) IEEE Trans. Acoust., Speach, Signal Processing, 37, 1190-1196.
52. Woessner, D.E. (1962) J. Chem. Phys., 3, 647-654.
53. Wrabl, J.O., Shortle, D. and Woolf, T.B. (2000) Proteins, 38, 123-133.
54. Yang, D. and Kay, L.E. (1996) J. Mol. Biol., 263, 369-382.
55. Ye, J., Mayer, K.L., Mayer, M.R. and Stone, M.J. (2001) Biochemistry 40, 7820-7831.