Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy

Journal of the American Chemical Society

Volumn 129, Issue 15, 2007, Pages 4724-4730

  Markwick, Phineus R L ^a   Bouvignies, Guillaume ^a   Blackledge, Martin ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; CONFORMATIONAL SUBSTATES; MILLISECOND TIMESCALE; MULTIPLE TIMESCALE MOTIONS;

BIOMOLECULES; COMPUTER SIMULATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PARAMETER EXTRACTION; PRINCIPAL COMPONENT ANALYSIS;

PROTEINS;

IMMUNOGLOBULIN G; PROTEIN GB3; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRINCIPAL COMPONENT ANALYSIS; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN LOCALIZATION; REACTION OPTIMIZATION; REPRODUCIBILITY;

COMPUTER SIMULATION; IMMUNOGLOBULIN G; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NERVE TISSUE PROTEINS; PROTEIN STRUCTURE, TERTIARY;

EID: 34247500337     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0687668     Document Type: Article

References (61)

1. Frauenfelder, H.; Sligar, S. G.; Wolynes, P. G. Science 1991, 254, 1598-1603.
2. Benkovic, S. J.; Hammes-Schiffer, S. Science 2003, 301, 1196-202.
3. Mittermaier, A.; Kay, L. E. Science 2006, 312, 224-228.
4. Kay, L. E.; Torchia, D. A.; Bax, A. Biochemistry 1989, 28, 8972-8979.
5. Palmer, A. G. Annu. Rev. Biophys. Biomol. Struct. 2001, 30, 129-155.
6. Bruschweiler, R. Curr. Opin. Struct. Biol. 2003, 13, 175-183.
7. Tousignant, A.; Pelletier, J. N. Chem. Biol. 2004, 11, 1037-1042.
8. Rousseau, F.; Schymkowitz, J. Curr. Opin. Struct. Biol. 2005, 15, 23-30.
9. Kern, D.; Zuiderweg, E. R. P. Curr. Opin. Struct. Biol. 2003, 13, 748-757.
10. Eisenmesser, E. Z.; Bosco, D. A.; Akke, M.; Kern, D. Science 2002, 295, 1520-1523.
11. Mulder, F. A.; Mittermaier, A.; Hon, B.; Dahlquist, F. W.; Kay, L. E. Nat. Struct. Biol. 2001, 8, 932-935.
12. Eisenmesser, E. Z.; Millet, O.; Labeikovsky, W.; Korzhnev, D. M.; Wolf-Watz, M.; Bosco, D. A.; Skalicky, J. J.; Kay, L. E.; Kern, D. Nature 2005, 438, 117-121.
13. Korzhnev, D. M.; Salvatella, X.; Vendruscolo, M.; Di Nardo, A. A.; Davidson, A. R.; Dobson, C. M.; Kay, L. E. Nature 2004, 430, 586-590.
14. Boehr, D. D.; McElheny, D.; Dyson, H. J.; Wright, P. E. Science 2006, 313, 1638-1642.
15. Tjandra, N.; Bax, A. Science 1997, 278, 1697-1697.
16. Tolman, J. R.; Flanagan, J. M.; Kennedy, M. A.; Prestegard, J. H. Nat. Struct. Biol. 1997, 4, 292-297.
17. Bax, A. Protein Sci. 2003, 12, 1-16.
18. Prestegard, J. H.; Bougault, C. M.; Kishore, A. I. Chem. Rev. 2004, 104, 3519-3540.
19. Prestegard, J. H.; al-Hashimi, H. M.; Tolman, J. R. Q. Rev. Biophys. 2000, 33, 371-424.
20. Blackledge, M. Prog. Nucl. Magn. Reson. Spectrosc. 2005, 46, 23-61.
21. Meiler, J.; Prompers, J. J.; Peti, W.; Griesinger, C.; Bruschweiler, R. J. Am. Chem. Soc. 2001, 123, 6098-6107.
22. Peti, W.; Meiler, J.; Bruschweiler, R.; Griesinger, C. J. Am. Chem. Soc. 2002, 124, 5822-5833.
23. Briggman, K. B.; Tolman, J. R. J. Am. Chem. Soc. 2003, 125, 10164-10165.
24. Ulmer, T. S.; Ramirez, B. E.; Delaglio, F.; Bax, A. J. Am. Chem. Soc. 2003, 125, 9179-9191.
25. Clore, G. M.; Schwieters, C. D. J. Am. Chem. Soc. 2004, 126, 2923-2938.
26. Bernado, P.; Blackledge, M. J. Am. Chem. Soc. 2004, 126, 4907-4920.
27. Bernado, P.; Blackledge, M. J. Am. Chem. Soc. 2004, 126, 7760-7761.
28. Bouvignies, G.; Bernado, P.; Blackledge, M. J. Magn. Reson. 2005, 173, 323-338.
29. Lienin, S. F.; Bremi, T.; Brutscher, B.; Bruschweiler, R.; Ernst, R. R. J. Am. Chem. Soc. 1998, 120, 9870-9879.
30. Bouvignies, G.; Bernado, P.; Meier, S.; Cho, K.; Grzesiek, S.; Bruschweiler, R.; Blackledge, M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13885-13890.
31. Derrick, J. P.; Wigley, D. B. J. Mol. Biol. 1994, 243, 906-918.
32. Karplus, M.; McCammon, J. A. Nat. Struct. Biol. 2002, 9, 646-652.
33. Karplus, M.; Kuriyan, J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6679-6685.
34. Levy, R. M.; Karplus, M.; Wolynes, P. G. J. Am. Chem. Soc. 1981, 103, 5998-6011.
35. Bruschweiler, R.; Roux, B.; Blackledge, M.; Griesinger, C.; Karplus, M.; Ernst, R. R. J. Am. Chem. Soc. 1992, 114, 2289-2302.
36. Case, D. A. Acc. Chem. Res. 2002, 35, 325-331.
37. Chandrasekhar, I.; Clore, G. M.; Szabo, A.; Gronenborn, A. M.; Brooks, B. R. J. Mol. Biol. 1992, 226, 239-250.
38. Schlitter, J.; Engels, M.; Kruger, P. J. Mol. Graph. 1994, 12, 84-89.
39. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu. Rev. Phys. Chem. 2002, 53, 291-318.
40. Amadei, A.; Linssen, A. B.; Berendsen, H. J. Proteins 1993, 17, 412-425.
41. Muller, E. M.; de Meijere, A.; Grubmuller, H. J. Chem. Phys. 2002, 116, 897-905.
42. Mitsutake, A.; Sugita, Y.; Okamoto, Y. J. Chem. Phys. 2003, 118, 6664-6675.
43. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199.
44. Kleinjung, J.; Bayley, P.; Fraternali, F. FEBS Lett. 2000, 470, 257-262.
45. Elber, R. Curr. Opin. Struct. Biol. 2005, 15, 151-156.
46. Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120, 11919-11929.
47. Hamelberg, D.; McCammon, J. A. J. Am. Chem. Soc. 2005, 127, 13778-13779.
48. Meier, S.; Haussinger, D.; Jensen, P.; Rogowski, M.; Grzesiek, S. J. Am. Chem. Soc. 2003, 125, 44-45.
49. Nederveen, A. J.; Bonvin, A. M. J. J. J. Chem. Theory Comp. 2005, 1, 363-374.
50. Hall, J. B.; Fushman, D. J. Biomol. NMR 2003, 27, 261-275.
51. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins: Struct., Funct., Bioinf. 2006, 65, 712-725.
52. Case, D. A. Curr. Opin. Struct. Biol. 1994, 4, 285-290.
53. Lange, O. F.; Grubmuller, H.; de Groot, B. L. Angew. Chem., Int. Ed. 2005, 44, 3394-3399.
54. Ding, K. Y.; Louis, J. M.; Gronenborn, A. M. J. Mol. Biol. 2004, 335, 1299-1307.
55. Voter, A. F. Phys. Rev. Lett. 1997, 78, 3908-3911.
56. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
57. Cheatham, T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4193-4194.
58. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1996, 118, 2309-2309.
59. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
60. Case et al. AMBER 8; University of California: San Francisco, CA. 2004.
61. Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546-4559.