Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions

Angewandte Chemie - International Edition

Volumn 44, Issue 22, 2005, Pages 3394-3399

  Lange, Oliver F ^a   Grubmüller, Helmut ^a   De Groot, Bert L ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Conformation analysis; Correlated motions; Molecular dynamics; NMR spectroscopy; Proteins

Indexed keywords

COMPUTER SIMULATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; RELAXATION PROCESSES;

CORRELATED MOTIONS; NMR RELAXATION EXPERIMENTS; PROTEIN MOTIONS;

PROTEINS;

GUANINE NUCLEOTIDE BINDING PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; MOTION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN TERTIARY STRUCTURE;

COMPUTER SIMULATION; GTP-BINDING PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, MOLECULAR; MOTION; PROTEIN STRUCTURE, TERTIARY;

EID: 20444424211     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/anie.200462957     Document Type: Article

References (34)

1. A. J. Wand, Nat. Struct. biol. 2001, 8, 926.
2. S. J. Benkovic, S. Hammes-Schiffer, Science 2003, 301, 1196.
3. P. K. Agarwal, S. R. Billeter, P. T. R. Rajagopalan, S. J. Benkovic, S. Hammes-Schiffer, Proc. Natl. Acad. Sci. USA 2002, 99, 2794.
4. J. N. Onuchic, Z. Luthey-Schulten, P. G. Wolynes, Annu. Rev. Phys. Chem. 1997, 48, 545.
5. J. D. Forman-Kay, Nat. Struct. Biol. 1999, 6, 1086.
6. A. L. Lee, A. J. Wand, Nature 2001, 411, 501.
7. R. Ishima, D. A. Torchia, Nat. Struct. Biol. 2000, 7, 740.
8. A. G. Palmer, Annu. Rev. Biophys. Biomol. Struct. 2001, 30, 129.
9. V. A. Daragan, K. H. Mayo, Prog. Nucl. Magn. Reson. Spectrosc. 1997, 31, 63.
10. G. Lipari, A. Szabo, J. Am. Chem. Soc. 1982, 104, 4546.
11. L. E. Kay, D. A. Torchia, A. Bax, Biochemistry 1989, 28, 8972.
12. A. G. Palmer, M. Rance, P. E. Wright, J. Am. Chem. Soc. 1991, 113, 4371.
13. K. L. Mayer, M. R. Earley, S. Gupta, K. Pichumani, L. Regan, M. J. Stone, Nat. Struct. Biol. 2003, 10, 962.
14. A. G. Palmer, Chem. Rev. 2004, 104, 3623.
15. A. E. Garcia, Phys. Rev. Lett. 1992, 68, 2696.
16. A. Amadei, A. B. M. Linssen, H. J. C. Berendsen. Proteins Struct. Funct. Genet. 1993, 17, 412.
17. A. M. Gronenborn, D. R. Filipula, N. Z. Essig, A. Achari, M. Whitlow, P. T. Wingfield, G. M. Clore, Science 1991, 253, 657.
18. D. Idiyatullin, V. A. Daragan, K. H. Mayo, J. Phys. Chem. B 2003, 107, 2602.
19. M. Philippopoulos, C. Lim, J. Mol. Biol. 1995, 254, 771.
20. D. C. Chatfield, A. Szabo, B. R. Brooks, J. Am. Chem. Soc. 1998, 120, 5301.
21. M. Philippopoulos, A. M. Mandel, A. G. Palmer, C. Lim, Proteins Struct. Funct. Genet. 1997, 28, 481.
22. D. A. Case, Acc. Chem. Res. 2002, 35, 325.
23. G. M. Clore, C. D. Schwieters, Biochemistry 2004, 43, 10678.
24. T. Gallagher, P. Alexander, P. Bryan, G. L. Gilliland, Biochemistry 1994, 33, 4721.
25. W. L. Jorgensen, D. S. Maxwell, J. Tirado-Rives, J. Am. Chem. Soc. 1996, 118, 11225.
26. E. Lindahl, B. Hess, D. Van der Spoel, J. Mol. Model. 2001, 7, 306; internet: http://www.gromacs.org.
27. B. Hess, H. Bekker, H. J. C. Berendsen, J. G. E. M. Fraaije, J. Comput. Chem. 1997, 18, 1463.
28. S. Miyamoto, P. A. Kollman, J. Comput. Chem. 1992, 13, 952.
29. T. Darden, D. York, L. Pedersen, J. Chem. Phys. 1993, 98, 10089.
30. H. J. C. Berendsen, J. P. M. Postma, A. DiNola, J. R. Haak, J. Chem. Phys. 1984, 81, 3684.
31. A. T. Brünger, P. D. Adams, G. M. Clore, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J. S. Jiang, J. Kuszewski, N. Nilges, N. S. Pannu, R. J. Read, L. M. Rice, T. Simonson, G. L. Warren, Acta Crystallogr. Sect. D 1998, 54, 905.
32. J. Kuszewski, A. M. Gronenborn, G. M. Clore, J. Am. Chem. Soc. 1999, 121, 2337.
33. S. Pfeiffer, D. Fushman, D. Cowburn, J. Am. Chem. Soc. 2001, 123, 3021.
34. O. Lange, H. Grubmüller, unpublished results.