Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex

Journal of the American Chemical Society

Volumn 128, Issue 28, 2006, Pages 8992-8993

  Kormos, Bethany L ^a   Baranger, Anne M ^a   Beveridge, David L ^a  

^a WESLEYAN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEIN U1A; RNA; UNCLASSIFIED DRUG;

ARTICLE; ATOM; ATOMIC PARTICLE; DNA PROTEIN COMPLEX; MOLECULAR DYNAMICS; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RNA BINDING; THERMODYNAMICS;

PROTEIN BINDING; PROTEIN CONFORMATION; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RNA; RNA-BINDING PROTEINS; THERMODYNAMICS;

EID: 33746104463     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0606071     Document Type: Article

References (32)

1. Green, M. R. Annu. Rev. Cell Biol. 1991, 7, 559-599.
2. Stark, H.; Dube, P.; Lührmann, R.; Kastner, B. Nature 2001, 409, 539-542.
3. Maris, C.; Dominguez, C.; Allain, F. H.-T. FEBS Lett. 2005, 272, 2118-2131.
4. Oubridge, C.; Ito, N.; Evans, P. R.; Teo, C. H.; Nagai, K. Nature 1994, 372, 432-438.
5. Allain, F. H.; Howe, P. W.; Neuhaus, D.; Varani, G. EMBO J. 1997, 16, 5764-5772.
6. Mittermaier, A.; Varani, L.; Muhandiram, D. R.; Kay, L. E.; Varani, G. J. Mol. Biol. 1999, 294, 967-979.
7. Varani, L.; Gunderson, S. I.; Mattaj, I. W.; Kay, L. E.; Neuhaus, D.; Varani, G. Nat. Struct. Biol. 2000, 7, 329-335.
8. Kranz, J. K.; Hall, K. B. J. Mol. Biol. 1998, 275, 465-481.
9. Kranz, J. K.; Hall, K. B. J. Mol. Biol. 1999, 285, 215-231.
10. Showalter, S. A.; Hall, K. B. J. Mol. Biol. 2002, 322, 533-542.
11. Nolan, S. J.; Shiels, J. C.; Tuite, J. B.; Cecere, K. L.; Baranger, A. M. J. Am. Chem. Soc. 1999, 121, 8951-8952.
12. Shiels, J. C.; Tuite, J. B.; Nolan, S. J.; Baranger, A. M. Nucleic Acids Res. 2002, 30, 550-558.
13. Tuite, J. B.; Shiels, J. C.; Baranger, A. M. Nucleic Acids Res. 2002, 30, 5269-5275.
14. Katsamba, P. S.; Bayramyan, M.; Haworth, I. S.; Myszka, D. G.; Laird-Offringa, I. A. J. Biol. Chem. 2002, 36, 33267-33274.
15. Law, M. J.; Chambers, E. J.; Katsamba, P. S.; Haworth, I. S.; Laird-Offringa, I. A. Nucleic Acids Res. 2005, 33, 2917-2928.
16. Crowder, S.; Holton, J.; Alber, T. J. Mol. Biol. 2001, 310, 793-800.
17. Scherly, D.; Kambach, C.; Boelens, W.; van Venrooij, W. J.; Mattaj, I. W. J. Mol. Biol. 1991, 219, 577-584.
18. Jessen, T. H.; Oubridge, C.; Teo, C. H.; Pritchard, C.; Nagai, K. EMBO J. 1991, 10, 3447-3456.
19. Hall, K. B.; Stump, W. T. Nucleic Acids Res. 1992, 20, 4283-4290.
20. Rimmele, M. E.; Belasco, J. G. RNA 1998, 4, 1386-1396.
21. Blakaj, D. M.; McConnelll,. K. J.; Beveridge, D. L.; Baranger, A. M. J. Am. Chem. Soc. 2001, 123, 2548-2551.
22. Pitici, F.; Beveridge, D. L.; Baranger, A. M. Biopolymers 2002, 65, 424-435.
23. Showalter, S. A.; Hall, K. B. Biophys. J. 2005, 89, 2046-2058.
24. Lockless, S. W.; Ranganathan, R. Science 1999, 286, 295-299.
25. Case, D. A.; et al. AMBER 8; University of California: San Francisco, 2004.
26. Kollman, P. A.; Dixon, R.; Cornell, W.; Fox, T.; Chipot, C.; Pohorille, A. In Computer Simulation of Biomolecular Systems; Wilkinson. A., Weiner, P., van Gunsteren, W. F., Eds.; Kluwer: London. 1997; Vol. 3, pp 83-96.
27. Ichiye, T.; Karplus, M. Proteins 1987, 2, 236-259.
28. Swaminathan, S.; Harte, W. E.; Beveridge, D. L. J. Am. Chem. Soc. 1991, 113, 2717-2721.
29. Harte, W. E., Jr.; Swaminathan, S.; Mansuri, M. M.; Martin, J. C.; Rosenberg, I. E.; Beveridge, D. L. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 8864-8868.
30. Harte, W. E., Jr.; Swaminathan, S.; Beveridge, D. L. Proteins: Struct., Funct., Genet. 1992, 13, 175-194.
31. Ichiye, T.; Karplus, M. Proteins: Struct., Funct., Genet. 1991, 11, 205-217.
32. Young, M. A.; Gonfloni, S.; Superti-Furga, G.; Roux, B.; Kuriyan, J. Cell 2001, 105, 115-126.