Dynamics of B-DNA on the microsecond time scale

Journal of the American Chemical Society

Volumn 129, Issue 47, 2007, Pages 14739-14745

  Pérez, Alberto ^a,b   Luque, F Javier ^c   Orozco, Modesto ^a,b,c  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b BARCELONA SUPERCOMPUTING CENTER   (Spain)

^c UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; CONFORMATIONS; MOLECULAR DYNAMICS;

GENETIC INFORMATION; STABLE STRUCTURE;

DNA;

CATION; DOUBLE STRANDED DNA; SODIUM;

ARTICLE; BINDING SITE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; DNA BINDING; DNA CONFORMATION; MOLECULAR DYNAMICS; MOLECULAR STABILITY; SIMULATION;

EID: 36749098380     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0753546     Document Type: Article

References (49)

1. Beveridge, D. L.; McConnell, K. J. Curr. Opin. Struct. Biol. 2000, 10 (2), 182-196.
2. Cheatham, T. E., III; Kollman, P. A. Annu. Rev. Phys. Chem. 2000, 51, 435-71.
3. Cheatham, T. E. Curr. Opin. Struct. Biol. 2004, 14 (3), 360-367.
4. Giudice, E.; Lavery, R. Acc. Chem. Res. 2002, 35 (6), 350-357.
5. Orozco, M.; Perez, A.; Noy, A.; Luque, F. J. Chem. Soc. Rev. 2003, 32 (6), 350-364.
6. Cheatham, T. E.; Young, M. A. Biopolymers 2000, 56 (4), 232-256.
7. Sponer, J.; Lankas, F. Computational Studies of RNA and DNA; Springer: Dordrecht, 2006; Vol. 2, p 636.
8. Fadrna, E.; Spackova, N.; Stefl, R.; Koca, J.; Cheatham, T. E.; Sponer, J. Biophys. J. 2004, 87 (1), 227-242.
9. Levitt, M. Cold Spring Harb. Symp. Quant. Biol. 1983, 47 Pt 1, 251-62.
10. Tidor, B.; Irikura, K. K.; Brooks, B. R.; Karplus, M. J. Biomol. Struct. Dyn. 1983, 1 (1), 231-52.
11. McCammon, J. A.; Gelin, B. R.; Karplus, M. Nature 1977, 267 (5612), 585-90.
12. Cheatham, T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117 (14), 4193-4194.
13. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98 (12), 10089-10092.
14. 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. 1995, 117 (19), 5179-5197.
15. Mackerell, A. D.; Wiorkiewiczkuczera, J.; Karplus, M. J. Am. Chem. Soc. 1995, 117 (48), 11946-11975.
16. Foloppe, N.; MacKerell, A. D. J. Comput. Chem. 2000, 21 (2), 86-104.
17. Cheatham, T. E.; Cieplak, P.; Kollman, P. A. J. Biomol. Struct. Dyn. 1999, 16 (4), 845-862.
18. Beveridge, D. L., et al. Biophys. J. 2004, 87 (6), 3799-3813.
19. Dixit, S. B.; Beveridge, D. L.; Case, D. A.; Cheatham, T. E.; Giudice, E.; Lankas, F.; Lavery, R.; Maddocks, J. H.; Osman, R.; Sklenar, H.; Thayer, K. M.; Varnai, P. Biophys. J. 2005, 89 (6), 3721-3740.
20. Dixit, S. B.; Beveridge, D. L. Bioinformatics 2006, 22 (8), 1007-1009.
21. Ponomarev, S. Y.; Thayer, K. M.; Beveridge, D. L. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (41), 14771-14775.
22. Varnai, P.; Zakrzewska, K. Nucleic Acids Res. 2004, 32 (14), 4269-4280.
23. Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92 (11), 3817-29.
24. Drew, H. R.; Dickerson, R. E. J. Mol. Biol. 1981, 151 (3), 535-556.
25. Dickerson, R. E.; Ng, H. L. Proc. Natl. Acad. Sci. U.S.A. 2001, 98 (13), 6986-6988.
26. Shields, G. C.; Laughton, C. A.; Orozco, M. J. Am. Chem. Soc. 1997, 119 (32), 7463-7469.
27. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23 (3), 327-341.
28. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79 (2), 926-935.
29. Meyer, T.; Ferrer-Costa, C.; Perez, A.; Rueda, M.; Bidon-Chanal, A.; Luque, F. J.; Laughton, C. A.; Orozco, M. J. Chem. Theory Comput. 2006, 2 (2), 251-258.
30. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26 (16), 1668-1688.
31. Lu, X. J.; Olson, W. K. Nucleic Acids Res. 2003, 31 (17), 5108-5121.
32. Andricioaei, I.; Karplus, M. J. Chem. Phys. 2001, 115 (14), 6289-6292.
33. Harris, S. A.; Gavathiotis, E.; Searle, M. S.; Orozco, M.; Laughton, C. A. J. Am. Chem. Soc. 2001, 123 (50), 12658-12663.
34. Amadei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Proteins: Struct., Funct., Genet. 1993, 17 (4), 412-425.
35. Perez, A.; Blas, J. R.; Rueda, M.; Lopez-Bes, J. M.; de la Cruz, X.; Orozco, M. J. Chem. Theory Comput. 2005, 1 (5), 790-800.
36. Lankas, F.; Sponer, J.; Langowski, J.; Cheatham, T. E. Biophys. J. 2003, 85 (5), 2872-2883.
37. Olson, W. K.; Gorin, A. A.; Lu, X. J.; Hock, L. M.; Zhurkin, V. B. Proc. Natl. Acad. Sci. U.S.A. 1998, 95 (19), 11163-11168.
38. Noy, A.; Perez, A.; Laughton, C. A.; Orozco, M. Nucleic Acids Res. 2007.
39. Rueda, M.; Chacon, P.; Orozco, M. Structure 2007, 15 (5), 565-575.
40. Gonzalez, C.; Stec, W.; Reynolds, M. A.; James, T. L. Biochemistry 1995, 34 (15), 4969-4982.
41. Hartmann, B.; Piazzola, D.; Lavery, R. Nucleic Acids Res. 1993, 21 (3), 561-568.
42. Bertrand, H. O.; Ha-Duong, T.; Fermandjian, S.; Hartmann, B. Nucleic Acids Res. 1998, 26 (5), 1261-1267.
43. Varnai, P.; Djuranovic, D.; Lavery, R.; Hartmann, B. Nucleic Acids Res. 2002, 30 (24), 5398-5406.
44. Giudice, E.; Varnai, P.; Lavery, R. Nucleic Acids Res. 2003, 31 (5), 1434-43.
45. Morreale, A.; de la Cruz, X.; Meyer, T.; Gelpi, J. L.; Luque, F. J.; Orozco, M. Proteins: Struct., Funct., Bioinf. 2004, 57 (3), 458-467.
46. Rueda, M.; Cubero, E.; Laughton, C. A.; Orozco, M. Biophys. J. 2004, 87 (2), 800-811.
47. Denisov, V. P.; Halle, B. Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (2), 629-633.
48. Williams, L. D. DNA Binders and Related Subjects 2005, 253, 77-88.
49. Duan, Y.; Kollman, P. A. Science 1998, 282 (5389), 740-744.