Conformational properties of the tata-box binding sequence of dna

Journal of Biomolecular Structure and Dynamics

Volumn 14, Issue 6, 1997, Pages 757-765

  Flatters, Delphine ^a   Young, Matthew ^b   Beveridge, David L ^b   Lavery, Richard ^a  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

^b WESLEYAN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TATA BINDING PROTEIN;

ARTICLE; CRYSTALLOGRAPHY; DNA CONFORMATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; TATA BOX;

EID: 0030958316     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1997.10508178     Document Type: Article

References (30)

1. Kim, Y., Gieger, J. H., Hahn, S., and Sigler, P. B., 1993. Nature, 365:512–520.
2. Kim, J. L., Nikolov, D. B., and Burley, S. K., 1993. Nature, 365:520–527.
3. Juo, Z. S., Chiu, T. K., Leiberman, P. M., Baikalov, I., Berk, A. J., and Dickerson, R. E., 1996. J. Mol. Biol., 261:239–254.
4. Guzikevich-Guerstein, G., and Shakked, Z., 1996. Nature Struct. Biol., 3:32–37.
5. Lavery, R., Zakrzewska, K., and Sklenar, H., 1995. Comp. Phys. Commun., 91:135–158.
6. Lebrun, A., Shakked, Z., and Lavery, R., Proc. Natl. Acad. Sci (USA) (1997) in press
7. Lebrun, A., and Lavery, R., 1996. Nucleic Acids Res., 24:2260–2270.
8. Shakked, Z., Rabinovitch, D., Cruse, W. B., Egert, E., Kennard, O., Sala, G., Salisbury, S. A., and Viswamitra, M. A., 1981. Proc. Roy. Soc. Lond., B213:479–487.
9. Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., 1986. J. Comp. Chem., 7:230–252.
10. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Jr, Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., 1995. J. Am. Chem. Soc., 117:5179–5197.
11. Flatters, D., Zakrzewska, K., and Lavery, R., 1997. J. Comp. Chem., in press
12. Hingerty, B., Richie, R. H., Ferrei, T. L., and Turner, T. E., 1985. Biopolymers, 24:427–439.
13. Jayaram, B., Swaminathan, S., and Beveridge, D. L., 1990. Macromolecules, 23:3156–3165.
14. Young, M. A., Jayaram, B., and Beveridge, D. L., 1997. J. Am. Chem. Soc., 119:59–69.
15. Jorgensen, W. L., 1981. J. Am. Chem. Soc., 103:341–345.
16. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L., 1983. J. Chem. Phys., 79:926–936.
17. Darden, T. A., York, D. M., and Pedersen, L. G., 1993. Chem. Phys., 98:10089–10092
18. Cheatham, T. E., III, Miller, J. L., Fox, T., Darden, T. A., and Kollman, P. A., 1995. J. Am. Chem. Soc., 117:4193–4194.
19. Berendsen, H. J.C., Postma, J. P.M., van Gunsteren, W. F., and DiNiola, A., 1984. J. Chem. Phys., 81:3684–3690.
20. Rychaert, J. P., Ciccotti, G., and Berendsen, H. J.C., 1977. J. Comp. Phys., 23:327–341.
21. van Gunsteren, W. F., and Berendsen, H. J.C., 1977. Mol. Phys., 34:1311–1327.
22. Lavery, R., and Sklenar, H., 1989. J. Biomol. Struct. Dyn., 6:655–667.
23. Amott, S., Chandrasekharan, R., Birdsall, D. L., Leslie, A. G.W., and Ratliff, R. L., 1980. Nature, 283:743746 and coordinates communicated to our laboratory by S. Arnott
24. McConnell, K. J., Ninnala, R., Young, M. A., Ravishankar, G., and Beveridge, D. L., 1994. J. Am. Chem. Soc., 116:4461–4462.
25. Cheatham, T. E., III and Kollman, P. A., 1996. J. Mol. Biol., 259:434–444.
26. Young, M. A., Ravishanker, G., and Beveridge, D. L., Biophys. J. (submitted)
27. Pastor, N., and Weinstein, H., (private communication)
28. Miaskiewicz, K., and Ornstein, R. L., 1996. J. Biomol. Struct. Dynam., 13:593–600.
29. Starr, D. B., Hoopes, B. C., and Hawley, D. K., 1995. J. Mol. Biol., 250:434–446.
30. Parvin, J. D., McCormick, R. J., Sharp, P. A., and Fisher, D. E., 1995. Nature, 373:724–727.