Recognition complex between the hmg domain of lef-1 and its cognate dna studied by molecular dynamics simulations with explicit solvation

Journal of Biomolecular Structure and Dynamics

Volumn 23, Issue 1, 2005, Pages 1-11

  Drumm, Markus ^a   Teletchéa, Stéphane ^a   Kozelka, Jiří ^a  

^a UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CURVED DNA; DOUBLE STRANDED DNA; LYMPHOID ENHANCER FACTOR 1; METHIONINE;

ARTICLE; COMPLEX FORMATION; DNA CONFORMATION; DNA HELIX; ENTROPY; HIGH MOBILITY GROUP BOX DOMAIN; HYDROGEN BOND; INTERCALATION COMPLEX; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; SOLVATION;

EID: 20944448583     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2005.10507042     Document Type: Article

References (27)

1. Travers, A., 2000. Curr. Op. Struct. Biol., 10:102–109.
2. Thomas, J. O., and Travers, A. A., 2001. Trends Biochem. Sci., 26:167–174.
3. Love, J. J., Li, X., Case, D. A., Giese, K., Grosschedl, R., and Wright, P. E., 1995. Nature, 376:791–795.
4. Werner, M. H., Huth, J. R., Gronenborn, A., and Clore, G. M., 1995. Cell, 81:705–714.
5. Allain, F. H.-T., Yen, Y.-M., Masse, J. E., Schultze, P., Dieckmann, T., Johnson, R. C., and Feigon, J., 1999. EMBO J., 18:2563–2579.
6. Murphy, F. V., and Churchill, S. R.M.M.E. A., 1999. EMBO J., 18:6610–6618.
7. Ohndorf, U. M., Rould, M. A., He, Q., Pabo, C. O., and Lippard, S. J., 1999. Nature, 399:708–712.
8. Cheatham, T. E., III and Kollman, P. A., 2000. Ann. Rev. Phys. Chem., 51:435–471.
9. Elizondo-Riojas, M.-A., and Kozelka, J., 2001. J. Mol. Biol., 314:1227–1243.
10. Darden, T. A., York, D., and Pedersen, L. G., 1993. J. Chem. Phys., 98:10089–10092.
11. Nadassy, K., Wodak, S. J., and Janin, J., 1999. Biochemistry, 38:1999–2017.
12. Tang, Y., and Nilsson, L., 1998. Proteins Struct. Funct. Gen., 31:417–433.
13. Love, J. J., Li, X., Chung, J., Dyson, J., and Wright, P. E., 2004. Biochemistry, 43:8725–8734.
14. Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Jr, Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Tsui, V., Radmer, R. J., Duan, Y., Pitera, J., Massova, I., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A., 1999. San Francisco:University of California.
15. Cheatham, T. E., III, Cieplak, P., and Kollman, P. A., 1999. J. Biomol. Struct. Dyn., 16:845–862.
16. Essman, U., Perera, L., Berkowitz, M., Darden, T. A., Lee, H., and Pedersen, L. G., 1995. J. Chem. Phys., 103:8577–8593.
17. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C., 1977. J. Comput. Phys., 23:327–341.
18. Arnott, S., Campbell-Smith, P., and Chandresekharan, P., 1976. CRC Handbook of Biochemistry, Vol., 2:411–414.
19. Lavery, R., and Sklenar, H., 1989. J. Biomol. Struct. Dyn., 6:655–667.
20. Hartmann, B., Piazzola, D., and Lavery, R., 1993. Nucleic Acids Res., 21:561–568.
21. Hartmann, B., Sullivan, M. R., and Harris, L. F., 2003. Biopolymers, 65:250–264.
22. Pearlman, D. A., and Kollman, P. A., 1991. J. Mol. Biol., 220:457–479.
23. Withka, J. M., Swaminathan, S., Beveridge, D. L., and Bolton, P. H., 1991. J. Am. Chem. Soc., 113:5041–5049.
24. Djuranovic, D., and Hartmann, B., 2003. J. Biomol. Struct. Dyn., 20:771–788.
25. Schwabe, J. W. R., 1997. Curr. Op. Struct. Biol., 7:126–134.
26. Levitt, M., and Park, B. H., 1993. Structure, 1:223–226.
27. Dalke, A., Humphrey, W., and Ulrich, J., 1997. VMD (Visual Molecular Dynamics). Theoretical Biophysics Group. Urbana. USA:University of Illinois and Beckman Institute.