Binding of net-fla, a netropsin-flavin hybrid molecule, to dna: Molecular mechanics and dynamics studies in vacuo and in water solution

Journal of Biomolecular Structure and Dynamics

Volumn 13, Issue 6, 1996, Pages 963-977

  Ketterlé, Christophe ^a   Gabarro Arpa, Jacques ^a   Ouali, Mohammed ^a   Bouziane, Mohammed ^a   Auclair, Christian ^a   Helissey, Philippe ^b   Giorgi Renault, Sylviane ^b   Bret, Marc Le ^a  

^a INSTITUT GUSTAVE ROUSSY   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CONGOCIDINE; DNA FRAGMENT; QUERCETIN; WATER;

ARTICLE; BASE PAIRING; DRUG DNA BINDING; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION;

BINDING SITES; COMPUTER SIMULATION; DNA; ENERGY TRANSFER; FLAVINS; MODELS, MOLECULAR; NETROPSIN; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SOLUTIONS; TIME FACTORS; VACUUM; WATER;

EID: 0029999388     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1996.10508911     Document Type: Article

References (50)

1. Hertzberg, R. P., and Dervan, P. B., 1982. J. Am. Chem. Soc., 104:313–315. Cleavage of double DNA by (methidiumpropyl-EDTA)iron (II)
2. Moser, H. E., and Dervan, P. B., 1987. Science, 238:645
3. François, J. C., Saison-Behmoaras, T., Barbier, C., Chassignol, M., Thuong, N. T., and Hélène, C., 1988. Proc. Natl. Acad. Sci. USA, 86:9702
4. Gaspairo, F. P., Havre, P. A., Olack, G. A., Gunther, E. J., and Glazer, P. M., 1994. Nucleic Acids Res., 22:2845
5. Shultz, P. G., Taylor, J. S., and Dervan, P. B., 1982. J. Am. Chem. Soc., 104:6861
6. Youngquist, R. S., and Dervan, P. B., 1985. Proc. Natl. Acad. Sci. USA, 8:2 2565
7. Hartley, J. A., McAdam, S. R., Das, S., Roldan, M. C., Haskell, M. K., and Lee, M., 1994. Anti-Cancer Drug Design, 9:181
8. Spielmann, H. P., Fagan, P. A., Bregant, T. M., Little, R. D., and Wemmer, D. E., 1995. Nucleic Acids Res., 23:1576
9. Saito, I., Takayama, M., Sugiyama, H., and Kawanishi, S., 1995. J. Am. Chem. Soc., 117:5590
10. Saito, I., Takayama, M., Sugiyama, H., Nakatani, K., Tsuchida, A., and Yamamoto, M., 1995. J. Am. Chem. Soc., 117:6406
11. Bouziane, M., Ketterlé, Ch., Helissey, P., Herfeld, P., Le Bret, M., Giorgi-Renault, S., and Auclair, C., 1995. Biochemistry, 34:14051
12. Zimmer, C., 1975. Prog. Nucl. Ac. Res. Mol. Biol., 15:285
13. Herfeld, P., Helissey, P., Giorgi-Renault, S., Goulaouic, H., Pager, J., and Auclair, C., 1994. Bioconjugate Chem., 5:67
14. Patel, D. J., 1979. Eur. J. Biochem., 99:369
15. Rosenberg, J. M., Seeman, N. C., Day, R. O., and Rich, A., 1976. Biochem. Biophys. Res. Commun., 69:979
16. Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P., and Dickerson, R. E., 1985. J. Mol. Biol., 183:553
17. Coll, M., Aymami, J., van der Marel, G. A., van Boom, J. H., Rich, A., and Wang, A. H.J., 1989. Biochemistry, 28:310
18. Gabarro-Arpa, J., Cognet, J. A.H., and Le Bret, M., 1992. J. Mol. Graph., 10:166
19. Le Bret, M., Gabarro-Arpa, J., Gilbert, J. C., and Lemanéchal, C., 1991. J. Chim. Phys., 88:2489
20. Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., 1986. J. Comput. Chem., 7:230
21. Weiner, P., and Kollman, P. A., 1981. J. Comput. Chem., 2:287
22. Pearlman, D. A., Case, D. A., Caldwell, J. C., Seibel, G. L., Singh, U. C., Weiner, P., and Kollman, P. A., 1991. AMBER Vol. 40, San Francisco:University of California.
23. Mouscadet, J.-F., Ketterlé, C., Goulaouic, H., Carteau, S., Subra, F., Le Bret, M., and Auclair, C., 1994. Biochemistry, 33:4187
24. McConnell, K. J., Nirmala, R., Young, M. A., Ravishanker, G., and Beveridge, D. L., 1994. J. Am. Chem. Soc., 116:4461
25. Jorgensen, W. L., Chandrasekhhar, J., Madura, J., Impeyer, R. W., and Klein, M. L., 1983. J. Chem. Phys., 79:926
26. Singh, U. C., Weiner, S. J., and Kollman, P., 1985. Proc. Natl. Acad. Sci. USA, 82:755
27. Laughton, C. A., Jenkins, T. C., Fox, K. R., and Neidle, S., 1990. Nucleic Acids Res., 18:4479
28. Goodsell, D. S., Kopka, M. L., and Dickerson, R. E., 1995. Biochemistry, 34:4983
29. Conte, M. R., Jenkins, T. C., and Lane, A. N., 1995. Eur. J. Biochem., 229:433
30. Caldwell, J., and Kollman, P. A., 1986. Biopolymers, 25:249
31. Zakrzewska, K., Lavety, R., and Pullman, B., 1987. J. Biomol. Struct & Dyn., 4:833
32. Tabernero, L., Verdaguer, N., Coll, M., Fita, I., van der Marel, G. A., van Boom, J. H., Rich, A., and Aymami, J., 1993. Biochemistry, 32:8403
33. Malcolm, A. D.B., and Snoulou, G., 1983. Cold Spring Harbor Symposia on Quantitative Biology (Vol. XLVII-Part I), 323
34. Ketterlé, C., 1995. PhD Thesis Orsay
35. Weerasinghe, S., Smith, P. E., Mohan, V., Cheng, Y.-K., and Pettitt, B. M., 1995. J. Am. Chem. Soc., 117:2147
36. Larsen, T. A., Goodsell, D. S., Cacio, D., Grzeskowiak, K., and Dickerson, R. E., 1989. J. Biomol. Struct. Dyn., 7:477
37. entry 6bna in the Brookhaven Protein Databank
38. Portugal, J., and Waring, M., 1987. Eur. J. Biochem., 167:281
39. Marky, L. A., and Breslauer, K. J., 1987. Proc. Natl. Acad. Sci. USA, 84:4359
40. Breslauer, K. J., Ferrante, R., Marky, L., Dervan, P. B., and Youngquist, R. S., 1988. Structure & Expression Vol. Edited by:Sarma, R. H., and Sarma, M. H., Vol. 2, 273Adenine Press.
41. Rentzeperis, D., Ho, J., and Marky, L. A., 1993. Biochemistry, 32:2564
42. Rentzeperis, D., Marky, L. A., Dwyer, T. J., Geierstanger, B. H., Pelton, J. G., and Wemmer, D. E., 1995. Biochemistry, 34:2937
43. Chalikian, T. V., Plum, G. E., Sarvazian, A. P., and Breslauer, K. J., 1994. Biochemistry, 33:8629
44. Eisenberg, H., 1987. Accounts Chem. Res., 20:276
45. Hirsh, J., and Schleif, R., 1976. J. Mol. Biol., 108:471
46. Podtelezhnikov, A. A., Kurakin, A. V., Vologodskii, A. V., and Chemy, D. I., 1994. Micron, 25:439
47. Landau, L., and Lifchitz, E., 1967. Théorie de l'Elasticité (Mir)
48. Piriou, J. M., Ketterlé, Ch., Gabarro-Arpa, J., Cognet, J. A.H., and Le Bret, M., 1994. Biophys. Chem., 50:323
49. Klevit, R. E., Wemmer, D. E., and Reid, B. R., 1986. Biochemistry, 25:3296
50. Kumar, S., Joseph, T., Singh, M. P., Bathini, Y., and Lown, J. W., 1992. J. Biomol. Struct & Dyn., 9:853