How NF-κB can be attracted by its cognate DNA

Journal of Molecular Biology

Volumn 293, Issue 1, 1999, Pages 139-150

  Tisné, Carine ^a   Delepierre, Muriel ^a   Hartmann, Brigitte ^b  

^a CNRS   (France)

^b INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

Accessible surface; DNA; Electrostatic potential; NF B; Specific recognition

Indexed keywords

DNA FRAGMENT; DOUBLE STRANDED DNA; DNA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PHOSPHATE;

ARTICLE; BASE PAIRING; BINDING SITE; DNA SEQUENCE; DNA STRUCTURE; ELECTRICITY; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; TRANSCRIPTION REGULATION; CHEMISTRY; CONFORMATION; GENETICS; MUTATION; VIRUS GENE;

EUKARYOTA; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

BINDING SITES; DNA; ELECTROSTATICS; GENES, VIRAL; HIV-1; MAGNETIC RESONANCE SPECTROSCOPY; MUTATION; NF-KAPPA B; NUCLEIC ACID CONFORMATION; PHOSPHATES;

EID: 0033568921     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3157     Document Type: Article

References (45)

1. Bertrand H.-O., Ha-Duong T., Fermandjian S., Hartmann B. Flexibility of B-DNA backbone: Effects of local and neighbouring sequences on pyrimidine-purine steps. Nucl. Acids Res. 26:1998;1261-1267.
2. Chen F. E., Huang D.-B., Chen Y.-Q., Ghosh G. Crystal structure of p50/p65 heterodimer of transcription factor NF-κB bound to DNA. Nature. 391:1998;410-413.
3. Chen Y.-Q., Ghosh S., Ghosh G. A novel DNA recognition mode by the NF-κB p65 homodimer. Nature Struct. Biol. 5:1998;67-73.
4. Cho Y., Gorina S., Jeffrey P. D., Pavletich N. P. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science. 265:1994;346-355.
5. Cornell W. D., Cieplak P., Bayly C. I., Gould I. R., Merz K. M. J., Ferguson D. M., Spellmeyer D. C., Fox T., Caldwell J. W., Kollman P. A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
6. Cramer P., Larson C. J., Verdine G. L., Müller C. W. Structure of the human NF-κB p52 homodimer-DNA complex at 2.1 Å resolution. EMBO J. 16:1997;7078-7090.
7. 1H NMR of the HIV-1 enhancer: the transcription factor NF-κB and Sp1 binding domains. Magn. Reson. Chem. 34:1996;s67-s80.
8. de Souza O. N., Ornstein R. L. Inherent DNA curvature and flexibility correlate with TATA box functionality. Biopolymers. 46:1998;1998.
9. Dickerson R. E., Bansal M., Calladine C. R., Dieckmann S., Hunter W. N., Kennard O., Lavery R., Nelson H. C. M., Olson W., Saenger W., Shakked Z., Sklenar H., Soumpasis D. M., Tung C.-S., von Kitzing E. et al. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 205:1989;787-791.
10. Flatters D., Young M., Beveridge D. L., Lavery R. Conformational properties of the TATA box binding sequence of DNA. J. Biomol. Struct. Dynam. 14:1997a;757-765.
11. Flatters D., Zakrzewska K., Lavery R. Internal coordinate modeling of DNA: force field comparisons. J. Comput. Chem. 18:1997b;1043-1055.
12. Friedman R. A., Honig B. The electrostatic contribution to DNA base-stacking interactions. Biopolymers. 32:1992;145-159.
13. Fritsch V., Westhof E. Three-center hydrogen bonds in DNA: molecular dynamics of poly(dA). poly(dT). J. Am. Chem. Soc. 113:1991;8271-8277.
14. Ghosh G., Van Duyne G., Ghosh S., Sigler P. S. Structure of NF-κB p50 homodimer bound to a κB site. Nature. 373:1995;303-310.
15. Gilson M. K., Sharp K. A., Honig B. H. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comput. Chem. 9:1988;327-335.
16. 31P NMR. Chem. Rev. 94:1994;1315-1338.
17. Gurlie R., Zakrzewska K. DNA curvature and phosphate neutralisation: an important aspect of specific protein binding. J. Biomol. Struct. Dynam. 49:1998;313-327.
18. Gurlie R., Ha-Duong T., Zakrzewska K. The role of DNA-protein salt bridges in molecular recognition: a model study. Biopolymers. 49:1999;313-327.
19. Hartmann B., Piazzola D., Lavery R. BI-BII transitions in B-DNA. Nucl. Acids Res. 21:1993;561-568.
20. Jayaram B., Sharp K. A., Honig B. The electrostatic potentials of B -DNA. Biopolymers. 28:1989;975-993.
21. Klapper I., Hagstrom R., Fine R., Sharp K., Honig B. Focussing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins: Struct. Funct. Genet. 1:1986;47-59.
22. Kunsch C., Ruben S. M., Rosen C. A. Selection of optimal κB/Rel DNA-binding motifs: interaction of both subunits of NF-κB with DNA is required for transcriptional activation. Mol. Cell. Biol. 12:1992;4412-4421.
23. Lavery R. DNA bending and curvature. Olson W. K., Sarma R. H., Sundaralingam M. Structure and Expression. 1988;191-211 Adenine Press, New York.
24. Lavery R., Pullman A., Pullman B. Steric accessibility of reactive centers in B -DNA. Int. J. Quant. Chem. 20:1981;49-62.
25. Lavery R., Parker I., Kendrick J. A general approach to the optimization of the conformation of ring molecules with an application to valynomicin. J. Biomol. Struct. Dynam. 4:1986a;443-461.
26. Lavery R., Sklenar H., Zakrzewska K., Pullman B. The flexibility of the nucleic acids: (II) the calculation of internal energy and applications to mononucleotide repeat DNA. J. Biomol. Struct. Dynam. 3:1986b;989-1014.
27. Lavery R., Zakrewska K., Sklenar H. JUMNA (junction minimisation of nucleic acids). Comput. Phys. Commun. 91:1994;135-158.
28. Lefebvre A., Mauffret O., Hartmann B., Lescot E., Fermandjian S. The structural behaviour of the CpG step in two related oligonucleotides reflects its malleability in solution. Biochemistry. 34:1995;12019-12029.
29. Mazur J., Jernigan R. L. Distance-dependent dielectric constants and their application to double-helical DNA. Biopolymers. 31:1991;1615-1629.
30. Müller C. W., Rey F. A., Sodeoka M., Verdine G. L., Harrison S. C. Structure of the NF-κB p50 homodimer bound to DNA. Nature. 373:1995;311-317.
31. Nabel G., Baltimore D. An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature. 326:1987;711-713.
32. Pastor N., Pardo L., Weinstein H. Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein. Biophys. J. 73:1997;640-652.
33. Pullman A., Pullman B. Molecular electrostatic potential of the nucleic acids. Quart. Rev. Biophys. 14:1981;289-380.
34. Sharp K. Incorporating solvent and ion screening into molecular dynamics using the finite difference Poisson-Boltzmann method. J. Comput. Chem. 12:1991;454-468.
35. Sharp K., Honig B. Calculating total electrostatic energies with the non-linear Poisson-Boltzmann equation. J. Phys. Chem. 94:1990;7684-7692.
36. Strauss-Soukup J. K., Maher L. J. III. Electrostatic effects in DNA bending by GCN4 mutants. Biochemistry. 37:1998;1060-1066.
37. Tisné C., Hantz E., Hartmann B., Delepierre M. Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 κB site: evidences for BI-BII equilibrium inducing a global dynamic curvature of the duplex. J. Mol. Biol. 279:1998a;127-142.
38. 31P NMR conformational studies of non-palindromic DNA duplexes related to HIV-1 enhancer. J. Chim. Phys. 2:1998b;417-422.
39. Tisné C., Hartmann B., Delepierre M. NF-κB binding mechanism: an NMR and molecular modelling study of a GGG→CTC mutation. Biochemistry. 38:1999;3883-3894.
40. Tomky L. A., Strauss-oukup J. K., Maher I. L. J. Effects of phosphate neutralization on the shape of the AP-1 transcription factor binding site in duplex DNA. Nucl. Acids Res. 26:1998;2298-2305.
41. Weiner S. J., Kollman P. A., Case D. A., Singh U. C., Ghio C., Alagona G., Profeta S. J., Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784.
42. Winkler F. K., Banner D. W., Oefner C., Tsernoglou D., Brown R. S., Heathman S. P., Bryan R. K., Martin P. D., Petratos K., Wilson K. The crystal structure of Eco RV endonuclease and its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1993;1781-1795.
43. Wolfe S. A., Zhou P., Dötsch V., Chen L., You A., Ho S. N., Crabtree G. R., Wagner G., Verdine G. L. Unusual Rel-like architecture in the DNA-binding domain of the transcription factor NFATc. Nature. 385:1997;172-176.
44. Zakrzewska K., Madami A., Lavery R. Poisson-Boltzmann calculations for nucleic acids and nucleic acids complexes. Chem. Phys. 204:1995;263-269.
45. Zhou P., Sun L. J., Dötsch V., Wagner G., Verdine G. L. Solution structure of the core NFATC1/DNA complex. Cell. 92:1998;687-696.