The role of the phosphorus BI-BII transition in protein-DNA recognition: The NF-κB complex

Nucleic Acids Research

Volumn 30, Issue 20, 2002, Pages 4452-4459

  Wecker, K ^a   Bonnet, M C ^a   Meurs, E F ^a   Delepierre, M ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA FRAGMENT; DOUBLE STRANDED DNA; ESTER DERIVATIVE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PHOSPHORUS; PHOSPHORUS 31;

5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA BINDING; DNA FLANKING REGION; DNA SEQUENCE; GEL MOBILITY SHIFT ASSAY; GENE MUTATION; GENE STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR RECOGNITION; MOUSE; NONHUMAN; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ANALYSIS;

ANIMALS; BASE SEQUENCE; BINDING SITES; CELL LINE; DNA; ELECTROPHORETIC MOBILITY SHIFT ASSAY; MACROMOLECULAR SUBSTANCES; MOLECULAR SEQUENCE DATA; NF-KAPPA B; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PHOSPHORIC ACID ESTERS; PHOSPHORUS; PROTEIN BINDING;

ANIMALIA; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0037109266     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (38)

1. Nabel,G. and Baltimore,D. (1987) An inductible transcription factor activates expression of human immunodeficiency virus in T cells. Nature, 326, 711-713.
2. Clark,L., Matthews,J.R. and Hay,R.T. (1990) Interaction of enhancer-binding protein EBP1(NF-kappa B) with the human immunodeficiency virus type 1 enhancer. J. Virol., 64, 1335-1344.
3. Virelizier,J.L. (1990) Cellular activation and human immunodeficiency virus infection. Curr. Opin. Immunol., 2, 409-413.
4. Brown,K., Gerstberger,S., Carlson,L. and Franzoso,G. (1995) Control of I kappa B-alpha proteolysis by site-specific, signal-induced phosphorylation. Science, 267, 1485-1488.
5. DiDonato,J.A., Mercurio,F. and Karin,L. (1995) Phosphorylation of I kappa B alpha precedes but is not sufficient for its dissociation from NF-kappa B. Mol. Cell. Biol., 15, 1302-1311.
6. Müller,C.W., Rey,F.A., Sodeoka,M., Verdine,G.L. and Harrison,S.C. (1995) Structure of the NF-kappa B p50 homodimer bound to DNA. Nature, 373, 311-317.
7. Ghosh,G., van Duyne,G., Ghosh,S. and Sigler,P.B. (1995) Structure of NF-kappa B p50 homodimer bound to a kappa B site. Nature, 373, 303-310.
8. Chen,Y.-Q., Ghosh,S. and Gosh,G. (1998) A novel DNA recognition mode by the NF-kappa B p65 homodimer. Nature Struct. Biol., 5, 67-73.
9. Cramer,P., Larson,C.J., Verdine,G.L. and Muller,C.W. (1997) Structure of the human NF-κB p52 homodimer-DNA complex at 2.1 Å resolution. EMBO J., 16, 7078-7090.
10. Chen,F.E., Huang,D.B., Chen,Y.-Q. and Ghosh,G. (1998) Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature, 391, 410-413.
11. Schreck,R., Zorbas,H., Winnacker,E.L. and Baeuerle,P.A. (1990) The NF-kappa B transcription factor induces DNA bending which is modulated by its 65-kD subunit. Nucleic Acids Res., 18, 6497-6502.
12. Tisné,C., Hantz,E., Hartmann,B. and Delepierre,M. (1998) Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BI1 equilibrium inducing a global dynamic curvature of the duplex. J. Mol. Biol., 279, 127-142.
13. Tisné., Hartmann,B. and Delepierre,M. (1999) NF-kappa B binding mechanism: a nuclear magnetic resonance and modeling study of a GGG→CTC mutation. Biochemistry, 38, 3883-3894.
14. Lavery,R. and Sklenar,H. (1998) The definition of generalised helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn., 6, 63-91.
15. Lavery,R. (1998) DNA bending and curvature. In Olson,W.K., Sarma,R.H. and Sundaralingam,M. (eds), Structure and Expression. Adenine Press, New York, NY, Vol. 3, pp. 191-211.
16. Lavery,R. (1998) Junctions and bends in nucleic acids: a new theoretical modelling approach. In Olson,W.K., Sarma,R.H. and Sundaralingam,M. (eds), Structure and Expression. Adenine Press, New York, NY, Vol. 3, pp. 191-211.
17. Lavery,R., Zabrewska,K. and Sklenar,H. (1994) JUMNA (junction minimisation of nucleic acids). Comput. Phys. Commun., 91, 135-158.
18. Bertrand,H., Ha-Duong,T., Fermandjian,S. and Hartmann,B. (1998) Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps. Nucleic Acids Res., 26, 1261-1267.
19. Hartmann,B., Piazzola,D. and Lavery,R. (1993) BI-BII transitions in B-DNA. Nucleic Acids Res., 11, 561-568.
20. 31P NMR spectra and backbone torsional angles of wild-type and mutant Lac operator fragments. Biochemistry, 28, 8292-8303.
21. Lefebvre,A., Mauffret,O., Hartmann,B. Lescot,E. and Fermandjian,S. (1995) Structural behaviour of the CpG step in two related oligonucleotides reflects its malleability in solution. Biochemistry, 34, 12019-12028.
22. 31P chemical shifts of double-helical nucleic acids. Biochemistry, 27, 7223-7237.
23. States,D.J., Haberkorn,R.A. and Ruben,D.J. (1982) A two-dimensional nuclear Overhauser experiment with pure absorption phase in four quadrants. J. Magn. Reson., 48, 286.
24. 1H spin system identification in macromolecules. J. Am. Chem. Soc., 110, 7870.
25. Bax,A. and Davis,D.G. (1985) MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson., 65, 355-360.
26. Desvaux,H., Berthault,P., Birlirakis,N., Goldman,M. and Piotto,M. (1995) Improved version of dynamic ROESY. J. Magn. Reson., 113, 47-52.
27. Wilker,W., Leibftitz,D., Kerssebaum,R. and Bermel,W. (1993) Gradient selection in inverse heteronuclear correlation spectroscopy. Magn. Reson. Chem., 31, 287-292.
28. 1H-15N spectroscopy. J. Magn. Reson., 87, 488-501.
29. 31P coupling constants in double-stranded DNA fragments. J. Am. Chem. Soc., 25, 7525-7526.
30. Kupce,E. and Freeman,R. (1995) Short selective pulses for biochemical applications. J. Magn. Reson., 112, 134-137.
31. Clore,G. and Gronenborn,A.M. (1985) Probing the three-dimensional structures of DNA and RNA oligonucleotides in solution by nuclear Overhauser enhancement measurements. FEBS Lett., 179, 187-198.
32. Wüthrich,K. (1986) NMR of Proteins and Nucleic Acids. John Wiley & Sons, New York, NY.
33. Van de Ven,F.J.M. and Hilbers,C.W. (1988) Resonance assignments of non-exchangeable protons in B type DNA oligomers, an overview. Nucleic Acids Res., 16, 5713-5720.
34. Wijmenga,S.S., Mooren,M.M.W. and Hilbers,C.W. (1993) NMR of nucleic acids; from spectrum to structure. In NMR in Macromolecules: A Practical Approach, Oxford University Press, Oxford, UK, pp. 217-288.
35. 1H3′ coupling constant. Magn. Reson. Chem., 34, 115-124.
36. Weisz,K., Shafer,RH., Egan,W. and James,T.L. (1994) Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations. Biochemistry, 11, 354-366.
37. Rozenberg,H., Rabinovich,D., Frolow,F., Hegde,R.S. and Shakked,Z. (1988) Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. Proc. Natl Acad. Sci. USA, 95, 15194-15199.
38. Hizver,J., Rozenberg,H., Frolow,F., Rabinovich,D. and Shakked,Z. (2001) DNA bending by an adenine-thymine tract and its role in gene regulation. Proc. Natl Acad. Sci. USA, 98, 8490-8495.