Abstract
We have applied bioinformatic analysis of X-ray 3D structures of complexes of transcription factor NF-κB with DNAs. We determined the number of possible Van der Waals contacts and hydrogen bonds between amino acid residues and nucleotides. Conservative contacts in the NF-κB dimer-DNA complex composed of p50 and/or p65 NF-κB subunit and DNA sequences like 5′-GGGAMWTTCC-3′ were revealed. Based on these results, we propose a novel scheme for interactions between NF-κB p50 homodimer and the κB region of the immunoglobulin light chain gene enhancer (Ig-κB). We applied a chemical cross-linking technique to study the proximity of some Lys and Cys residues of NF-κB p50 subunit with certain reactive nucleotides into its recognition site. In all cases, the experimentally determined protein-DNA contacts were in good agreement with the predicted ones.
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Abbreviations
- IVBP:
-
interior variable base pairs
- PDG(pSS):
-
phosphoryldisulfide group
- PDB:
-
protein structure databank
- Pu:
-
A or G
- Py:
-
T or C
- N:
-
any of nucleotides
- M:
-
A or C
- W:
-
A or T
- RHR:
-
Rel homology region, the high-homology region of Rel family proteins
- U*(C*):
-
2′-O-(2-oxoethyl)uridine (2′-O-(2-oxoethyl)cytidine)
- U :
-
2′-deoxy-2′-iodoacetamidouridine
- iU:
-
5-iodo-2′-deoxyuridine
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Translated from Biokhimiya, Vol. 70, No. 11, 2005, pp. 1474–1487.
Original Russian Text Copyright © 2005 by Romanenkov, Ustyugov, Zatsepin, Nikulova, Kolesnikov, Metelev, Oretskaya, Kubareva.
Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM04-338, March 27, 2005.
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Romanenkov, A.S., Ustyugov, A.A., Zatsepin, T.S. et al. Analysis of DNA-Protein Interactions in Complexes of Transcription Factor NF-κB with DNA. Biochemistry (Moscow) 70, 1212–1222 (2005). https://doi.org/10.1007/s10541-005-0249-2
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DOI: https://doi.org/10.1007/s10541-005-0249-2