Analysis of DNA-protein interactions in complexes of transcription factor NF-kappaB with DNA.
We have applied bioinformatic analysis of X-ray 3D structures of complexes of transcription factor NF-kappaB 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-kappaB dimer-DNA complex composed of p50 and/or p65 NF-kappaB subunit and DNA sequences like 5 -GGGAMWTTCC-3 were revealed. Based on these results, we propose a novel scheme for interactions between NF-kappaB p50 homodimer and the kappaB region of the immunoglobulin light chain gene enhancer (Ig-kappaB). We applied a chemical cross-linking technique to study the proximity of some Lys and Cys residues of NF-kappaB 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.
Romanenkov
A S
AS
Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.
Ustyugov
A A
AA
Zatsepin
T S
TS
Nikulova
A A
AA
Kolesnikov
I V
IV
Metelev
V G
VG
Oretskaya
T S
TS
Kubareva
E A
EA
D000595:Amino Acid Sequence; D001483:Base Sequence; D004247:DNA / Q000378:metabolism*; D017931:DNA Primers; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006801:Humans; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017386:Sequence Homology, Amino Acid
D017931:DNA Primers; D004268:DNA-Binding Proteins; D016328:NF-kappa B; D004247:DNA