Analysis of DNA-protein interactions in complexes of transcription factor NF-κB with DNA

A. S. Romanenkov, A. A. Ustyugov, T. S. Zatsepin, A. A. Nikulova, I. V. Kolesnikov, V. G. Metelev, T. S. Oretskaya, E. A. Kubareva

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1212-1222
Number of pages11
JournalBiochemistry (Moscow)
Volume70
Issue number11
DOIs
Publication statusPublished - Nov 2005
Externally publishedYes

Keywords

  • Affinity modification
  • DNA-protein interaction
  • Hydrogen bond
  • Modified DNA
  • Transcription factor NF-κB
  • Van der Waals contact

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