Analysis of DNA-Protein Interactions in Complexes of Transcription Factor NF-kappaB with DNA

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A. S. Romanenkov¹, A. A. Ustyugov², T. S. Zatsepin¹, A. A. Nikulova², I. V. Kolesnikov³, V. G. Metelev¹, T. S. Oretskaya¹, and E. A. Kubareva^4*

¹Faculty of Chemistry and ²Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; fax: (7-095) 939-3181

³Bioline GmbH, Im Biotechnologiepark TGZ 2, Luckenwalde 14943, Germany; fax: +49 (0) 337-168-1244

⁴Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; fax: (7-095) 939-3181; E-mail: kubareva@belozersky.msu.ru

^* To whom correspondence should be addressed.

Received November 10, 2004; Revision received December 9, 2004

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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.

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KEY WORDS: transcription factor NF-kappaB, DNA-protein interaction, hydrogen bond, Van der Waals contact, modified DNA, affinity modification

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