[Correlations between clusters of protein-DNA binding sites and the binding experimental data allow to predict a structure of regulatory modules].

Here we analyzed an option to predict the structure of cis-regulatory modules that consist of binding sites of different proteins (heterogeneous cis-regulatory modules) using mutual positional correlations between protein-DNA binding experimental data and computationally identified clusters of binding sites for each of the proteins.

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.

[A discrepancy between the experimental and theoretical data on energy migration from B800 to B850 in LH-2 antennary complexes in purple bacteria]. / Nesootvetstvie éksperimental'nykh i teoreticheskikh dannykh po migratsii énergii ot B800 k B850 v antennykh kompleksakh LH-2 purpurnykh bakterii.

A discrepancy between the times of excitation transfer from B800 to B850 bacteriochlorophyll fractions in LH-2 complexes of purple bacteria was revealed. The experimental value (0.7-0.8 ps from literature sources) are at least four times lower than that (> 3.2 ps) calculated theoretically on the basis of recently obtained atomic structure of LH2. Possible reasons for this discrepancy are discussed.