Anna A. Nikulova

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Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory 'grammar', or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be(More)
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(More)
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(More)
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.
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