Deppdb--DNA electrostatic potential properties database: electrostatic properties of genome DNA

Protein-DNA recognition mechanisms and specificity

The accumulated knowledge about the structure of protein-DNA complexes allowed us to understand the mechanisms of protein-DNA recognition and searching for a specific site on DNA. Obviously, the mechanism of specific DNA recognition by a protein must satisfy two requirements. First, the probability of incorrect binding should be very small. Second, the time to find the "correct" binding site should not be too long. If we assume that protein recognition of a precise site on DNA occurs at some distance from DNA and calculate global minima, we can avoid local minima at short distances. The only long-range interaction is the interaction of charges. The location of charges on DNA in three-dimensional space depends on the local conformation of DNA and thus reflects the DNA sequence and sets the spatial pattern for recognition. Various factors such as counter ion concentration, ionic strength, and pH can affect protein recognition of DNA. Nowadays, the theory of long-range interactions makes it possible to calculate the best mutual spatial arrangement of protein and DNA molecules by charged groups and avoid misplaced binding.

Comparative Analysis of Mycoplasma gallisepticum vlhA Promoters

Mycoplasma gallisepticum is an intracellular parasite affecting respiratory tract of poultry that belongs to class Mollicutes. M. gallisepticum features numerous variable lipoprotein hemagglutinin genes (vlhA) that play a role in immune escape. The vlhA promoters have a set of distinct properties in comparison to promoters of the other genes. The vlhA promoters carry a variable GAA repeats region at approximately 40 nts upstream of transcription start site. The promoters have been considered active only in the presence of exactly 12 GAA repeats. The mechanisms of vlhA expression regulation and GAA number variation are not described. Here we tried to understand these mechanisms using different computational methods. We conducted a comparative analysis among several M. gallisepticum strains. Nucleotide sequences analysis showed the presence of highly conserved regions flanking repeated trinucleotides that are not linked to GAA number variation. VlhA genes with 12 GAA repeats and their orthologs in 12 M. gallisepticum strains are more conserved than other vlhA genes and have narrower GAA number distribution. We conducted comparative analysis of physicochemical profiles of M. gallisepticum vlhA and sigma-70 promoters. Stress-induced duplex destabilization (SIDD) profiles showed that sigma-70 group is characterized by the common to prokaryotic promoters sharp maxima while vlhA promoters are hardly destabilized with the region between GAA repeats and transcription start site having zero opening probability. Electrostatic potential profiles of vlhA promoters indicate the presence of the distinct patterns that appear to govern initial stages of specific DNA-protein recognition. Open state dynamics profiles of vlhA demonstrate the pattern that might facilitate transcription bubble formation. Obtained data could be the basis for experimental identification of mechanisms of phase variation in M. gallisepticum.

DEPPDB - DNA electrostatic potential properties database. Electrostatic properties of genome DNA elements

Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB - DNA Electrostatic Potential (and other Physical) Properties Database - provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids genomes according to the NCBI RefSeq, and some model eukaryotic genomes. Data for promoters, regulation sites, binding proteins, etc., are incorporated from established DBs and literature. The database is complemented by analytical tools. User sequences calculations are available. Case studies discovered electrostatics complementing DNA bending in E.coli plasmid BNT2 promoter functioning, possibly affecting host-environment metabolic switch. Transcription factors binding sites gravitate to high potential regions, confirming the electrostatics universal importance in protein-DNA interactions beyond the classical promoter-RNA polymerase recognition and regulation. Other genome elements, such as terminators, also show electrostatic peculiarities. Most intriguing are gene starts, exhibiting taxonomic correlations. The necessity of the genome electrostatic properties studies is discussed.