Doxycycline Sensitive Two-Promoter Integrator Based on the TET-ON 3G Transactivator

Molecular Biology - A synthetic genetic chain was created—a two-promoter integrator, the activity of the output signal of which is high only with the high activity of two promoters at the...     

Computational method for predicting protein functional sites with the use of specificity determinants

The currently available body of decoded amino acid sequences of various proteins exceeds manifold the experimental capabilities of their functional annotation. Therefore, in silico annotation using bioinformatics methods becomes increasingly important. Such annotation is actually a prediction; however, this can be an important starting point for further laboratory research. This work describes a new method for predicting functionally important protein sites, SDPsite, on the basis of identification of specificity determinants. The algorithm proposed utilizes a protein family aglinment and a phylogenetic tree to predict the conserved positions and specificity determinants, map them onto the protein structure, and search for clusters of the predicted positions. Comparison of the resulting predictions with experimental data and published predictions of functional sites by other methods demonstrates that the results of SDPsite agree well with experimental data and exceed the results obtained with the majority of previous methods. SDPsite is publicly available at http://bioinf.fbb.msu.ru/SDPsite.     

Entropy Change for Free Polypeptide Chain upon Hydrogen Bonding

Formation probabilities of different hydrogen bonds between carbonyl oxygen and amide hydrogen were determined by Monte Carlo simulations using a computer model in the space of sterically allowable conformations of alanine and glycine oligopeptides, and the corresponding entropy losses for the peptide backbone, TS, were calculated. The model was studied at different criteria of steric interactions. Comparison with the data of other authors showed the values of TSto be mainly determined by overall extent and type of the state space and to be only slightly dependent on its energy profile. Both short-range and long-range steric interactions were shown to prevent hydrogen bonding, especially in alanine peptides. In the model studied, the initiation of (R)-helices is associated with TS= 8–10 kT, and prior formation of a 3/10-turn or one three-center H-bond does not appreciably decrease this entropy barrier. Elongation of the (R)-helix by one residue leads to TS= 3.0–3.7 kT, the helices begin to stabilize after at least three sequential H-bonds are formed. The difference in the probability of insertion of Ala and Gly into the helix is lower than it follows from comparison of their mobility. The results could be explained assuming that factors different from helical H-bonds take part in the stabilization of the helices. One may suppose upon modeling of folding that even three sequential H-bonds are unable to fix the structure of a flexible peptide loop, while the elongation of (R)-helices in the supersecondary helix-loop-helix structure is favorable as long as the loop conformation remains nearly optimal.     

Purine Regulon of Gamma-Proteobacteria: A Detailed Description

The structure of the purine regulon was studied by a comparative genomic approach in seven genomes of gamma-proteobacteria: Escherichia coli, Salmonella typhimurium, Yersinia pestis, Haemophilus influenzae, Pasteurella multocida, Actinobacillus actinomycetemcomitans, and Vibrio cholerae. The palindromic binding site of the purine repressor (consensus ACGCAAACGTTTGCGT) is fairly well conserved upstream genes encoding enzymes that participate in the synthesis of inosine monophosphate from phosphoribozylpyrophosphate and in transfer of one-carbon units, and also upstream of some transport protein genes. These genes may be regarded as the main part of the purine regulon. In terms of physiology, the regulation of the purC and gcvTHP/folD genes seems to be especially important, because the PurR site was found upstream nonorthologous but functionally replaceable genes. However, the PurR site is poorly conserved upstream orthologs of some genes belonging to the E. coli purine regulon, such as genes involved in general nitrogen metabolism, biosynthesis of pyrimidines, and synthesis of AMP and GMP from IMP, and also upstream of the purine repressor gene. It is predicted that purine regulons of the examined bacteria include the following genes: upp participating in synthesis of pyrimidines; uraA encoding an uracil transporter gene; serA involved in serine biosynthesis; folD responsible for the conversion of N5,N10-methenyl tetrahydrofolate into N10-formyltetrahydrofolate; rpiA involved in ribose metabolism; and genes with an unknown function (yhhQ and ydiK). The PurR site was shown to have different structure in different genomes. Thus, the tendency for a decline of the conservatism of site positions 2 and 15 was observed in genomes of bacteria belonging to the Pasteurellaceae and Vibrionaceae groups.     

The channel in transporters is formed by residues that are rare in transmembrane helices

Transmembrane transport is an essential component of the cell life. Many genes encoding known or putative transport proteins are found in bacterial genomes. In most cases their substrate specificity is not experimentally determined and only approximately predicted by comparative genomic analysis. Even less is known about the 3D structure of transporters. Nevertheless, the published experimental data demonstrate that channel-forming residues determine the substrate specificity of secondary transporters and analysis of these residues would provide better understanding of the transport mechanism. We developed a simple computational method for identification of channel-forming residues in transporter sequences. It is based on the analysis of amino acids frequencies in bacterial secondary transporters. We applied this method to a variety of transmembrane proteins with resolved 3D structure. The predictions are in sufficiently good agreement with the real protein structure.