[Machine learning study of DNA binding by transcription factors from the LacI family].

We studied 1372 LacI-family transcription factors and their 4484 DNA binding sites using machine learning algorithms and feature selection techniques. The Naive Bayes classifier and Logistic Regression were used to predict binding sites given transcription factor sequences and to classify factor-site pairs on binding and non-binding ones. Prediction accuracy was estimated using 10-fold cross-validation. Experiments showed that the best prediction of nucleotide densities at selected site positions is obtained using only a few key protein sequence positions. These positions are stably selected by the forward feature selection based on the mutual information of factor-site position pairs.

[Computational method for prediction of protein functional sites using specificity determinants].

The current available data on protein sequences largely exceeds the experimental capabilities to annotate their function. So annotation in silico, i.e. using computational methods becomes increasingly important. This annotation is inevitably a prediction, but it can be an important starting point for further experimental studies. Here we present a method for prediction of protein functional sites, SDPsite, based on the identification of protein specificity determinants. Taking as an input a protein sequence alignment and a phylogenetic tree, the algorithm predicts conserved positions and specificity determinants, maps them onto the protein's 3D structure, and searches for clusters of the predicted positions. Comparison of the obtained predictions with experimental data and data on performance of several other methods for prediction of functional sites reveals that SDPsite agrees well with the experiment and outperforms most of the previously available methods. SDPsite is publicly available under http://bioinf.fbb.msu.ru/SDPsite.

[Comparative genomics analysis of nitrate and nitrite respiration in gamma proteobacteria].

Nitrate and nitrite are preferred respiration oxidants during anaerobic conditions. In Escherichia coli such nitrate- and nitrite respiration is controlled by homologous transcriptional factors NarL and NarP. Although this system was intensively studied during the last two decades, the exact mechanisms of regulation and the structure of the NarL binding signals remained elusive. By the use of comparative genomics approach it was determined that most of the gammaproteobacteria contained only NarP protein. Regulog analysis revealed that whole structure of NarP regulons varied in different genomes and only regulation of nitrate and nitrite reduction system seemed to be highly conservative. Correlation between changes in the respiration system and the presence of the single regulatory system was shown. Conservative NarP binding sites upstream of fnr gene and genes for aerobic metabolism point to alteration in NarP role in respiration control during evolution. Thirty five new regulog members were determined and autoregulation of narQP operon in Vibrionaceae genomes was predicted.

[Purine regulon of gamma-proteobacteria: a detailed description]. / Purinovyi regulon gamma-proteobakterii. Detal'noe opisanie.

The structure of the purine regulon was studied by a comparative genomic approach in seven genomes of gamma-proteobacteria: Escherichia coli, Salmonella typhi, Yersinia pestis, Haemophilus influenzae, Pasteurella multocida, Actinobacillus actinomycetemcomitans, and Vibrio cholerae. The palindromic binding site of the purine repressor (consensus ACGCAAACGTTTGCGT) is fairly well retained of genes encoding enzymes that participate in the synthesis of inosinemonophosphate from phosphoribozylpyrophosphate and in transfer of unicarbon groups, 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 of nonorthologous but functionally replaceable genes. However, the PurR site is poorly retained in front of 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 protein 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.

[Change in entropy of the free polypeptide chain during formation of hydrogen bonds]. / Izmenenie éntropii svobodnoi polipeptidnoi tsepi pri obranzovanii vodorodnykh sviazei.

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, T delta S, were calculated. The model was studied at different criteria of steric interactions. Comparison with the data of other authors showed the values of T delta S to 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 alpha(R)-helices is associated with T delta S = 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 alpha(R)-helix by one residue leads to T delta S = 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 alpha(R)-helices in the supersecondary helix-loop-helix structure is favorable as long as the loop conformation remains nearly optimal.

Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria.

Comparative approach is a powerful tool for analysis of gene regulation in bacterial genomes. Here we apply it to analysis of regulation of the multidrug resistance transport (MDRT) systems in enterobacteria Escherichia coli, Salmonella typhi, Klebsiella pneumoniae and Yersinia pestis. Comparison of nucleotide sequences upstream of MDRT genes was performed in order to predict new regulatory sites (operators) and identify candidate regulons. Since the regulatory sites diverge slower than the non-coding regions in general, they are visible as strongly conserved islands. This analysis resulted in description of a regulatory network for known and hypothetical MDRT systems and porins. New candidate members of the MarA regulon were detected. Putative binding sites for EmrR and AcrR were suggested. A new hypothetical MarX regulon was described that includes some multidrug transporters and porins.

Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria.

The comparative approach is a powerful tool for the analysis of gene regulation in bacterial genomes. It can be applied to the analysis of regulons that have been studied experimentally as well as that of regulons for which no known regulatory sites are available. It is assumed that the set of co-regulated genes and the regulatory signal itself are conserved in related genomes. Here, we use genomic comparisons to study the regulation of transport and utilization systems for sugar acids in gamma purple bacteria Escherichia coli, Salmonella typhi, Klebsiella pneumoniae, Yersinia pestis, Erwinia chrysanthemi, Haemophilus influenzae and Vibrio cholerae. The variability of the operon structure and the location of the operator sites for the main transcription factors are demonstrated. The common metabolic map is combined with known and predicted regulatory interactions. It includes all known and predicted members of the GntR, UxuR/ExuR, KdgR, UidR and IdnR regulons. Moreover, most members of these regulons seem to be under catabolite repression mediated by CRP. The candidate UxuR/ExuR signal is proposed, the KdgR consensus is extended, and new operators for all transcription factors are identified in all studied genomes. Two new members of the KdgR regulon, a hypothetical ATP-dependent transport system OgtABCD and YjgK protein with unknown function, are detected. The former is likely to be the transport system for the products of pectin degradation, oligogalacturonides.

Simulated annealing for alpha-helical protein folding: searches in vicinity of the "molten globule" state.

A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on a vicinity of "molten globule" states of a protein. In contrast to the majority of the known approaches for estimation of a protein free energy we introduce a simplified potential of interactions with solvent and consider conformational energy of the loops in addition to mean-force potential. The model was applied to several globular alpha-helical proteins and demonstrated high prediction accuracy in comparison with other known models.

Interhelical contacts determining the architecture of alpha-helical globular proteins.

An approach based on a presentation of alpha-helical protein topology as a graph is presented. The approach allows to estimate a role of each interhelical contact in the whole protein topology and to classify the contacts. It is shown that a consideration of only about a half of the whole pool of interhelical contacts exposed in the protein is enough for a determination of protein architecture. Such contacts are called as major and their quantitative characteristics are obtained. Moreover, providing a clear and simple presentation of the protein topology, the approach can be applied for a description of structural domain/subdomain arrangement of alpha-helical proteins and illustration of their folding/denaturation paths.

Amino acid sequence pattern in the regulatory peptides.

The essential properties of the primary structure of regulatory peptides, i.e. amino acid residues and their combinations, which are characteristic of the whole population of regulatory peptides, have been revealed using statistical methodology. These properties are as follows: increased content of certain residues (Gly, Pro, Phe, Arg, Tyr, Met and Trp) as well as an increased rate of occurrence of certain pairs of residue as compared with proteins, a random sequence of residues and "nonregulatory" peptides. By representing regulatory peptides as a sequence of hydrophobic (2 types) and hydrophilic (3 types) segments, the pattern for alternation of these segments in regulatory peptides has been determined. The segments were classified into 5 types according to the peculiarities of mutual localization of hydrophobic and hydrophilic residues within the primary structure of regulatory peptides. As compared with proteins, "nonregulatory" peptides and a random sequence of segments, regulatory peptides were characterized by an increased frequency of 4 particular pairs of segments among 12 theoretically possible pairs. These 4 pairs are fragments of the periodic segment sequence with periods of 4 segments. The revealed pattern indicates that there exists a general principle of the regulatory peptide primary structure organization and possibly a common type of the regulatory peptides flexible peptide chain folding at the ligand-receptor complex formation.

[Configuration and properties of a binding site for thyroid hormones on a specific receptor]. / Konfiguratsiia i svoistva oblasti sviazyvaniia tireoidnykh gormonov na spetsificheskom retseptore.

An analysis has been carried out of data available in literature on structure-function relationships for thyroid hormones, namely thyroxine, triiodothyronine and their analogues. The configuration and dimensions of the hormone-binding site of the receptor in a hormone-receptor complex are described. The receptor is shown to have a strained conformation in the complex. The analysis is indicative of the existence of two types of hormone-receptor complexes, a particular type being determined by the dimensions of analogues.

[Induction of ion transport coupled to oxidative reactions in the membranes of mitochondria and liposomes]. / Induktsiia ionnogo transporta, sopriazhennaia s okislitel'nymi reaktsiiami v membranakh mitokhondrii i liposom.

The mechanism of induction of potassium permeability for mitochondrial membranes under special conditions was under study. Conditions were such as: 1--incubation of mitochondria in medium with low meaning of pH (6,0--6,5), 2--incubation in preseace of electrophylic agent--p-(N,N-di-2-chloroethyl) aminophenylacetic acid, which is hydrolized to HCl and 3-lipidsoluble acid, 2,4-dinitrophenol. It is shown that the named mechanism in any case requires the oxidation of lipids of mitochondrial membranes.

[Model for auxin receptor]. / Postroenie modeli retseltora auksinov.

Literary data on correlation between the structure and auxin activity of aryl-, arylalkan- and aryloxyalkancarboxylic acids and those of 3-indolylacetic acid are reviewed. The structure of auxins is compared to that of their inactive structural analogs in terms of a literary hypothesis on the bifunctional binding of auxins to the receptor, which allowed to construct a model for the structure of the auxin receptor (site responsible for intrinsic binding of auxins). The geometric parameters of this receptor site and specific arrangement of specific auxin binding sites have been proposed. It is demonstrated that during auxin absorption on the receptor the conformation of the latter is changed, which may be accounted for as a primary functional effect of auxins on the receptor.