[Disallowed conformations of polypeptide chain exemplified by the β-bend of the β-hairpin in the α-spectrin CH3-domain].

The work presents the results of an exhaustive conformational analysis of β-turns involving amino acid residues with disallowed backbone conformation of the polypeptide chain. It is known that the first residue of the β-turn (Asn47) of the distal β-hairpin in the α-spectrin SH3-domain is characterized by sterically disallowed main chain conformation (values of the dihedral angles (φ and ψ are in the right bottom quadrant of the Ramachandran plot). All α-spectrin structures with the anomalous elements deposited in the PDB were analysed.

[On efficient in vitro purification of cell suspensions containing malignant cells].

We propose a method for magnetic sorting of cell suspensions able to differentiate not only cells with single specific antigen on their surface, but also cells with a group of pre-defined antigens. Individually, each antigen of this group may be present on surfaces of non-selected cells. However, only the simultaneous presence of all given antigens on the cell surface means that such a cell should be separated.

[Conformationally stable segments in helical structures of polypeptide chains of proteins and their role in high level structures formation].

In the work the arguments are presented in favor of the idea on the role of conformationally stable oligo-peptides in specific long-distance interactions in phenomena of molecular recognition during various biological processes. Original authors' and literature data are taken into account. The examples of conformationally stable short oligopeptides participation in alpha-helix and collagen type structures formation are given simultaneously with theoretical approaches.

[Classification of amino acids based on a comparative analysis of contacts in DNA-protein complexes and specific DNA-protein interactions].

The classification of amino acid residues based on the events of contact formation between distinct amino acid and selected nucleotides was constructed. Thus, the most integral properties, that characterize interactions in organization of DNA-protein complexes, were used. We applied the Voronoi-Delaunay tessellation to draw statistics of contacts and area of contacts for the set included 1937 DNA-protein complexes.

[Estimation of the quality of global alignment of amino acid sequences based on evolution criterion].

The aim of the work is to develop the common method for estimating the pairwise alignment quality versus the evolution distance (a degree of homology) between the sequences being comparing, and the type of the alignment procedure. 3D alignments as well as any data on 3D protein structure are not used in the study. Based on the accepted protein sequences evolution model it is possible to estimate the capability of the concrete alignment algorithm to recover the genuine alignment.

[DNA sequencing using specific long-range interaction between macromolecules].

On the basis of the theory of specific long-range interaction between long molecules the approach has been elaborated for the "fast reading" of nucleotide sequences in sole DNA molecule. Firstly, a stretching force applies to the molecule that causes its unwinding from B-form to so called S-form. Then, a molecule disposes in a stretched state on the background.

[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.

[Splice sites are overrepresented in Pasilla binding motif clusters in D. melanogaster genes].

For RNA-binding protein Pasilla, which has been shown to play a role in alternative splicing regulation, binding sites and clusters of binding sites are found in silico in the whole genome of D. melanogaster. The current study analyzes the occurrence of splice sites in binding site clusters.

[On the optimal folding of protein molecules].

The process of globular structure formation from a long molecular chain has been examined. In the course of this process, various regions of the chain interact with one another. We classify the bonds formed during this process as "correct" and "erroneous" ones.

[Vascular endothelial growth factor and vascular endothelial growth factor receptor 2 in the blood serum, tumor and renal parenchyma of patients with renal cell carcinoma].

Serum, tumor and renal parenchyma levels of VEGF and VEGFR2 were compared in patients with renal carcinoma (RC) with reference to basic clinicomorphological characteristics of the disease. VEGF and VEGFR2 were estimated in 37 RC patients and 57 healthy controls (serum levels only). VEGF and VEGFR2 were detected in all the samples.

[Periodicities in nucleotide distribution in the locus of the light chain of Gallus gallus immunoglobulins].

Fourier spectra of nucleotide sequences from chromosome 15 of Gallus gallus have been obtained. The periodical structures of several Ig locus fragments have been characterized. The uniqueness of Fourier spectra of the locus of the Ig light chain and its fragments (such as a variable region, a constant region, an enhancer, and several other fragments) among Fourier spectra of other fragments of chromosome 15 is demonstrated.

[Left helix of polyproline II type and genesis of beta-structures in spidroins 1 and 2 and their recombinant analogs].

The distribution of secondary structures along the polypeptide chains of spider proteins spidroins 1 and 2 and their recombinant analogs has been studied by statistical methods. It was found that these proteins in the monomolecular form contain only trace amounts of beta-structures. At the same time, the regions of the sequence including Ala and Gly are predicted as helical-containing (with alpha-helices and left-helices of polyproline II type).

[Left-handed helix of polyproline II type in linker regions of DNA-binding proteins].

Using the databases of proteins and linkers, a search has been undertaken with the aim to find linker segments adopting the polyproline II conformation in DNA-protein complexes. Seventy three linker-DNA complexes were found. It was shown that the mean length of polyproline II segment comprises six residues, praline being not dominant.

[On the mechanisms of the influence of imino acids on the physical characteristics of collagens].

The influence of imino acids on the thermodynamic characteristics of collagen type structures in various collagens has been analyzed. It was shown that the basic mechanism of entropy increase in the protein-water system consists in the alteration in the number of cooperative segments accompanying the increase in imino acids content, which can be observed during the melting of the fibrous macromolecule. The range of variation in the physical characteristics of cooperative units is determined, in particular, by the variability of hydrogen bond parameters.

[A new approach to estimating the significance of identification of deletion inserts in pairwise alignment].

Within the framework of the unique method of estimating the significance of pairwise alignment of nucleotide sequences, developed by the authors, a new approach to the analysis of deletion inserts in pairwise alignment has been realized. It was shown that the decrease in the average integral length of deletion inserts in alignments obtained using the modern algorithms, as compared with true alignments, is related to a decrease in the number of some deletion inserts rather than a decrease in their average length.

[Geometrical analysis of protein-DNA interactions on the basis of the Voronoĭ-Delaune tessellation].

A new method for the rigorous analysis of DNA-protein contacts has been developed on the basis of Voronoi tessellation. This method permits one to determine close neighbors on the atomic level and compute the area of contact by edges of Voronoi polyhedra. Based on the results of the study of 1109 protein-DNA complexes from PDB, it was demonstrated that about one third of the contacts are the contacts with positively charged Arg and Lys.

[Study of beta-turns in globular proteins].

The formation of beta-turns in globular proteins has been studied by the method of molecular mechanics. Statistical method of discriminant analysis was applied to calculate energy components and sequences of oligopeptide segments, and after this prediction of I type beta-turns has been drawn. The accuracy of true positive prediction is 65%.

[An analysis of the secondary structure of spider spidroins I and II belonging to different species].

We have analyzed the secondary structure of spidroin proteins of I and II types, related to spiders of different species. We used standard methods of secondary structure prediction NNPREDICT and JPRED and also analyzed the occurrences of oligopeptides with a preferred secondary structure with the help of the OLIGON program. We have demonstrated that local segments of the polypeptide chain can adopt alpha- and beta-conformations as well as the left-handed helix of polyproline II type.

[Analysis of side group conformations in molecular mechanics. Possibility of reduction of the side group conformation library in alpha-helical proteins].

A new reduced library of side-chain conformations in proteins has been formed with the aim to apply it as a start point in the molecular mechanics calculations. The adequacy of this library was demonstrated by computation of X-ray determined a-helical protein (PDB code 1BB1) as example.

[A study of periodicity in the primary structure of spidroin 1 and spidroin 2 from spiders belonging to various species].

Sequences of spidroin 1 and 2 from spiders belonging to various species were analyzed by Fourier analysis. Specific periodical patterns were found in various segments of the sequences. These characteristic periodicities vary within the same proteins as well as between spidroin 1 and spidroin 2 sequences.

[Computation of the structure of collagen molecule fragments].

Step-by-step computations of octapeptide structures was performed for human collagens I and III. It was shown that computational results (coordinates of atoms) practically coincide with X-ray data for the collagen fragment.

[A non-statistical approach to the prediction of regular structures in proteins by the example of alpha-helices].

A new approach to the analysis of regular structures in proteins that is based on the method of molecular mechanics is proposed. The method uses only the information about the amino acid sequence. The alpha-helical conformation was simulated using the ICM program of molecular mechanics.

[Left-handed helix conformation of poly-L-proline II type in globular proteins. Statistics of incidence and a role of sequence].

Regions of left-handed polyproline II type conformation in globular proteins were studied throughout the PDB bank. The length and sequence of corresponding fragments were analyzed. It was found that a lot of tetrapeptides (from combinatorial possible ones) show the tendency to be included in the left-handed helices.

[Mapping of active site of alcohol dehydrogenase with low-molecular ligands].

In search of an active alcohol dehydrogenase inhibitor, the structure of which may serve as the basis for a potential drug design, the active site of alcohol dehydrogenase containing NAD and Zn2+ ions was mapped using the method of molecular mechanics. Molecular docking was performed using a number of ligands containing characteristic functional groups: formate ion, ammonia, ammonium ion, methanol, and methylamine. Sites of preferable binding were revealed for each ligand and arranged in order of decreasing energy of binding to the enzyme.

[How do point amino acid substitutions affect the protein structure?].

In order to estimate the influence of point mutations on the protein structure, 552 pairs of structurally aligned proteins with pairwise sequence identities greater than 60% were analyzed. We selected all isolated point mismatches from these alignments. The statistics of local conformational changes corresponding to these mismatches was studied.