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

The work presents the results of an exhaustive conformational analysis of ß-turns involving amino acid residues with disallowed backbone conformation of the polypeptide chain. It is known that the first residue of the ß-turn (Asn47) of the distal ß-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. We hypothesized that the formation of disallowed conformation may occur through the fixation (due to the SH3 domain structure) of the adjacent to the ß-turn amino acid residues with the ß-structure. These residues are disposed in such a manner that ß-turn conformation of the residues contributes just to the disallowed local conformation of this residue whereas any other ß-turn conformations (with allowed local conformation) are impossible. To test this hypothesis an exhaustive conformational analysis of the ß-bend has been performed by altering internal coordinates (two pairs of φ and ψ angles and two Ω angles). The conformations were selected as a result of grid search procedure with. 1 degrees step that corresponded to stereochemically allowed local deformations of the polypeptide chain segment forming the ß-turn. In all conformations obtained the local conformation of Asn47 rests in the disallowed region. The conformations found include conformations coinciding with experimentally determined structures from the PDB as well as an additional variant that differs from X-ray structure in values of a pair of φ and ψ angles of the second residue belonging to the ß-bend. Values of these angles fall in the region of the Ramachandran plot near the line φ = 0 (and negative values of ψ) i.e. in strongly disallowed region without experimental points. Therefore the additional variants of the ß-turn local deformation are impossible to observe in experiment. Thus, the idea that disallowed conformation is intruded to the ß-bend by fixation of adjacent residues receives confirmation in this work. The topological limitations in a context of the structure in such kind of ß-hairpins exclude the allowed local conformations.

[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. The method is of interest, for purification of cell suspensions from malignant cells, in particular, for purification of bone marrow material for autologous transplantation in leukemia.

[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. In this study a classical Needleman and Wunsch global alignment algorithm has been tested on a set of sequences from the Prefab database. Dependences of accuracy and confidence of a global alignment procedure were calculated as consequences of insertions/deletions and mutations shares.

[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. Similarities of amino acid residues have been searched for based on the comparison of corresponded rows and matrixes of contacts and areas of contacts. Nine measures of distance were used for estimation of rows similarity degree. The procedure of clustering amino acids in groups included three hierarchical and two nonhierarchical methods. A total tree was built using nine techniques of estimating distance with three hierarchical clustering methods. It was shown that clustering centers in the main groups are always constant while other relationships between objects vary. Clustering of binary associations was found for the most amino acids. Major classes of up to six amino acids correspond to the certain local structures of the polypeptide chain in the context of amino acid composition. These data should be taken into account when designing DNA-protein ligands.

[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. The conformationally stable oligopeptides obtained in the course of PDB bank analysis are discussed. The role of amino acids sequence in collagen helix formation is shown.

[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.

[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. After this, the electrostatic potential is estimated in the space along the DNA filament. Information obtained is sufficient for the deduction of the nucleotide sequence in DNA. Another approach to the "reading" of information reduces to the measurement of the filament element deformation induced by electrostatic field from the electrode that stretches the filament by alternating current applied.

[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. The term "correct" bonds implies the bonds characteristic for a completely formed native globular structure. All other bonds can be treated as "erroneous". It was demonstrated that the process of globule formation may proceed actually without the formation and the following decay of "erroneous" bonds. Our model permits one to avoid the examination of numerous "erroneous" variants since, between the regions of the chain that form "correct" bonds, long-distance interactions characterized simultaneously by high selectivity take place. The existence of interactions of this kind facilitates the drawing together and subsequent interaction of just these regions of the chain that yield "correct" bonds. Based on the data bank analysis, it was demonstrated that the model elaborated is valid not only for abstract structures but also for real polypeptide chains capable of forming protein globules and superhelical fibrils.

[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. Several hundred thousand binding site motifs and thousands of significant motif clusters were identified. It was discovered that exon-intron borders in D. melanogaster genes are reliably found within Pasilla binding motif clusters, with a higher frequency than could be otherwise expected based on a random model. Additionally, donor splice sites are found in Pasilla clusters twice as often as acceptor sites. This phenomena is observed both for exons annotated as alternatively spliced and for exons annotated as constitutive. These observations support the hypothesis that Pasilla plays a functional role in splicing regulation of D. melanogaster.

[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. Their concentrations in the serum were the same in the patients and controls. The tumor tissue contained more VEGF than renal parenchyma. In unfavorable clinicomorphological features the tumor contained higher content of VEGF, higher VEGF/VEGFR2, lower VEGFR2. Thus, angiogenic factors studied closely correlate with clinicomorphological characteristics of renal carcinoma: primary tumor size, stage of the disease, tumor differentiation, tumor pseudocapsule invasion.

[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). An analysis of literature data and our data obtained in this study shows that the main conformation of the polypeptide chain solutions of spidroins 1 and 2 and their recombinant analogs in water solutions is the left-helix of polyproline II type with some contaminations of alpha-helices and a very small share of beta-structures. The transition to the state with extended conformations, which are peculiar to mature filaments of spider webs, requires the dehydration of the polypeptide chain backbone. Thus, the genesis of beta-structure in spider web proteins is determined by the conditions of conformation transitions between the main regular conformations of the polypeptide chain backbone.

[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. This is displayed in a broadening of the bands of NH-valence vibrations and the half-widths of transitions in post-denatured structures. Thus, the basic mechanism of the influence of imino acids on thermodynamic characteristics of collagens is related to the complex nature of the melting process. The dehydration-hydration mechanisms of native and denatured states become significantly different upon replacement of any amino acid by an imino acid.

[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 Voronoi-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. There is distinct amino acid prevalence for nucleotides: for A - Pro; for T - His; for G - Asp; for C - Trp, Asp, Glu. Therefore, GC pairs prefer to interact with negatively charged residues, and alanine and methionine, whereas AT pairs prefer to interact with histidine and unpolar residues.

[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. The symmetry of praline disposition in these regions prevents the formation of the cooperative water net involving amide groups. An example of specific distribution of proline in some proteins of the motility apparatus is presented.

[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%. Components of conformational energy considerably affecting beta-turn formation were delineated. There are torsional energy, energy of hydrogen bonds, and van der Waals energy.

[Computation of the structure of collagen molecule fragments]. / Raschet struktury fragmentov molekuly kollagena.

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 study of periodicity in the primary structure of spidroin 1 and spidroin 2 from spiders belonging to various species]. / Issledovanie periodichnostei v posledovatel'nostiakh aminokislot spidroinov pervogo i vtorogo tipov iz paukov razlichnykh vidov.

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. It is possible that alterations in periodicity help to recognize contact sites between the molecules. Spidroins of 2 type have similar sequence structure consisting of four parts with a particular periodical pattern. These parts are a constant C-terminal part, a long-periodical part, a short-periodical part, and a constant N-terminal part.

[An analysis of the secondary structure of spider spidroins I and II belonging to different species]. / Analiz vtorichnykh struktur spidroinov pervogo i vtorogo tipov iz paukov, prinadlezhashchikh razlichnym vidam.

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. Periodical patterns found in the amino acid distribution indicate that there is a possibility of development of a macroscopic order accompanied by local conformational transitions.