[Regulation of the binding of the BMP-2 growth factor with collagen by blood plasma fibronectin].

The release kinetics of recombinant human bone morphogenic factor 2 (rhBMP-2) from collageneous hydrogel in the presence of human blood plasma have been studied. The expulsion of rhBMP-2 from the collagen-BMP-2 complex by the competitive adhesion of collagen-binding proteins penetrating from plasma was firstly recognized. It was experimentally proven that that blood plasma fibronectin is the main collagen-binding protein, which is responsible for the controlled release of rhBMP-2. As a result, a new collageneous hydrogel with the incorporation of fibronectin was created which retained rhBMP-2 for a twice longer period as compared to the ordinary collageneous hydrogel. A distinctive feature of this new collagen-fibronectin matrix is the slow release of rhBMP-2 in the first three days which allows for the avoiding of adverse effects in clinics caused by the rapid release of large amounts of rhBMP-2 from collageneous hydrogel.

[The choice of the targets and the search for their inhibitors by means of computer simulation for the development of innovative preparations to treat of chronic bacterial infections].

Persistence is a form of interaction of pathogenic bacteria with a host aimed to promote their long-term survivalby means of inactivation of the host's protective systems via modulation of intracellular signal pathways. Persistent forms of a pathogen are refractory to traditional antibiotic therapy and cause chronic infectious diseases. Directed search for protein targets and new antibacterial drugs using computer simulation and experimental testing for the development of innovative preparations to treat chronic bacterial infections appears to have good prospects as a method for the management of persistent infections. A stepwise strategy for realization of such approach is exemplified by the search of preparations against chlamydial infection.

[Secondary structure of SsoII-like (cytosine-5)-DNA methyltransferases N-terminal region determined by circular dichroism spectroscopy].

(Cytosine-5)-DNA methyltransferase SsoII (M.SsoII) has a long N-terminal region (1-71 residues) preceding the sequence with conservative motifs, which are characteristic for all DNA methyltransferases of such kind. The presence of this region provides M.SsoII capability to act as a transcription regulator in SsoII restriction-modification system. To perform its regulatory function, M.SsoII binds specifically to a 15-mer inverted repeat in the promoter region of SsoII restriction-modification system genes. In the present work, properties of the protein delta(72-379)M.Ecl18kI are studied, which is a deletion mutant of the SsoII-like DNA-methyltransferase M.Ecl18kI and is homologous to M.SsoII N-terminal region. delta(72-379)M.Ecl18kI capability to bind specifically a DNA duplex containing the regulatory site is demonstrated. However, such a binding takes place only in the presence of high protein excess relative to DNA, which could indicate an altered structure in the deletion mutant in comparison with the full-length M.SsoII. Circular dichroism spectroscopy demonstrated that delta(72-379)M.Ecl18kI has a strongly pronounced secondary structure and contains 32% a-helices and 20% beta-sheets. Amino acid sequences alignment of M.SsoII N-terminal region and transcription factors of known spatial structure is made. An assumption is made how alpha-helices and beta-sheets are arranged in M.SsoII N-terminal region.

[Development and use of a domestic test system for diagnosis of tuberculous infection on the basis of quantitative analysis of interferon-gamma induction in whole blood samples in vitro, by using specific recombinant antigens].

A test system was developed to detect tuberculous infection by qualitative analysis of interferon-gamma (IFN-gamma) in the plasma samples after 20-24-hour incubation of whole blood samples in the presence of Mycobacterium tuberculosis (MBT) antigens: tuberculin PPD and a mixture of the MBT-specific recombinant antigens ESAT-6 and CFP-10. The analysis used 3 test tubes each containing 1 ml of heparinized venous blood, one of which served as a control; the other two test tubes were employed to measure antigen-induced IFN-gamma production. Whether this test system might be used to determine primary tuberculous infection was studied in 277 children and adolescents. The threshold diagnostic IFN-gamma induction level determined in the test tube containing a mixture of the antigens ESAT-6 and CFP-10 was ascertained. Postvaccine allergy was detectable if there was IFN-gamma induction in the test tube containing tuberculin and if there was no diagnostic IFN-gamma level in that containing the antigens ESAT-6 and CFP-10. The diagnostic sensitivity of detection of primary tuberculous infection was 97.6% with 94.4% specificity, which enabled this condition to be differentiated from postvaccine allergy. The level of antigen-induced IFN-gamma may be lower in relatively disseminated forms of pulmonary tuberculosis.

[Production of the recombinant human bone morphogenetic protein-2 in Escherichia coli and testing of its biological activity in vitro and in vivo].

Bone morphogenetic protein-2 (rhBMP-2) represents the osteoinductive protein factor which plays a dominant role in growth and regeneration of a bone tissue. In clinical practice the bone grafting materials on the basis of rhBMP-2 are widely applied; the Russian analogues of similar materials are not produced. The fragment of the bmp2gene coding for a mature protein was cloned in Escherichia coli. The effective overproducing strain of rhBMP-2 was created on a basis of the E. coli BL21 (DE3). The rhBMP-2 production was about 25% of total cell protein. The biologically active dimeric form of rhBMP-2 was obtained by isolation and purification of protein from inclusion bodies with subsequent refolding. The rhBMP-2 sample with more than 80% of the dimeric form was obtained, which is able to interact with specific antibodies to BMP-2. Biological activity of the received rhBMP-2 samples was shown in the in vitro experiments by induction of alkaline phosphatase synthesis in C2C12 and C3H10T1/2 cell cultures. On model of the ectopic osteogenesis it was shown that received rhBMP-2 possesses biological activity in vivo, causing tissue calcification in the place of an injection. The protein activity in vivo depends on way of protein introduction and characteristics of protein sample: rhBMP-2 may be introduced in an acid or basic buffer solution, with or without the carrier. The offered method of rhBMP-2 isolation and purification results in increasing common protein yield as well as the maintenance of biologically active dimeric form in comparison with the analogues described in the literature.

[Target-directed search of anti-virulence drugs].

Modern medicine now encounters with problem of the absence of effective antibacterial drugs, which are able to render therapeutic effect on chronic form of infectious process. Thus, the actual objective is to develop essentially new generation of drugs, on the basis of which should lie identification of new bacterial targets playing key role in process of chronization of infection as well as selection of new physiologically active substances, which are able to render highly specific inhibitory effect on selected target. Solving of this objective is possible during realization of new approaches for search and design of new drugs and, first of all, during usage of bioinformatics methods, which enable to identify new biotargets, select most effective chemical compounds-inhibitors and optimize their pharmacological and pharmacokinetic properties. The most promising bacterial target is secretion systems of pathogenic microorganisms participating in realization of their virulent characteristics and playing major role in transition of infectious process in chronic phase. We performed synthesis of and screening for 80 compounds, which allowed to select a range of inhibitors rendering specific target-directed effect on type 3 secretion system of Chlamydia. Obtained data allow to further assess of biological and therapeutic activity of these compounds on developed models of infectious process in vivo.

[Isolation and characterization of collagen-binding domains from human von Willebrand factor].

DNA fragments encoding for two collagen binding decapeptides from the human von Willebrand factor (vWF-H1 and vWF-H2) were cloned in the Escherichia coil culture. Overproducing strains of the chimeric proteins vWF(H1)-CBD and vWF(H2)-CBD consisting of the corresponding decapeptide, Gly-Ser spacer and a cellulose binding domain (CBD) from Anaerocellum thermophilum were constructed. Using one-stage purification on cellulose, the highly purified samples of vWF(H1)-CBD and vWF(H2)-CBD proteins were obtained and the ability of these proteins to bind collagen was studied. These constructions are planned to be used for development of the recombinant collagen binding proteins with different biological activities, which, in its turn, will be used for development of the new generation products and materials for medicine, such as different kinds of implants, the coats, etc.

[Effector proteins of Clamidia].

The review summarizes the recent published data on molecular mechanisms of Chlamidiae - host cell interaction, first of all on chlamydial effector proteins. Such proteins as well as III transport system proteins that transfer many effector proteins into host cytoplasm are attractive targets for drug therapy of chlamydial infections. The majority of the data concerns two species, Chlamydia trachomatis and Chlamydophila pneumoniae. C. trachomatis protein TARP, which is presynthesized in elementary bodies, plays an essential role in the initial stages of the infection. Patogen proteins participating in the next stage, that is the intracellular inclusion traffic to the centrosome, are CT229 of C. trachomatis and Cpn0585 of C. pneumoniae, which interact with cellular Rab GTPases. In C. trachomatis, IncA protein plays a key role in chlamydial inclusions fusion, CT847 modulates life cycle of the host cell, LDA3 is essential in acquisition of nutrients. CPAF protease and inclusion membrane proteins IncG and CADD participate in suppression of apoptosis of infected cells. The proteases CPAF and CT441, as well as deubiquitinating ChlaDub1 protein, contribute to avoiding the immune response.

[Some practical notes about performing polymerase chain reaction and electrophoretic fractionation of amplificated products].

Practical aspects concerning standardization of molecular-genetic expertise performing with the use of the method of DNA are considered. Examples of difficulties, which can occur at nonobservance of requirements of polymerase chain reaction and electrophoresis performing, are described; practical recommendations of their elimination are given.

[Mechanism of interaction of tumor necrosis factor (TNF-alpha) of macroorganism with the Salmonella enterica cells (ser. Typhimurium)].

The goal of this work was to elucidate the mechanism of direct interaction of bacterial cells with tumor necrosis factor (TNF-alpha; cytokine). It was shown earlier that this interaction facilitated activation of bacterial growth and recultivation of non-cultivated forms in vitro and in vivo. It was shown in experiments with mice deficient in the genes encoding eucaryotic TNF-alpha receptors and infected with salmonella that addition of exogenous TNF-alpha to suspension of infection cells caused a one-day acceleration in the infection start (bacteria planting from spleen) in both knockouted and control mice relative to the same animals infected with the same bacteria without cytokine. Thus, bacteria are able to interact with cytokine even in the absence of eucaryotic receptors. Specificity of the bacterium-cytokine interaction and bacterial protein EF-Tu mediating direct interaction of bacteria with cytokine were identified using the method of immobilization of recombinant protein TNF-alpha-spacer-CSD on cellulose.

[Immunization with cellulose-immobilized antigens. The development of A. E. Gurvitch concept].

A highly purified TUL4-CBD chimeric protein was obtained by one stage purification method. TUL4-CBD protein consists of TUL4 Francisella tularensis mature peptide sequence, Gly-Ser spacer and cellulose binding domain (CBD) of Anaerocellum thermophilum. The TUL4-CBD protein was shown to induce production of specific antibodies to TUL4 protein in laboratory animals.

[The need of regulation of production of components for forensic-medical molecular-genetic technologies and improvement of legal basis of forensic-medical molecular-genetic expert examinations in the Russian Federation].

Of late, Ministry of Health of Russian Federation has developed instructions concerning forensic-medical molecular genetic methods of analysis promoting creation of standardized forensic-medical genetic service. However, some legal uncertainty exists in respect to design and production of the materials for forensic-medical molecular-genetic technologies, unification and standardization of molecular-genetic kits and methods. It is thought necessary to regulate legally forensic medical molecular-genetic technologies from foreign countries and production and use of domestic components for forensic medical molecular-genetic expert examinations.

DNA-methyltransferase SsoII as a bifunctional protein: features of the interaction with the promoter region of SsoII restriction-modification genes.

DNA duplexes bearing an aldehyde group at the 2'-position of the sugar moiety were used for affinity modification of (cytosine-5)-DNA methyltransferase SsoII. It is shown that lysine residues of M.SsoII N-terminal region are located in proximity to DNA sugar-phosphate backbone of a regulatory sequence of promoter region of SsoII restriction-modification enzyme coding genes. The ability of the two M.SsoII subunits to interact with DNA regulatory sequence has been demonstrated by affinity modification using DNA duplexes with two 2'-aldehyde groups. Changes in nucleotide sequence of one half of the regulatory region prevented cross-linking of the second M.SsoII subunit. The results on sequential affinity modification of M.SsoII by two types of modified DNA ligands (i.e. by 2'-aldehyde-containing and phosphoryldisulfide-containing) have demonstrated the possibility of covalent attachment of the protein to two different DNA recognition sites: regulatory sequence and methylation site.

[Possible unfavourable effects of using in-house components for forensic expert molecular-genetic technologies].

So-called in-house production of reagents, components and kits for DNA analysis which are made without strict quality control and standards are now widely practiced in forensic molecular-genetic examinations. Markers of molecular mass were studied to illustrate problems which may arise in use of such in-house components. Other difficulties and negative sequelae of in-house products are also demonstrated.

[Genomics and gene engineering: rationale to the development of new means of tuberculosis control]. / Genomika i gennaia inzheneriia: ratsional'nye podkhody dlia razrabotki novykh sredstv bor'by s tuberkulezom.

The review contains information on modern approaches to the development of antituberculosis vaccines and remedies. Data on the comparative effectiveness of different subunit and DNA vaccines against tuberculosis are presented. The use of comparative and structural genomics for the search and characterization of new Mycobacterium tuberculosis genes, whose products may prove to be important antigens for the development of vaccines or target proteins for remedies against tuberculosis, is considered.

[Covalent binding of Cys142 from SsoII methyltransferase with DNA duplexes, containing a phosphoryldisulfide internucleotide group]. / Kovalentnoe sviazyvanie Cys142 metiltransferazy SsoII s DNK-dupleksami, soderzhashchimi fosforildisulfidnuiu mezhnukleotidnuiu grupppu.

DNA duplexes containing a single phosphoryldisulfide link in place of the natural internucleotide phosphodiester bond were employed in affinity modification of Cys142 in cytosine-C5 DNA methyltransferase SsoII (M.SsoII). The possibility of duplex-M.SsoII conjugation as a result of disulfide exchange was demonstrated. The crosslinking efficiency proved to depend on the DNA primary structure, modification position, and the presence of S-adenosyl-L-homocysteine, a nonreactive analog of the methylation cofactor. The SH group of M.SsoII Cys142 was assumed to be close to the DNA sugar-phosphate backbone in the DNA-enzyme complex.

[An analysis of methyltransferase SsoII-DNA contacts in the enzyme-substrate complex]. / Analiz kontaktov metiltransferazy SsoII s DNK v ferment-substratnom komplekse.

The functional groups of the DNA methylation site that are involved in the DNA interaction with methyltransferase SsoII at the recognition stage were identified. The contacts in the enzyme-substrate complex were analyzed in the presence of S-adenosyl-L-homocysteine using the interference footprinting assay with formic acid, hydrazine, dimethyl sulfate, or N-ethyl-N-nitrosourea as a modifying reagent. It was shown that the replacement of the central A.T by the G.C pair in the methylation site did not affect the enzyme-DNA interaction, whereas the use of a substrate with one chain methylated (monomethylated substrate) instead of the unmethylated substrate dramatically changes the DNA contacts. The binding constants of unmethylated and monomethylated substrates with methyltransferase SsoII in the presence of S-adenosyl-L-homocysteine were calculated.

[Structural aspects of homeodomain interactions with DNA]. / Strukturnye aspekty vzaimodeistviia gomeodomenov s DNK.

This review is devoted to the structural aspects of interaction of homeodomains with DNA. Presented are the list of all homeodomains with known spatial structure and the alignment of their amino acid sequences. The structure of homeodomains and contacts of their amino acid residues with DNA bases and sugar-phosphate backbone are described. The role of water molecules in DNA binding is discussed. Structures of multicomponent protein complexes on DNA including homeodomains are characterized.

[Theoretical approaches for evaluation of DNA-protein interactions]. / Teoreticheskie podkhody k otsenke spetsificheskogo DNK-belkovogo vzaimodeistviia.

The notion of the DNA-recognizing segment of a protein for three-dimensional structures of DNA-protein complexes was formalized. Algorithms for calculating two parameters, hydrogen bonds and hydrophobic contacts, that characterize the interaction of the DNA-recognizing segment of the protein with the groove DNA major were proposed. DNA-recognizing protein segments in three-dimensional structures (of complexes) were classified according to these two parameters. These data were compared with the classification of the corresponding DNA-recognizing domains according to structure. The contribution of each pair amino acid residue-base to the interaction of protein with the DNA major groove was calculated.