Search

The molecular docking method was used to study the structural characteristics determining the competitive transport in the blood, and also the subsequent binding with enzymes of tocopherols and their metabolites to yield a specific biological activity. The target proteins were α-tocopherol-transport protein (α-TTP), tocopherol-associated protein 1 (TAP1), cyclooxygenase-2 (COX-2), protein phosphatase 2A (PP2A) and 3-hydroxy- 3-methylglutaryl-Coenzyme A (HMG-CoA) reductase. RRR-tocopherol (α-, β-, γ- and δ-forms), RRR-13'-carboxychromanol (α-, β-, γ- and δ-forms) and carboxyethyl hydroxychromanol (α-, β-, γ- and δ-forms) were used as ligands in this research. The conducted studies confirmed that among all homologues the α-tocopherol had the greatest affinity for the transport proteins α-TTP and TAP1 (ΔG=-11.40 and ΔG=-10.28 kcal/mol, respectively). It was shown that in all cases carboxyethyl hydroxychromanol metabolites had the greatest free binding energy (ΔG>-8 kcal/mol), that was why it has been concluded that they were not effective ligands for the proteins under study. In contrast, the metabolites of 13'-carboxychromanol, when bound to both α-TTP and TAP1 proteins, preferentially formed more stable complexes than their precursors. It was shown for the first time that γ-13'-carboxychromanol with TAP1 has less free binding energy (ΔG=-10.64 kcal/mol) in comparison to the α-tocopherol complex (ΔG=-10.28 kcal/mol). It has also been shown that 13'-carboxychromanole metabolites were more efficiently bound to COX-2 enzymes (ΔG=-9.56 kcal/mol for α-13'-carboxychromanol complex) and HMG-CoA reductase (ΔG=-9.46 kcal/mol for the complex with δ-13'-carboxychromanol). In relation to the PP2A protein, 13'-carboxychromanol metabolites had similar affinities as their precursors. The results of the work indicate the possibility of 13'-carboxychromanols to competitively bind to α-tocopherol transporters and act as effective ligands of COX-2 and HMG-CoA, that can be used to correct nutritional status in conditions accompanied by deficiency of tocopherols., Competing Interests: The authors declare no overt and potential conflict of interest related to the publication of this article., (Copyright© GEOTAR-Media Publishing Group.)

With the method of molecular dynamics, pairs of amino acid residues have been identified on the surface of the interacting formin mDial domains: DID-DAD, which are responsible for the autoinhibition of formin, and the GTPase Rho-DID domain, and control activation. It was found that the most stable interactions are ionic interactions between Glu178 residue and Arg248 residue, as well as hydrophobic interactions between Thr175 and Phe247. The strongest interactions proved to be between the DID domain with Rho-GTPase. These interactions are mediated by specific triple ionic interactions between positively charged amino acid in Rho, and a triplet of amino acids in DID, consisting of two negatively charged amino acids, separated by one uncharged. Binding sites for Rho-GTPase and DAD partially overlap, but various amino acids on the DID participate in interactions with different domains. We discuss the possible conformational changes in formin domains during activation and inactivation.

The genome of Melioribacter roseus, one of two members of the recently described phylum Ignavibacteriae, was searched for the genes encoding proteins associated with copper transport or containing copper as cofactors, and the effect of Cu2+ concentration in the medium on M. roseus growth was investigated. Genomic analysis revealed a variety of copper-containing oxidoreductases in this facultative anaerobe. Three ATPases responsible for copper transport were identified. One of them (MROS_1511) was.probably involved in assembly of the copper-containing cytochrome c oxidase, while two others (MROS_0327 and MROS_0791) probably carried out a detoxification function. The presence of several copper-containing oxidoreductases and copper homeostasis systems in M. roseus is in agreement with the previously hypothesized origin of the phylum Ignavibacteriae from an aerobic ancestor common with those of Bacteroidetes and Chlorobi.

Evolutionary conserved TIP49a and TIP49b ATPases belong to the AAA+ superfamily of DNA-dependent ATPases that are involved in many cellular processes such as chromatin remodeling, regulation of transcription and cell division during mitosis, the maintenance of genome stability, snoRNP biogenesis, and participate in the formation of active form of telomerase. These proteins are involved in the complex networks of protein-protein interactions and, in spite of high structural similarity, in some cases, can perform opposite functions. Despite of the variety of their different activities, the exact mechanisms of action of TIP49a and TIP49b are still poorly understood. In this paper, by means of molecular docking approaches we first modeled the structures of hetero-hexameric TIP49 complexes with short ds-DNA fragments (20 base pairs with different GC content) within the central channel of hexameric ring. Using molecular dynamics simulations in the periodic water box (MD) we investigated conformational dynamics and mechanisms of DNA unwinding activity of these proteins. We shown that: a) the interaction between the positively charged protein loops and DNA within the central channel of protein ring leads to the partial unwinding of the DNA helix; b) DNA unwinding occurs only in the region within the protein ring, while the terminal parts of DNA outside the protein complex remain in its initial b-form conformation; c) the presence of ATP in the active sites of protein complex affects both the dynamics and the structure of DNA, leading to the breakage of some complementary bonds in AT-rich DNA sequences.

The review summarizes the current data about the hepatitis C viral genome and polyprotein organization. The functional role of the structural and non-structural viral proteins including their interaction with cellular regulatory proteins and cell structural elements is discussed. Specific peculiarities of the life cycle of the hepatitis C virus important for the understanding of the viral hepatitis C pathogenesis are summarized.

The goal of the study was to identify amino acid replacements in the structure of penicillin-binding protein PBP2, which may influence on the development of resistance N. gonorhoeae to the III cephalosporins generation. The gene penA of 50 strains of N. gonorrhoeae was sequenced: 20 strains with high sensitivity to ceftriaxone (MIC, Minimum Inhibitory Concentration, = 0.002 mg/L) and 30 strains with decreased sensitivity to ceftriaxone (MIC = 0.03-0.25 mg/L). The difference of MIC sensitivity between these strains was 30-250 times. Then nucleotide sequence was transformed into the amino acid sequence of PBP2 protein. Mutations in the gene penA and amino acid replacements in the protein PBP2 were found in 16 of 20 strains (80%) with high sensitivity to ceftriaxone and in all strains with decreased sensitivity to ceftriaxone. Amino acid replacements in the PBP2 protein were compared with amino acid replacements in groups, which characterize the PBP2 structure in accordance with the international classification Ito M. The amino acid replacement of PBP2 at positions 346, 505, 511, 517, 543, 567, 575, 576 are associated with V group by Ito M and have features of resistance of N. gonorrhoeae to ceftriaxone authentically (OR = 3.9 ± 2.5; χ2 = 4.9; p < 0.05). It was shown that the replacement of glycine to serine at position 543 of PBP2 in the analyzed strains induced the multiple increase of resistance to ceftriaxone. These data may be significant as showing strong influence of amino acid replacements at positions 346, 505, 511, 517, 567, 575 and, in particular, 543 for development of resistance N. gonorrhoeae strains to ceftriaxone.

The review presents both our and literature data of results of studies of pathways of evolution of the so-called multinuclear blue copper-proteins (MBCP) that have the domain organization. The MBCP are widely spread in living nature, they have been revealed in cells of archais, bacteria, and eukaryotes. Included in the MBCP composition are such different by their functions copper-proteins as oxidases, reductase, blood coagulation factors V and VIII. Most likely, MBCP have been originated from the low-molecular protein-precursor similar topologically with blue electron-transporting protein of the type of cupredoxin, as a result of action of various evolutionary mechanisms: amplification of genes, formation of protein structures by different combinations of domains, a change of size of domains, the segment elongation at the expense of the activational domain, formation and loss of various copper-binding centres, variation of amino acid ligands in such centres, the appearance of centres of binding of other proteins, glycosylation, etc.

Review is devoted to the challenging direction in modem molecular biology and bioengineering - the properties of alternative scaffold proteins (ASP) and methods for obtaining ASP binding molecules. ASP molecules incorporate conservative protein core and hypervariable regions, providing for the binding function. Structural classification of ASP includes several types which differ also in their molecular targets and potential applications. Construction of artificial binding proteins on the ASP basis implies a combinatorial library design with subsequent selection of specific binders with the use of phage display or the modem cell-free systems. Alternative binding proteins on non-immunoglobulin scaffolds find broad applications in different fields ofbiotechnology and molecular medicine.

A novel lipid transfer protein called Ec-LTP was isolated from resting caryopsis of weed barnyard grass Echinochloa crusgalli (L.) Beauv.; its molecular weight, amino acid content and N-terminal amino acid sequence were determined. Ec-LTP was a 9150 Da protein, containing eight cysteine residues, which formed four disulfide bonds. The isolated protein could significantly inhibit the development of pathogenic fungi Phytophthora infestans and Helminthosporium sativum, causing the late blight of potato and tomato and the root rot of herbs, respectively.

A novel lipid-transporting protein (Ns-LTP1) has been isolated from seeds of the garden fennel flower Nigella sativa. The molecular mass, N-terminal amino acid sequence, and amino acid composition of the protein have been determined. Ns-LTP1 has a molecular mass of 9602 Da and contains eight cysteine residues which form four disulfide bridges. The protein is capable of suppressing the development of some phytopathogenic fungi and oomycetes.

Lactoferrin (LF), the glycoprotein transferring Fe+ ions, is contained in barrier liquids, human blood and milk. LF is an acute phase protein and one of the most important factors of nonspecific defense. The protein has unique set of biological functions. Using the methods of small-angle X-ray scattering and light-scattering it was shown for the first time that addition of DNA and oligosaccharides to LF with different level of initial oligomerization leads to an enhance in the oligomerization rate. 1M NaCl stimulates almost a complete dissociation of LF oligomeric complexes obtained in the pesence of DNA, oligosaccharides, or early founded oligomerization effectors (nucleotides). It was shown that LF oligomeric complexes obtained in the presence of different oligomerization effectors have different stability. Incubation with 50 mM MgCl2 leads to complete destruction of the protein complexes formed by ATP and oligosaccharide but partially dissociate the complexes with following formation of new in the case of AMP- and d(pT)10-dependent associates, which possess higher stability i n presence of the salt. A possible role of LF oligomerization for different biological functions of the protein is discussed.

The results of the intraspecific typing of group A streptococci (SGA), isolated from patients with different manifestations of group A streptococcal infection, carried out in Russia for the first time, are presented. The genotypic method of emm-typing, based on sequencing the DNA area coding the variable part of the molecule of SGA M-protein was used. The data obtained in this study made it possible to follow changes in the pattern of SGA M-types in Moscow and the specific features of SGA in comparison with the analogous data on other territories. New emm-types of SGA circulating on the territory of Russia were detected and described.

Sequencing of fragments of genes coding for silicic acid transport (SIT) proteins of diatoms of evolutionary distant classes (centric Chaetoceros muelleri Lemmermann, pennate araphid Synedra acus Kützing, pennate raphid Phaeodactylum tricornutum Bohlin, and pennate with keeled raphe system Cylindrotheca fusiformis Reimann et Lewin), revealed the presence in these proteins of a conservative amino acid motif CMLD. Hydropathy profiles suggest that CMLD occupies a position between two transmembrane strands which do not contain lysine and arginine residues. The two strands are good candidates for the role of the channel along which transport of silicic acid occurs. CMLD is a rare motif. Diatoms are known to need Zn2+ for the incorporation of silica. Presumably, CMLD is the site of Zn2+ binding of SITs. We found that the growth of diatoms is inhibited by a negatively charged alkylating reagent 5-(2-iodoacetamidoethyl)aminonaphtalene-1-sulfonic acid which cannot penetrate through the cell membrane. Cysteine of CMLD can be a target of this reagent. Synthetic peptide NCMLDY forms a complex with Zn2+, as revealed by the fact that the ion considerably reduces the rate of alkylation of the peptide.

Changes in the molecular weight and functional properties of the C and X proteins from skeletal muscles and the C protein from the cardiac muscle of hibernating ground squirrels Citellus undulatus at different stages of the hibernation were studied. A decrease in the molecular weight of the C protein from fast fibers of skeletal muscles of hibernating ground squirrels compared with awakening and active animals was revealed. The appearance of shorter molecules of the C protein upon hibernation was accompanied by a lowering of its capacity to enhance the actin-activated ATPase activity of control myosin and by the inhibition of its Ca(2+)-sensitivity. No similar changes were observed for the skeletal X protein and the cardiac C protein. The influence of the skeletal C protein on the main functional properties of myosin allows one to draw a conclusion about its contribution to the inhibition of contractile activity of skeletal muscles upon hibernation. The physiological significance of the changes in the C protein upon hibernation is discussed in connection with similar changes in some cardiomyopathies.

We report here the cloning of human cDNA of Aup1 gene (ancient uniquitous protein 1), its genomic organization and preliminary characterization of human AUP1 protein. Genomic length of the human Aup1 gene is composed of 12 exons and 11 introns spanning 3047 bp. A single open reading frame of 1230 bp starts with the first ATG from nucleotide 5630 of the genomic sequence, in accordance with the Kazak rule, and stops with TGA on nucleotide 8500 of the genomic sequence AC005041.2. The 3 noncoding region has a 152 bp length followed by poly(A)tail. All exon-intron junctions conform to 5' donor and 3' acceptor consensus. Exon and intron sizes range from 69 to 187 bp, and from 180 to 262 bp, resp. We have cloned a full-length human Aup1 cDNA. For preliminary characterization of human AUP1 protein, we cloned the full-length human Aup1 cDNA in pcDNA3 vector. In vitro transcription/translation of the cloned cDNA yielded a 45 kDa protein. Human Aup1 coding region demonstrates 90% homology to its rat and mouse homologous at the nucleotide level, and 82% at the amine acid level.

The 11-kDa product of adenovirus early region 4 (E4) open reading frame (ORF) 3 participates in many processes occurring in infected cell, including post-transcriptional steps in late viral gene expression and viral DNA synthesis. In addition, E4ORF3 from adenovirus type 5 (Ad5) displays the features of a viral oncoprotein. It initiates focal transformation of primary rat cells in cooperation with Ad5 El genes and confers multiple additional transformed properties on E1-expressing cells. Biochemical details of E4ORF3 activities in these processes are not well understood. A large body of evidence indicates that its lytic and transforming functions are mediated by physical interactions with viral and cellular components involved in DNA transcription and repair, as well as by host cell factors that regulate the integrity of nuclear multiprotein complexes known as PML oncogenic domains (PODs). In this study we have employed the two-hybrid screen in yeast to isolate human cDNAs encoding for E4ORF3-interacting proteins. Among 15 positive clones five cDNAs encode for a cellular protein called AUP1. In vitro-binding assays demonstrated that AUP1 fused to glutathione S-transferase (GST) specifically binds to E4ORF3 from Ad5, Ad9 and Ad40 generated in a coupled transcription-translation system, whereas no interactions was observed with ORF3 from Ad12. Interestingly, GST-AUP1 interacted also specifically with in vitro translated Ad5 E1A proteins. Regions involved in the Ad5 E4ORF3/AUP1 interaction in vitro map to the central part of E4 protein and the carboxy-terminal region of AUP1, while E1A binds to an amino-terminal segment of the cell protein. Taken together, these studies indicate that AUP1 may represent a cellular target of both adenovirus E4ORF3 and E1A proteins. Additional studies are currently under way to confirm the significance of these interactions in living cells in vivo.

Reductive cleavage of the riboflavin-binding glycoprotein from hen egg white with LiBH4/tert-BuOH followed by NaBH4 treatment gave rise to oligosaccharide alditols. After fractionation by HPLC two individual oligosaccharide alditols of a hybrid type were isolated. Their structures were proved by 1H NMR 500 MHz spectroscopy and methylation analysis. One of the oligosaccharides has earlier been found in ovalbumin, whereas the other is identified in glycoproteins for the first time.

cAMP-binding protein was isolated from the plaque agent and purified to the homogeneous state. Purification process included filtration of the initial preparation through the membrane able to transmit particles with mol. weight to 300,000 Da, chromatography on cellulose "DE-52" and biogel HTP. The protein homogeneity was confirmed by electrophoresis in polyacrylamide gel and precipitation with commercial plague agglutinating serum. The protein with mol. weight of 180,000 Da consisted of two identical subunits (90,000 Da. each) which could dissociate with formation of monomers (mol. weight approximately 18,000 Da), Cu2+, Co2+, Mn2+ ions stimulated activity of cAMP-binding protein of a plague microbe while Fe3+, Ca2+, Zn2+ ions inhibited it by 30-70%. A monospecific rabbit serum to the homogeneous preparation of cAMP-binding protein was obtained. It helped finding the similar protein in the close relative bacterium Yersinia pseudotuberculosis but not in Y. enterocolitica.

Using LiBH4/ButOH treatment, oligosaccharides were cleaved off the hen egg white riboflavin-binding glycoprotein. HPLC led to the isolation of four fucose-containing oligosaccharide alditols, whose structure was elucidated by means of 1H NMR 500 MHz spectroscopy. The main fucosylated oligosaccharide, also present in hen ovomucoid, was found to be a biantennary carbohydrate chain of N-acetyllactosamine type.