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71.
Tat'yana A. Guschina Svetlana E. Soboleva Georgy A. Nevinsky 《Journal of molecular recognition : JMR》2013,26(3):136-148
The general principles of recognition of nucleic acids by proteins are among the most exciting problems of molecular biology. Human lactoferrin (LF) is a remarkable protein possessing many independent biological functions, including interaction with DNA. In human milk, LF is a major DNase featuring two DNA‐binding sites with different affinities for DNA. The mechanism of DNA recognition by LF was studied here for the first time. Electrophoretic mobility shift assay and fluorescence measurements were used to probe for interactions of the high‐affinity DNA‐binding site of LF with a series of model‐specific and nonspecific DNA ligands, and the structural determinants of DNA recognition by LF were characterized quantitatively. The minimal ligands for this binding site were orthophosphate (Ki = 5 mM), deoxyribose 5'‐phosphate (Ki = 3 mM), and different dNMPs (Ki = 0.56–1.6 mM). LF interacted additionally with 9–12 nucleotides or nucleotide pairs of single‐ and double‐stranded ribo‐ and deoxyribooligonucleotides of different lengths and sequences, mainly through weak additive contacts with internucleoside phosphate groups. Such nonspecific interactions of LF with noncognate single‐ and double‐stranded d(pN)10 provided ~6 to ~7.5 orders of magnitude of the enzyme affinity for any DNA. This corresponds to the Gibbs free energy of binding (ΔG0) of ?8.5 to ?10.0 kcal/mol. Formation of specific contacts between the LF and its cognate DNA results in an increase of the DNA affinity for the enzyme by approximately 1 order of magnitude (Kd = 10 nM; ΔG0 ≈ ?11.1 kcal/mol). A general function for the LF affinity for nonspecific d(pN)n of different sequences and lengths was obtained, giving the Kd values comparable with the experimentally measured ones. A thermodynamic model was constructed to describe the interactions of LF with DNA. Copyright © 2013 John Wiley & Sons, Ltd. 相似文献
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74.
N. L. Starodubtseva V. V. Sobolev A. G. Soboleva A. A. Nikolaev S. A. Bruskin 《Russian Journal of Genetics》2011,47(9):1117-1123
Using real-time polymerase chain reaction (RT-PCR), we measured mRNA amounts of matrix metalloproteinases (MMPs): MMP-1, MMP-2, MMP-9, and MMP-12 genes in psoriatic lesions and unaffected skin of the same patients. We observed significant (about 15-fold) increase in
the expression level of matrix metalloproteinase MMP-1 and MMP-12 genes associated with psoriasis. The results of our studies of MMP gene expression in cultured primary human keratinocytes treated with interleukin (IL)-17 have shown upregulation of MMP gene expression both in cultured keratinocytes and in psoriatic skin lesions. Therefore, upregulation of MMP genes in the skin affected by psoriasis could result from IL-17 effects on skin cells. 相似文献
75.
Alexander G. Nevinskii Svetlana E. Soboleva Fedor V. Tuzikov Valentina N. Buneva Georgy A. Nevinsky 《Journal of molecular recognition : JMR》2009,22(4):330-342
Using small‐angle X‐ray scattering (SAXS), light scattering (LS), and soft laser ablation we have shown that lactoferrin (LF) in solution at neutral pH is oligomerized in the absence of salt or at physiological salt concentrations. The level of oligomerization depends on the concentration of LF, KCl or NaCl, and on the duration of the protein storage in solution. At the concentrations comparable with those in human milk (1 ÷ 6 mg/ml), the average radius of gyration (Rg) values of LF can attain 400 ÷ 480 Å´, while fresh solution of previously lyophylized LF demonstrate a lower average Rg (50 ÷ 100 Å´), and Rg value characterizing the LF monomer formed at 1 M NaCl is 26.7 Å´. The addition of oligonucleotides, oligosaccharides, or mononucleotides to LF in the presence or in the absence of KCl with different level of initial oligomerization accelerates the oligomerization rate and increases the Rg values up to ~600 ÷ 700 Å´, which correspond to associates containing ten or more protein molecules. During gel filtration on Sepharose 4B, high‐degree LF oligomers dissociate nearly completely forming different degraded complexes, but in some cases it is possible to reveal small amount of a decamer. A possible role for oligomerization of LF, a highly polyfunctional protein, for its different biological activities is discussed. Copyright © 2009 John Wiley & Sons, Ltd. 相似文献
76.
Soboleva A. V. Krasnoshtanova A. A. Krylov I. A. 《Applied Biochemistry and Microbiology》2004,40(3):236-240
The kinetics of the conversion of the sulfur-containing amino acids L-cystine and L-cysteine to taurin by the enzyme system of cattle liver cells was studied and a mathematical model was developed. It was shown that the conversions of L-cystine and L-cysteine obeyed the Michaelis–Menten equations of serial–sequential conversions with regard to inhibition by the final product and inactivation. The yield of taurin under the optimized conditions of L-cystine and L-cysteine conversion (temperature, 40°C; pH 1.5 and 3.0, respectively; and the addition of enzyme preparations in five equal portions at 2-h intervals) was in the range of 80–85% of the substrate weight. 相似文献
77.
Golub V. B. Syromyatnikov M. Yu. Kokina A. V. Soboleva V. A. Nesterova E. V. Popov V. N. 《Entomological Review》2020,100(6):827-836
Entomological Review - The paper presents an improved key to the co-occurring species of Polymerus Hahn, 1831 (Heteroptera, Miridae) based on morphological characters and our new data on the... 相似文献
78.
Van Wey AS Cookson AL Soboleva TK Roy NC McNabb WC Bridier A Briandet R Shorten PR 《Biotechnology and bioengineering》2012,109(5):1280-1292
The ability for a biofilm to grow and function is critically dependent on the nutrient availability, and this in turn is dependent on the structure of the biofilm. This relationship is therefore an important factor influencing biofilm maturation. Nutrient transport in bacterial biofilms is complex; however, mathematical models that describe the transport of particles within biofilms have made three simplifying assumptions: the effective diffusion coefficient (EDC) is constant, the EDC is that of water, and/or the EDC is isotropic. Using a Monte Carlo simulation, we determined the EDC, both parallel to and perpendicular to the substratum, within 131 real, single species, three-dimensional biofilms that were constructed from confocal laser scanning microscopy images. Our study showed that diffusion within bacterial biofilms was anisotropic and depth dependent. The heterogeneous distribution of bacteria varied between and within species, reducing the rate of diffusion of particles via steric hindrance. In biofilms with low porosity, the EDCs for nutrient transport perpendicular to the substratum were significantly lower than the EDCs for nutrient transport parallel to the substratum. Here, we propose a reaction-diffusion model to describe the nutrient concentration within a bacterial biofilm that accounts for the depth dependence of the EDC. 相似文献
79.
A. L. Konevega N. G. Soboleva V. I. Makhno A. V. Peshekhonov V. I. Katunin 《Molecular Biology》2006,40(4):597-610
The modified nucleotide 3′ of the tRNA anticodon is an important structural element that regulates the codon-anticodon interaction in the ribosome by stacking with codon-anticodon bases. The presence and identity (pyrimidine, purine, or modified purine) of this nucleotide significantly affects the energy of stacking in the A and P sites of the ribosome. Modification of nucleotide 37 does not contribute to stacking in the A site of the 70S ribosome, while its effect is substantial in the P site. The enthalpies of tRNA interactions with the A and P sites in the ribosome are similar and considerably lower than the enthalpy of the interactions of two tRNAs with the cognate anticodons in solution, suggesting that the ribosome contributes to the enthalpy-related portion of the free energy of tRNA binding by directly forming additional interactions with tRNA or by indirectly stabilizing the conformation of the codon-anticodon complex. In addition to stacking, tRNA binding in the A and P sites is further stabilized by interactions that involve magnesium ions. The number of ions involved in the formation of the tRNA-ribosome complex depends on the identity of tRNA nucleotide 37. 相似文献
80.
Sharapova NE Kotnova AP Galushkina ZM Lavrova NV Poletaeva NN Tukhvatulin AE Tukhvatullin AE Semikhin AS Gromov AV Soboleva LA Ershova AS Zaĭtsev VV Sergienko OV Lunin VG Kariagina AS 《Molekuliarnaia biologiia》2010,44(6):1036-1044
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. 相似文献