Vassily E Stefanov

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A model for topological coding of proteins is proposed. The model is based on the capacity of hydrogen bonds (property of connectivity) to fix conformations of protein molecules. The protein chain is modeled by an n -arc graph with the following elements: vertices (alpha -carbon atoms), structural edges (peptide bonds) and connectivity edges (virtual edges(More)
Nitric oxide (II) diffusion through a model two-component (phosphatidylcholine and phosphatidylethanolamine molecules) biological membrane is investigated using the molecular dynamics method. It is shown that NO molecules are rotating in the process of diffusion into the phospholipid bilayer. The calculated diffusion coefficient D[NO] = 0.35 (±0.23) × 10−5(More)
MD DFT:B3LYP (6-31G** basis set, T = 310 K) method is used to study interactions [singlet (S) and triplet (T) reaction paths] between adenosinetriphosphate, ATP4−, and [Mg(H2O)6]2+ in water environment, modeled with 78 water molecules. Computations reveal the appearance of low and high-energy states (stable, quasi-stable, and unstable), assigned to(More)
38 One of debatable questions of enzymology is the question of the physical nature of the unique ability of magnesium cation to initiate polymerization reactions involving nucleosides (NTPs). Recently, a fast (com pared to hydrolytic) ion radical mechanism of NTP decomposition has been discovered theoretically and then indirectly confirmed in experiments(More)
Protein-ligand docking and molecular dynamics studies have shown that the key event initiated by 3′:5′-AMP binding to the A- and B-domains of protein kinase A Iα regulatory subunit is formation of a hydrogen bond between 3′:5′-AMP and A202(A326) (the residue in parentheses being from the B-domain). The A202(A326) amide group movement associated with the(More)
The review presents both our own and literature data on 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 archei, bacteria, and eukaryotes. The MBCP composition includes the copper-proteins such(More)
We have performed a comparative molecular dynamics simulation of the diffusion process of the heterocyclic compound pyrazine and its methylated derivatives into the model membrane phospholipid bilayer. Several structural and dynamical bilayer parameters were measured, and qualitative interrelations between parameter changes and the substituted pyrazine(More)
The goal of the work was to perform by the method of molecular dynamics a comparative analysis of conformational mobility of evolutionary related peptides—insulin, proinsulin, IGF1, and IGF2. The proinsulin molecule has been shown to have the highest mobility, whereas IGF1—the lowest. Rotation radius (Rg) of insulin, IGF1, and IGF2 changes insignificantly,(More)
Activity of many enzymes is directly determined by nonprotein compounds or cofactors [1]. Metal cations (particularly Mg 2+ ) are common inorganic cofactors. The list of magnesium-dependent enzymatic reactions is extraordinarily long [2]. For example, magnesium cations have been shown to initiate hydrolysis of ATP and GTP. The energy released in these(More)