Tatiana Vasilevskaya

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In order to elucidate effects of 24-epibrassinolide (EB) on the efficiency of in vitro regeneration of highbush blueberry (Vaccinium corymbosum L., cv. Brigitta blue), we analyzed variability of seven bioproductive parameters in regenerant plants cultured on nutrient media differing in hormonal composition. The additive action of EB, cytokinin (2iP), and(More)
The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase-2 (MMP-2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all-atom three-dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide(More)
We address methodological issues in quantum mechanics/molecular mechanics (QM/MM) calculations on a zinc-dependent enzyme. We focus on the first stage of peptide bond cleavage by matrix metalloproteinase-2 (MMP-2), that is, the nucleophilic attack of the zinc-coordinating water molecule on the carbonyl carbon atom of the scissile fragment of the substrate.(More)
Quantum mechanics/molecular mechanics (QM/MM) simulations of reactions in solutions and in solvated enzymes can be performed using the QM/MM-Ewald approach with periodic boundary conditions (PBC) or a nonperiodic treatment with a finite solvent shell (droplet model). To avoid the changes in QM codes that are required in standard QM/MM-Ewald implementations,(More)
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