Tatiana Vasilevskaya

  • Citations Per Year
Learn More
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)
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)
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)
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)
Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly(More)
In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1-matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as(More)
  • 1