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Your search keyword '"Dmitry D. Lykoshin"' showing total 4 results
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4 results on '"Dmitry D. Lykoshin"'

1. Heparin-Induced Changes of Vascular Endothelial Growth Factor (VEGF165) Structure

Author

Ekaterina L. Nemashkalova, Marina P. Shevelyova, Andrey V. Machulin, Dmitry D. Lykoshin, Roman S. Esipov, and Evgenia I. Deryusheva

Subjects
vascular endothelial growth factor, heparin, protein aggregation, differential scanning calorimetry, Microbiology, QR1-502
Abstract

Vascular endothelial growth factor-A (VEGF-A), a secreted homodimeric glycoprotein, is a critical regulator of angiogenesis in normal and pathological states. The binding of heparin (HE) to VEGF165 (the major form of VEGF-A) modulates the angiogenesis-related cascade, but the mechanism of the observed changes at the structural level is still insufficiently explored. In the present study, we examined the effect of HE on the structural and physicochemical properties of recombinant human VEGF165 (rhVEGF165). The HE binding results in an increase of hydrophobic surface exposure in rhVEGF165 without changes in its secondary structure. Differential scanning calorimetry measurements for intact and HE-bound rhVEGF165 reveals the absence of any pronounced thermally induced transitions in the protein in the temperature range from 20 to 100 °C. The apolar area increase during the heparin binding explains the pronounced HE-induced oligomerization/aggregation of rhVEGF165, as studied by chemical glutaraldehyde cross-linking and dynamic light scattering. Molecular modeling and docking techniques were used to model the full structure of dimeric VEGF165 and to reveal putative molecular mechanisms underlying the function of the VEGF165/HE system. In general, the results obtained can be a basis for explaining the modulating effect of HE on the biological activity of VEGF-A.

Published
2023
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2. Rational Mutagenesis in the Lid Domain of Ribokinase from E. coli Results in an Order of Magnitude Increase in Activity towards D-arabinose

Author

Evgeniy A. Zayats, Ilya V. Fateev, Maria A. Kostromina, Yulia A. Abramchik, Dmitry D. Lykoshin, Daria O. Yurovskaya, Vladimir I. Timofeev, Maria Ya. Berzina, Barbara Z. Eletskaya, Irina D. Konstantinova, and Roman S. Esipov

Subjects
Inorganic Chemistry, Organic Chemistry, General Medicine, Physical and Theoretical Chemistry, enzyme genetic improvement, rational design, active site modification, site-directed mutagenesis, ribokinase, cascade synthesis, modified nucleoside, arabinoside, arabinose, Molecular Biology, Spectroscopy, Catalysis, Computer Science Applications
Abstract

Development of efficient approaches for the production of medically important nucleosides is a highly relevant challenge for biotechnology. In particular, cascade synthesis of arabinosides would allow relatively easy production of various cytostatic and antiviral drugs. However, the biocatalyst necessary for this approach, ribokinase from Escherichia coli (EcoRK), has a very low activity towards D-arabinose, making the synthesis using the state-of-art native enzyme technologically unfeasible. Here, we report the results of our enzyme design project, dedicated to engineering a mutant form of EcoRK with elevated activity towards arabinose. Analysis of the active site structure has allowed us to hypothesize the reasons behind the low EcoRK activity towards arabinose and select feasible mutations. Enzyme assay and kinetic studies have shown that the A98G mutation has caused a large 15-fold increase in kcat and 1.5-fold decrease in KM for arabinose phosphorylation. As a proof of concept, we have performed the cascade synthesis of 2-chloroadenine arabinoside utilizing the A98G mutant with 10-fold lower amount of enzyme compared to the wild type without any loss of synthesis efficiency. Our results are valuable both for the development of new technologies of synthesis of modified nucleosides and providing insight into the structural reasons behind EcoRK substrate specificity.

Published
2022
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4. Comparative Analysis of Enzymatic Transglycosylation Using

Author

Mikhail S, Drenichev, Vladimir E, Oslovsky, Anastasia A, Zenchenko, Claudia V, Danilova, Mikhail A, Varga, Roman S, Esipov, Dmitry D, Lykoshin, and Cyril S, Alexeev

Subjects
Purine-Nucleoside Phosphorylase, Purines, Escherichia coli, Nucleosides, Pentosyltransferases, Ribonucleosides, Phosphates, Thymidine
Abstract

A comparative analysis of the transglycosylation conditions catalyzed by

Published
2022

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