MSc. Denys Biriukov, PhD
+420 220 183 185
Vybrané publikace
Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity
Carbohydrate Polymers 325: 121568 (2024)
Hyaluronan is a natural carbohydrate polymer with a negative charge that fosters gel-like conditions crucial for its cellular functions and industrial applications. As a recognized ligand for proteins, understanding their mutual interactions provides solid ground to tune hyaluronan\'s gel properties using biocompatible peptides. This work employs NMR and molecular dynamics simulations to identify molecular motifs relevant to hyaluronan–peptide interactions using arginine, lysine, and glycine oligopeptides. Arginine-rich peptides exhibit the strongest binding to hyaluronan according to chemical shift perturbation measurements, followed distantly by the similarly charged lysine. This difference highlights the significance of electrostatics and the peculiarities of the guanidinium side chain in arginine, capable of non-polar interactions that further stabilize the binding. Additional nuclear Overhauser effect measurements do not show stable interaction partners, precluding strong and…
Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field
Journal of Chemical Theory and Computation 20 (17): 7546–7559 (2024)
The “good,” the “bad,” and the “hidden” in neutron scattering and molecular dynamics of ionic aqueous solutions
Journal of Chemical Physics 156 (19): 194505 (2022)
Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints
Journal of Chemical Theory and Computation 19 (18): 6332–6341 (2023)
Nejnovější publikace
Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions
Journal of Chemical Information and Modeling 64 (18): 7122–7134 (2024)
Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field
Journal of Chemical Theory and Computation 20 (17): 7546–7559 (2024)
Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity
Carbohydrate Polymers 325: 121568 (2024)
Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints
Journal of Chemical Theory and Computation 19 (18): 6332–6341 (2023)