Hydration of T-antigen Galβ(1-3)GalNAc and the isomer Galβ(1-3)GlcNAc by molecular dynamics simulations

Abstract

We present a 250 ps molecular dynamics simulation of the T-antigen Galβ(1-3)GalNAc and its isomer Galβ(1-3)GlcNAc in the classic Gibbs Ensemble, Number of particles, Pressure and Temperature (NPT) with explicit representation of 432 water molecules. We computed the radial distribution function, equilibrium conformation, intramolecular and intermolecular hydrogen bonds, and water residence time to characterize the hydration pattern of these sugars, which are not very different and exhibit hydrophilic behavior. Based on hydration dynamics, it was concluded that these sugars should be classified as negative hydrated. Formation of an intramolecular hydrogen bond between the ring oxygen atom O5 of the first unit and the OH4′ group of glycoside of the second unit might influence interaction with the antigenic receptor and could explain the main difference of affinities between them.