Studies on the conformational behaviour of GlcNAc-Man3-GlcNAc2 oligosaccharides using molecular dynamics simulations

Three-dimensional structures of the natural substrate unit for the enzyme N-acetylglucosamine-transferase II, GIcNAc-Man3-GlcNAc2, were investigated by molecular modelling methods. Molecular dynamics (MD) and molecular mechanics calculations on two hexasaccharides, namely GlcNAc-Man3-GlcNAc2-Asn and GlcNAc-Man3-GlcNAc2-OMe were performed by the Biosym/MSI software using the CVFF and CFF95 force fields in vacuum. The MD simulations were calculated for 3 ns at different simulation temperatures and for two values of dielectric constant, epsilon=1 and epsilon=4. From each 3 ns trajectory, 3050 structures have been optimized. The local minima obtained have been clustered into families exhibiting similar values of glycosidic torsional angles phi, psi, and omega. The influence of the simulation conditions and force fields used on the conformational behaviour and structure of the title oligosaccharides is discussed.