STUDIES ON THE CONFORMATIONAL BEHAVIOR OF GLCNAC-MAN(3)-GLCNAC(2) OLIGOSACCHARIDES USING MOLECULAR-DYNAMICS SIMULATIONS

Three-dimensional structures of the natural substrate unit for the enz yme N-acetylglucosamine-transferase II, GlcNAc-Man(3)-GlcNAc(2), were investigated by molecular modelling methods. Molecular dynamics (MD) a nd molecular mechanics calculations on two hexasaccharides, namely Glc NAc-Man(3)-GlcNAc(2)-Asn and GlcNAc-Man(3)-GlcNAc(2)-OMe were performe d by the Biosym/MSI software using the CVFF and CFF95 force fields in vacuum. The MD simulations were calculated for 3 ns at different simul ation 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, an d omega. The influence of the simulation conditions and force fields u sed on the conformational behaviour and structure of the title oligosa ccharides is discussed.