CONFORMATIONAL-ANALYSIS OF GM1 OLIGOSACCHARIDE IN WATER SOLUTION WITHA NEW SET OF PARAMETERS FOR THE NEU5AC MOIETY

An unconstrained Monte Carlo/energy minimization (MC/EM) conformationa l search was performed on ganglioside GM1 oligosaccharide, and the res ults were compared to the known solution conformation of this molecule . The search was performed using the continuum dielectric water solvat ion model as implemented in MacroModel/Batchmin and the force field AM BER. The latter was modified to include new parameters for the Neu5Ac residue contained in GM1. The parameters were developed based on mole cular orbital calculations on simple model systems and therefore shoul d have general validity for molecular mechanics calculations on sialyl oligosaccharides. A nice agreement was reached between the computed G M1 structure and the available NMR data.