Conformational Analysis of GM1 Oligosaccharide in Water Solution with a New Set of Parameters for the Neu5Ac Moiet

An unconstrained Monte Carlo/energy minimization (MC/EM) conformational search was performed on ganglioside GM1 oligosaccharide, and the results were compared to the known solution conformation of this molecule. The search was performed using the continuum dielectric water solvation model as implemented in MacroModel/Batchmin and the force field AMBER*. The latter was modified to include new parameters for the Neu5Ac residue contained in GM1. The parameters were developed based on molecular orbital calculations on simple model systems and therefore should have general validity for molecular mechanics calculations on sialyl oligosaccharides. A nice agreement was reached between the computed GM1 structure and the available NMR data.