5 nanosecond molecular dynamics and NMR study of conformational transitions in the sialyl-Lewis X antigen

The range of internal motions of the sialyl Lewis-X (SLe(x)) tetrasaccharide (NeuNAc alpha 2-->3Gal beta 1-->4(Fuc alpha 1-->3)GlcNAc) [where Fuc is L-fucopyranose, Gal is D-galactopyranose, GlcNAc is 2-acetamido-2-deoxy-D-glucopyranose and NeuNAc is D-neuraminic acid (sialic acid)] was studied by restrained simulated annealing and restrained molecular dynamics (MD) calculations. Transitions between predominantly two conformational states were observed for the NeuNAc alpha (2-->3)Gal linkage, consistent with previous observations for this linkage in sialyl-N-acetyllactosamine. The MD trajectory was simulated for 5 ns of real time, in order to observe a statistically significant number of these relatively low-frequency transitions. The Fuc alpha(1-->3)GlcNAc and Gal beta (1-->4)GlcNAc linkages, however, showed more restricted flexibility within a single energy well (RMS differences for the time-averaged glycosidic torsion angles, and , were 50% lower than for the NeuNAc alpha(2-->3)Gal linkage), and approximate to a rigid conformation. NMR parameters [relative rotating-frame Overhauser enhancement (r.O.e.) and inter-glycosidic 3JCH] back-calculated from the MD simulation were in close agreement with experimentally measured values for the free reducing oligosaccharide in D2O solution.