Conformational studies of the backbone (poly-N-acetyllactosamine) and the core region sequences of O-linked...

The AMBER forcefield with added carbohydrate specific parameters for potential types, charges and anomericity has been used to explore the conformational space sampled by oligosaccharides of repeating (Gal beta 1-4GlcNAc beta 1-3)n sequence and those having alpha chain terminating substituents on a Gal beta 1-3GalNAc alpha, O-glycosylated core. The 17 lowest energy forms of the 16-mer N-acetyllactosaminic sequence included fully extended units and spring-like coils with dielectric constant 80 to simulate a water environment. More restricted stereochemistry was exhibited by the glycosylation adjacent to the core as has been previously predicted by n.m.r. studies.