Predicting helical structures of the exopolysaccharide produced by Lactobacillus sake 0-1

The viscous exopolysaccharide (EPS) produced by Lactobacillus sake 0–1 is a high molecular mass polymer (Mm 6 × 106 Da) consisting of pentasaccharide repeating units with a composition of D-glucose, L-rhamnose, and sn-glycerol 3-phosphate in molar ratios of 3:2:1. One of the rhamnose residues in the repeating unit is partially 2-O-acetylated. The O-deacetylated, deglycerophosphorylated EPS has been investigated by molecular mechanics calculations. A complete conformational analysis of each of the constituent disaccharide fragments has been performed using the flexible residue approach with the MM3(92) force field. Furthermore, using the same force field, CICADA analyses were accomplished on hexa- and octasaccharide substructures of the polysaccharide. Based on these analyses, insight was obtained into nine conformational minima for the polysaccharide. The low energy conformations found by CICADA were extrapolated to regular polysaccharide structures using a polysaccharide builder program. The generated helices exhibit either 2-fold or 3- or 4-fold righthanded chiralities, and in each case the helices are highly extended