Molecular modeling study of highly branching (1-3)-alpha-D-glucan, a model polysaccharide for cariogenic glucan, using the N-H mapping method

A systematic search for possible regular helical structures of a highly branching (l to 3)-alpha-D-glucan was done using the n-h mapping technique, combined with MM3-generated relaxed-residue energy map calculations with respect to the conformations of the backbone glycosidic linkages. The alpha-D-glucan, consisting of a (1 to 3)-alpha-linked backbone with alpha-D-glucose side residues attaching to an O6 atom of every second backbone residue, was considered as a model polysaccharide of a branching part of the glucan produced by oral bacteria, which was known to be related to dental plaque formation and to contribute to dental caries. The potential energy surfaces of the trisaccharide repeating unit of the branching alpha-D-glucan indicated that (1 to 6)-alpha-linked side residues did not appear to interfere significantly with the backbone stereochemistry, probably due to a further separation of the three-bond-linked side residue compared with an ordinary two-bond-linked residue. Based on the n-h maps of the branching alpha-D-glucan, the side residues, when involved in a complete helix, mostly contributed additional stabilizations to particular helical structures. It was found by checking the typical helix models that formation of hydrogen bonds involving side residues was probably a major cause of the stabilization. This hydrogen bonding was expected to increase insolubility for the glucan chain - a typical, physical property observed for the bacterial alpha-D-glucan - by introducing its backbone stereochemistry as an additional stiff feature