Conformational analysis and molecular modelling of the branching point of amylopectin

The conformational properties of 6(2) alpha-D-glucosylmaltotriose have been studied using energy calculations that include van der Waals interactions, hydrogen bond stabilization, exo-anometric effect and torsional potential contributions. The calculations focused mainly on the conformational properties displayed at the alpha(1----6) linkage within the tetrasaccharide for which the conformational space is reported. The tetrasaccharide molecule was then considered as a model compound of the branching point in amylopectin. From molecular modelling, some basic structural features associated with branching were clearly established. It was found that, among the low energy arrangements, the side chain would fold back onto the main backbone, thereby producing dense three-dimensional structures in which a 'parallel' arrangement is achieved. The branching between two strands of the double helix, as found in the crystalline moiety of A and B starches, was further investigated. It was found that one particular set of conformations about the glycosidic linkages in the two different strands, could result in an arrangement such that strands could be connected through an alpha(1----6) glycosidic linkage, with a minimum of distortion. The three-dimensional features derived from the molecular modelling agree with the physical properties and mode of biogenesis within the starch granule; they are in accord with a 'cluster' type of structure.