Modeling of Interactions of Polysaccharide Chains

This paper describes a method for predicting the packing relationship of two polysaccharide chains and its use in studying polymorphism in starch. Given a rigid model of an isolated double helix, its interaction with a second double helix is studied at varied helix-axis translations and mutual rotational orientations while keeping the helices in van der Waals contact. The stability of each structure is evaluated by an energy calculated using atom-atom potentials that includes compensation for hydrogen bonding. Models for starch were based on the fiber repeat distance on fiber diffraction patterns and are double-helices composed of left-handed single strands related by two-fold rotational symmetry. Two stable relationships were found for both the parallel and antiparallel models. The structure predicted to be most stable corresponds to a duplex of parallel double-helices as found in both the crystalline A and B allomorphs. From this result, an explanation of the transition from B to A is proposed.