Modeling the α(1→6) branch point of amylopectin in solution

We have investigated the structure and dynamics of the branching motif of amylopectin, the major component of starch. The trisaccharide panose and the tetrasaccharide 6(2) alpha-D-glucosylmaltotriose have been chosen as minimal model compounds for the alpha(1-->6) branch point and molecular dynamics (MD) simulations of these have been run with explicit water. Calculation of NMR longitudinal relaxation times for panose shows good agreement with experimental values, thereby validating our simulation dynamics. Compared with the disaccharides maltose and isomaltose the addition of extra residues appears to provide more interresidue interactions, causing the branch models to explore a wider range of glycosidic conformational space, particularly for the alpha(1-->6) linkage; nonetheless, there remain two distinct regions separated by a high-energy barrier. The correlation time for dynamics about the alpha(1-->6) linkage torsion angles depends strongly on which of these regions is being sampled. We calculate the diffusion constants for water as a function of distance from the solute: the calculations show that these regions of structured water close to the solute diffuse more slowly than bulk water. We then show that the solvated saccharides are surrounded by a layer of structured, spatially localized water by comparing the diffusion of the solvent with its configurational probability distribution. Finally, the implications of the model compound properties for the full structure of amylopectin were investigated by calculating geometric properties of the branch point.