QM/MM distortion energies in Di- and oligosaccharides complexed with proteins

Abstract

To investigate whether linkages between monosaccharide residues are unusually distorted by their interactions with proteins, φ and Ψ values for fragments of cellulose and starch were taken from the Protein Data Bank. These experimental conformations were then plotted on energy surfaces that were calculated with a hybrid of HF/6-31G* and MM3(96) energies. Energy values corresponding to each crystallographic conformation were then pooled. Nearly 70% of the 210 structures had energies of 1 kcal mol-1 or less. A cumulative frequency analysis showed that most points fell on a curve that had an exponential decrease in the number of observed structures as the energy increased. This is analogous to a Boltzmann distribution but at higher temperature. This analysis showed that more than 90% of the linkages were not unusually distorted, and the distribution was similar to that found for small-molecule crystals of carbohydrates. However, above 2 kcal mol-1, the observed points deviated from the curve. Most of these high-energy observations were from linkages being broken by enzymatic attack, but others were not, and some scissile linkages were not unusually distorted.