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

To investigate whether linkages between monosaccharide residues are unusual ly distorted by their interactions with proteins, phi and psi values for fr agments of cellulose and starch were taken from the Protein Data Bank. Thes e 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. Nearl y 70% of the 210 structures had energies of 1 kcal mol(-1) or less. A cumul ative frequency analysis showed that most points fell on a curve that had a n exponential decrease in the number of observed structures as the energy i ncreased. This is analogous to a Boltzmann distribution but at higher tempe rature. This analysis showed that more than 90% of the linkages were not un usually distorted, and the distribution was similar to that found for small -molecule crystals of carbohydrates. However, above 2 kcal mol-1, the obser ved points deviated from the curve. Most of these high-energy observations were from linkages being broken by enzymatic attack, but others were not, a nd some scissile linkages were not unusually distorted. (C) 2001 John Wiley & Sons, Inc.