QM/MM Distortion Energies in Di- and Oligosaccharides Complexed with Proteins
French, A. D.; Johnson, G. P.; Kelterer, A.-M.; Dowd, M. K.; Cramer, C. J.
Int. J. Quantum Chem. 2001, 84, 416.
To investigate whether linkages between monosaccharide residues are unusually distorted by their interactions with proteins, N and R 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.
To request a copy of this article, send e-mail to the Research Reports Coordinator at the Minnesota Supercomputer Institute (email@example.com). Please provide a mailing address and specify that you would like UMSI report 2001/113.