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United States Department of Agriculture

Agricultural Research Service

Title: Qm/mm Distortion Energies in Di and Oligosaccharides Complexed with Proteins

Authors
item French, Alfred
item Johnson, Glenn
item Kelterer, Anne-Marie - TECHNISCHE UNIV GRAZ
item Dowd, Michael
item Cramer, Christopher - UNIVERSITY OF MINNESOTA

Submitted to: International Journal of Quantum Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 27, 2001
Publication Date: N/A

Interpretive Summary: Enzymes are widely used in the processing of agricultural crops such as cotton and corn, which are made up in large part of cellulose and starch, respectively. Enzymes are used to break down the long starch and cellulose molecules into the subunit glucose for various practical reasons such as preserving the color on dyed fabric or making alcohol from corn. More and more is known about how the enzymes work on carbohydrates, but much remains to be understood. For example, it is known that the carbohydrate is bound in a complex with the enzyme, which is a protein. Also, part of the breakdown reaction involves a preliminary change in the shape of the glucose ring in the chain. That distortion is proposed to make the reaction occur more rapidly. This work investigates how the linkage between the glucose units might be distorted in an analogous manner to also facilitate the breakage of the long molecules. The amounts of energy required to change the shapes of the carbohydrates were studied by theoretical computer calculations, and these energies were compared with experimentally determined structures. Criteria for assessing non-random distortion were developed and several such distorted linkages between the glucose units were identified. This information should be of use to scientists who are trying to develop more efficient enzymes for utilization of agricultural carbohydrate materials. It is also of wider-ranging use for understanding enzyme reactions of all types.

Technical Abstract: To investigate whether linkages between monosaccharide residues are unusually distorted by their interactions with proteins, the carbohydrate linkage torsion 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 energies. Energy values corresponding to each crystallographic conformation were then pooled. Nearly 70% of the 209 structures had energies of 1 kcal/mol or less. A cumulative frequency analysis showed that most points fell on a curve that showed an exponential decrease in the number of observed structures as the energy increased, 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 the observed points deviated from the curve. Some of these high-energy shapes were from linkages being broken by enzymatic attack, but others were not, and some scissile linkages were not unusually distorted.

Last Modified: 12/22/2014
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