|Dowd, Michael - Mike|
Submitted to: Proteins: Structure, Function, and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/1996
Publication Date: N/A
Citation: Interpretive Summary: Glucoamylase is an important enzyme for the corn processing industry. It is used to convert corn starch into glucose, which is converted to the sweetener fructose or used as media for many fermentation processes to produce ethanol, vitamins, and amino acids. The program AutoDock (version 2.1) was developed to locate regions of enzymes and proteins that interact with small molecules. We used this computational method to study how small carbohydrates bind to glucoamylase. Based on comparisons with several known crystal structures, the modeling results correctly placed the carbohydrates into the glucoamylase binding site. Calculated interaction energies did not agree with the relative order of binding as indicated by known binding constants. This disagreement is due the lack of flexibility of the enzyme and carbohydrate rings as well as the simple approach that AutoDock uses to calculate interaction energies.
Technical Abstract: To investigate glucoamylase's interaction with monosaccharide substrates and analogues, MM3(92)-optimized structures were docked into glucoamylase's active site using AutoDock 2.1. The results were compared to structures of glucoamylase complexes obtained by protein crystallography. Charged forms of some substrate analogues were also docked to access the degree of protonation possessed by glucoamylase inhibitors. Many forms of methyl alpha-acraviosinide were conformationally mapped using MM3(92), characterizing the conformational pH dependence found for the acarbose family of glucosidase inhibitors. Their significant conformers, representing the most common states of the inhibitor, were used as initial structures for docking. This constitutes a new approach for the exploration of binding modes of carbohydrate chains. Docking results differ slightly from X-ray crystallographic data, the difference being of the order of the crystallographic error. Even though large approximations occur in the AutoDock force field, the estimated energetic interactions agree in most cases with experimental binding kinetics.