Submitted to: Proteins: Structure, Function, and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/1997
Publication Date: N/A
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 was developed to locate regions of enzymes and proteins that interact with small molecules. We used this computational method to study how different disaccharides (carbohydrates containing two sugar rings) bind to glucoamylase. The results show that one of the rings always binds in the same manner while the other ring can bind in different ways. While some disaccharides (alpha-linked) easily docked to the enzyme, other disaccharides (beta-linked and alpha,alpha-linked) did not dock explaining why they are not substrates for glucoamylase.
Technical Abstract: To better understand the molecular basis of glucoamylase selectivity, low-energy conformers of glucosyl disaccharides obtained from relaxed residue conformational mapping were flexibly docked into the glucoamylase active site using AutoDock 2.2. This procedure assures that significant conformational space is searched and can produce bound structures comparable to those obtained by protein crystallography. Alpha-linked glucosyl disaccharides except alpha,alpha-trehalose dock easily into the active site while exclusively beta-linked disaccharides do not, explaining why only the former are glucoamylase substrates. The optimized docking modes are similar at the nonreducing end of the different substrates. Individual atomic energies of intermolecular interaction allow the definite identification of key hydroxyl groups for each substrate. This approach confirmed the versatility of the second subsite of the glucoamylase active site in binding different substrates.