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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Commodity Utilization Research » Research » Publications at this Location » Publication #86236
Title: AUTOMATED DOCKING OF A-(1,4)- AND A-(1,6)-LINKED GLUCOSYL TRISACCHARIDES INTHE GLUCOAMYLASE ACTIVE SITE

Author
item COUTINHO, PEDRO - IOWA STATE UNIVERSITY
item Dowd, Michael
item REILLY, PETER - IOWA STATE UNIVERSITY

Submitted to: Journal of Industrial and Engineering Chemical Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/5/1997
Publication Date: N/A
Citation: N/A

Interpretive Summary: The enzyme glucoamylase is used by the corn processing industry to convert starch into glucose, which is then used as substrate for fermentation or converted to fructose for sweeteners. AutoDock, a program used for studying interactions between molecules and proteins, was used to study the binding of trisaccharide starch fragments to this enzyme. The study showed dthat the third binding site preferentially accepted trisaccharides in whic the third glucose residues was linked to the remainder of the trisaccharide in an a-(1,4)-linkage. This explains why glycoamylase has difficulties in acting through the a-(1,6) branch points contained by starch. This information will be useful to scientists trying to genetically modify this enzyme to improve its catalytic properties.

Technical Abstract: Low-energy conformers of five a-(1,4)- and a-(1,6)-linked glucosyl trisaccharides were flexibly docked into the glucoamylase active site using AutoDock 2.2. To assure that all significant conformational space was searched the starting trisaccharide conformers for docking were all possible combinations of the corresponding disaccharide low-energy conformers. All docked trisaccharides occupied the first and second subsites in very similar modes to those of the corresponding nonreducing end disaccharides. For linear substrates, full binding at the third subsite occurred only when the substrate reducing end was a-(1,4)-linked, hydrogen-bonding with the hydroxymethyl group being the only polar interaction there. For the one docked branched substrate, steric hindrance in the a-(1,6)-glycosidic oxygen suggests that the active-site residues have to change position for hydrolysis to occur. The second subsite of the eglucoamylase active site allows flexibility in binding but, at least in Aspergillus glucoamylases, the third selectively binds substrates a-(1,4)-l between the second and third residues.