Automated Docking of α-(1,4)- and α-(1,6)-Linked Glucosyl Trisaccharides in the Glucoamylase Active Site

Thumbnail Image
Coutinho, Pedro
Dowd, Michael
Major Professor
Committee Member
Journal Title
Journal ISSN
Volume Title
Research Projects
Organizational Units
Organizational Unit
Chemical and Biological Engineering

The function of the Department of Chemical and Biological Engineering has been to prepare students for the study and application of chemistry in industry. This focus has included preparation for employment in various industries as well as the development, design, and operation of equipment and processes within industry.Through the CBE Department, Iowa State University is nationally recognized for its initiatives in bioinformatics, biomaterials, bioproducts, metabolic/tissue engineering, multiphase computational fluid dynamics, advanced polymeric materials and nanostructured materials.

The Department of Chemical Engineering was founded in 1913 under the Department of Physics and Illuminating Engineering. From 1915 to 1931 it was jointly administered by the Divisions of Industrial Science and Engineering, and from 1931 onward it has been under the Division/College of Engineering. In 1928 it merged with Mining Engineering, and from 1973–1979 it merged with Nuclear Engineering. It became Chemical and Biological Engineering in 2005.

Dates of Existence
1913 - present

Historical Names

  • Department of Chemical Engineering (1913–1928)
  • Department of Chemical and Mining Engineering (1928–1957)
  • Department of Chemical Engineering (1957–1973, 1979–2005)
    • Department of Chemical and Biological Engineering (2005–present)

    Related Units

Journal Issue
Is Version Of

Low-energy conformers of five α-(1,4)- and α-(1,6)-linked glucosyl trisaccharides were flexibly docked into the glucoamylase active site using AutoDock 2.2. To ensure 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 subsites −1 and +1 in very similar modes to those of corresponding nonreducing-end disaccharides. For linear substrates, full binding at subsite +2 occurred only when the substrate reducing end was α-(1,4)-linked, with hydrogen-bonding with the hydroxymethyl group being the only polar interaction there. Given the absence of other important interactions at this subsite, multiple substrate conformations are allowed. For the one docked branched substrate, steric hindrance in the α-(1,6)-glycosidic oxygen suggests that the active-site residues have to change position for hydrolysis to occur. Subsite +1 of the glucoamylase active site allows flexibility in binding but, at least inAspergillus glucoamylases, subsite +2 selectively binds substrates α-(1,4)-linked between subsites +1 and +2. Enzyme engineering to limit substrate flexibility at subsite +2 could improve glucoamylase industrial properties.


Posted with permission from Industrial & Engineering Chemistry Research, 37, no. 6 (1998): 2148–2157, doi:10.1021/ie9706976. Copyright 2012 American Chemical Society.

Thu Jan 01 00:00:00 UTC 1998