Automated docking to explore subsite binding by glycoside hydrolase family 6 cellobiohydrolases and endoglucanases

Biopolymers. 2007 Nov;87(4):249-60. doi: 10.1002/bip.20831.

Abstract

Cellooligosaccharides were computationally docked using AutoDock into the active sites of the glycoside hydrolase Family 6 enzymes Hypocrea jecorina (formerly Trichoderma reesei) cellobiohydrolase and Thermobifida fusca endoglucanase. Subsite -2 exerts the greatest intermolecular energy in binding beta-glucosyl residues, with energies progressively decreasing to either side. Cumulative forces imparting processivity exerted by these two enzymes are significantly less than by the equivalent glycoside hydrolase Family 7 enzymes studied previously. Putative subsites -4, -3, +3, and +4 exist in H. jecorina cellobiohydrolase, along with putative subsites -4, -3, and +3 in T. fusca endoglucanase, but they are less important than subsites -2, -1, +1, and +2. In general, binding adds 3-7 kcal/mol to ligand intramolecular energies because of twisting of scissile glycosidic bonds. Distortion of beta-glucosyl residues to the (2)S(O) conformation by binding in subsite -1 adds approximately 7 kcal/mol to substrate intramolecular energies.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Cellulase / chemistry*
  • Cellulose 1,4-beta-Cellobiosidase / chemistry*
  • Computer Simulation
  • Fungal Proteins / chemistry*
  • Glycoside Hydrolases / chemistry*
  • Hypocrea / enzymology*
  • Oligosaccharides / chemistry
  • Protein Conformation
  • Software*
  • Thermodynamics

Substances

  • Fungal Proteins
  • Oligosaccharides
  • Glycoside Hydrolases
  • Cellulase
  • Cellulose 1,4-beta-Cellobiosidase