title: Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum.
abstract: Molecular dynamics (MD) simulations were used to study substrate recognition by the family 48 exocellulase CelF from Clostridium cellulolyticum. It was hypothesized that residues around the entrance of the active site tunnel of this enzyme might serve to recognize and bind the substrate through an affinity for the cellulose monomer repeat unit, β-d-glucopyranose. Simulations were conducted of the catalytic domain of this enzyme surrounded by a concentrated solution of β-d-glucopyranose, and the full three-dimensional probability distribution for finding sugar molecules adjacent to the enzyme was calculated from the trajectory. A significant probability of finding the sugar stacked against the planar faces of Trp 310 and Trp 312 at the entrance of the active site tunnel was observed. Biotechnol. Bioeng. 2016;113: 1433-1440. © 2015 Wiley Periodicals, Inc.
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, 14853.
authors.forename: Mo
authors.initials: M
authors.lastname: Chen
authors.affiliation: Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Himmel
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York.
authors.forename: David B
authors.initials: DB
authors.lastname: Wilson
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, 14853. jwb7@cornell.edu.
authors.forename: John W
authors.initials: JW
authors.lastname: Brady
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D044602:Cellulases / Q000737:chemistry* / Q000378:metabolism*; D046973:Ruminiclostridium cellulolyticum / Q000201:enzymology*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D044602:Cellulases
keywords: MD simulations; cellulases; enzymatic hydrolysis; enzyme mechanisms; substrate binding; substrate recognition