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Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum
Author(s) -
Chen Mo,
Himmel Michael E.,
Wilson David B.,
Brady John W.
Publication year - 2016
Publication title -
biotechnology and bioengineering
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.136
H-Index - 189
eISSN - 1097-0290
pISSN - 0006-3592
DOI - 10.1002/bit.25909
Subject(s) - substrate (aquarium) , active site , molecular dynamics , monomer , chemistry , enzyme , cellulose , domain (mathematical analysis) , strain (injury) , stereochemistry , biochemistry , computational chemistry , biology , organic chemistry , mathematics , ecology , mathematical analysis , polymer , anatomy
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.