Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum
- Department of Food Science, Cornell University, Ithaca New York 14853
- Biosciences Center, National Renewable Energy Laboratory, Golden Colorado
- Department of Molecular Biology and Genetics, Cornell University, Ithaca New York
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, ..beta..-d-glucopyranose. Simulations were conducted of the catalytic domain of this enzyme surrounded by a concentrated solution of ..beta..-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.
- Research Organization:
- National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Office of Biological and Environmental Research
- DOE Contract Number:
- AC36-08GO28308
- OSTI ID:
- 1330002
- Report Number(s):
- NREL/JA-2700-67322
- Journal Information:
- Biotechnology and Bioengineering, Vol. 113, Issue 7; ISSN 0006-3592
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
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