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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, ..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.

Authors:
 [1];  [2];  [3];  [1]
  1. Department of Food Science, Cornell University, Ithaca New York 14853
  2. Biosciences Center, National Renewable Energy Laboratory, Golden Colorado
  3. Department of Molecular Biology and Genetics, Cornell University, Ithaca New York
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Office of Biological and Environmental Research
OSTI Identifier:
1330002
Report Number(s):
NREL/JA-2700-67322
Journal ID: ISSN 0006-3592
DOE Contract Number:  
AC36-08GO28308
Resource Type:
Journal Article
Journal Name:
Biotechnology and Bioengineering
Additional Journal Information:
Journal Volume: 113; Journal Issue: 7; Journal ID: ISSN 0006-3592
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; enzyme mechanisms; enzymatic hydrolysis; MD simulations; substrate recognition; substrate binding; cellulases

Citation Formats

Chen, Mo, Himmel, Michael E., Wilson, David B., and Brady, John W. Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum. United States: N. p., 2016. Web. doi:10.1002/bit.25909.
Chen, Mo, Himmel, Michael E., Wilson, David B., & Brady, John W. Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum. United States. doi:10.1002/bit.25909.
Chen, Mo, Himmel, Michael E., Wilson, David B., and Brady, John W. Thu . "Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum". United States. doi:10.1002/bit.25909.
@article{osti_1330002,
title = {Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum},
author = {Chen, Mo and Himmel, Michael E. and Wilson, David B. and Brady, John W.},
abstractNote = {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.},
doi = {10.1002/bit.25909},
journal = {Biotechnology and Bioengineering},
issn = {0006-3592},
number = 7,
volume = 113,
place = {United States},
year = {2016},
month = {1}
}