Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Strategies to reduce end-product inhibition in family 48 glycoside hydrolases

Abstract

Family 48 cellobiohydrolases are some of the most abundant glycoside hydrolases in nature. They are able to degrade cellulosic biomass and therefore serve as good enzyme candidates for biofuel production. Family 48 cellulases hydrolyze cellulose chains via a processive mechanism, and produce end products composed primarily of cellobiose as well as other cellooligomers (dp ≤ 4). The challenge of utilizing cellulases in biofuel production lies in their extremely slow turnover rate. A factor contributing to the low enzyme activity is suggested to be product binding to enzyme and the resulting performance inhibition. In this study, we quantitatively evaluated the product inhibitory effect of four family 48 glycoside hydrolases using molecular dynamics simulations and product expulsion free-energy calculations. We also suggested a series of single mutants of the four family 48 glycoside hydrolases with theoretically reduced level of product inhibition. As a result, the theoretical calculations provide a guide for future experimental studies designed to produce mutant cellulases with enhanced activity.

Authors:
 [1];  [2];  [2];  [2];  [2];  [2];  [1];  [2];  [2];  [2]
+ Show Author Affiliations
  1. Cornell Univ., Ithaca, NY (United States)
  2. National Renewable Energy Lab. (NREL), Golden, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Laboratory (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1240085
Report Number(s):
NREL/JA-2700-65427
Journal ID: ISSN 0887-3585
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Accepted Manuscript
Journal Name:
Proteins
Additional Journal Information:
Journal Volume: 84; Journal Issue: 3; Related Information: Proteins: Structure, Function, and Bioinformatics; Journal ID: ISSN 0887-3585
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; glycoside hydrolases; product inhibition; biofuels; cellulose; molecular dynamics

Citation Formats

Chen, Mo, Bu, Lintao, Alahuhta, Markus, Brunecky, Roman, Xu, Qi, Lunin, Vladimir V., Brady, John W., Crowley, Michael F., Himmel, Michael E., and Bomble, Yannick J. Strategies to reduce end-product inhibition in family 48 glycoside hydrolases. United States: N. p., 2016. Web. doi:10.1002/prot.24965.
Copy to clipboard
Chen, Mo, Bu, Lintao, Alahuhta, Markus, Brunecky, Roman, Xu, Qi, Lunin, Vladimir V., Brady, John W., Crowley, Michael F., Himmel, Michael E., & Bomble, Yannick J. Strategies to reduce end-product inhibition in family 48 glycoside hydrolases. United States. https://doi.org/10.1002/prot.24965
Copy to clipboard
Chen, Mo, Bu, Lintao, Alahuhta, Markus, Brunecky, Roman, Xu, Qi, Lunin, Vladimir V., Brady, John W., Crowley, Michael F., Himmel, Michael E., and Bomble, Yannick J. Mon . "Strategies to reduce end-product inhibition in family 48 glycoside hydrolases". United States. https://doi.org/10.1002/prot.24965. https://www.osti.gov/servlets/purl/1240085.
Copy to clipboard
@article{osti_1240085,
title = {Strategies to reduce end-product inhibition in family 48 glycoside hydrolases},
author = {Chen, Mo and Bu, Lintao and Alahuhta, Markus and Brunecky, Roman and Xu, Qi and Lunin, Vladimir V. and Brady, John W. and Crowley, Michael F. and Himmel, Michael E. and Bomble, Yannick J.},
abstractNote = {Family 48 cellobiohydrolases are some of the most abundant glycoside hydrolases in nature. They are able to degrade cellulosic biomass and therefore serve as good enzyme candidates for biofuel production. Family 48 cellulases hydrolyze cellulose chains via a processive mechanism, and produce end products composed primarily of cellobiose as well as other cellooligomers (dp ≤ 4). The challenge of utilizing cellulases in biofuel production lies in their extremely slow turnover rate. A factor contributing to the low enzyme activity is suggested to be product binding to enzyme and the resulting performance inhibition. In this study, we quantitatively evaluated the product inhibitory effect of four family 48 glycoside hydrolases using molecular dynamics simulations and product expulsion free-energy calculations. We also suggested a series of single mutants of the four family 48 glycoside hydrolases with theoretically reduced level of product inhibition. As a result, the theoretical calculations provide a guide for future experimental studies designed to produce mutant cellulases with enhanced activity.},
doi = {10.1002/prot.24965},
journal = {Proteins},
number = 3,
volume = 84,
place = {United States},
year = {Mon Feb 01 00:00:00 EST 2016},
month = {Mon Feb 01 00:00:00 EST 2016}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1002/prot.24965
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 8 works
Citation information provided by
Web of Science

Figures / Tables:

Table I Table I: Residues at the tunnel exit of the four family 48 glycoside hydrolases.
All figures and tables (9 total)
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

The Cellulosomes: Multienzyme Machines for Degradation of Plant Cell Wall Polysaccharides
journal, October 2004

Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes
journal, May 2012

  • Bu, Lintao; Nimlos, Mark R.; Shirts, Michael R.
  • Journal of Biological Chemistry, Vol. 287, Issue 29
  • DOI: 10.1074/jbc.M112.365510

Probing Carbohydrate Product Expulsion from a Processive Cellulase with Multiple Absolute Binding Free Energy Methods
journal, March 2011

  • Bu, Lintao; Beckham, Gregg T.; Shirts, Michael R.
  • Journal of Biological Chemistry, Vol. 286, Issue 20
  • DOI: 10.1074/jbc.M110.212076

High temperature pre-digestion of corn stover biomass for improved product yields
journal, December 2014

  • Brunecky, Roman; Hobdey, Sarah E.; Taylor, Larry E.
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/s13068-014-0170-2

Deletion of the Cel48S cellulase from Clostridium thermocellum
journal, September 2010

  • Olson, Daniel G.; Tripathi, Shital A.; Giannone, Richard J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 41, p. 17727-17732
  • DOI: 10.1073/pnas.1003584107

Alleviating product inhibition in cellulase enzyme Cel7A: Alleviating Product Inhibition in Cel7A
journal, September 2015

  • Atreya, Meera E.; Strobel, Kathryn L.; Clark, Douglas S.
  • Biotechnology and Bioengineering, Vol. 113, Issue 2
  • DOI: 10.1002/bit.25809

Major characteristics of the cellulolytic system of Clostridium thermocellum coincide with those of the purified cellulosome
journal, January 1985

The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum Cellulosome
journal, July 2002

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
journal, July 1983

  • Brooks, Bernard R.; Bruccoleri, Robert E.; Olafson, Barry D.
  • Journal of Computational Chemistry, Vol. 4, Issue 2
  • DOI: 10.1002/jcc.540040211

Crystal Structures of the Cellulase Cel48F in Complex with Inhibitors and Substrates Give Insights into Its Processive Action † , ‡
journal, September 2000

  • Parsiegla, G.; Reverbel-Leroy, C.; Tardif, C.
  • Biochemistry, Vol. 39, Issue 37
  • DOI: 10.1021/bi001139p

Product inhibition of the recombinant CelS, an exoglucanase component of the Clostridium thermocellum cellulosome
journal, December 1995

  • Kruus, K.; Andreacchi, A.; Wang, W. K.
  • Applied Microbiology and Biotechnology, Vol. 44, Issue 3-4
  • DOI: 10.1007/BF00169935

Revealing Nature's Cellulase Diversity The Digestion Mechanism of Caldicellulosiruptor bescii CelA
journal, December 2013

Catalytically Enhanced Endocellulase Cel5A from <I>Acidothermus cellulolyticus</I>
journal, January 2005

  • Baker, John O.; McCarley, James R.; Lovett, Rebecca
  • Applied Biochemistry and Biotechnology, Vol. 121, Issue 1-3
  • DOI: 10.1385/ABAB:121:1-3:0129

Catalytic mechanism of enzymic glycosyl transfer
journal, November 1990

Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production
journal, February 2007

  • Himmel, M. E.; Ding, S.-Y.; Johnson, D. K.
  • Science, Vol. 315, Issue 5813, p. 804-807
  • DOI: 10.1126/science.1137016

Updating the sequence-based classification of glycosyl hydrolases
journal, June 1996

  • Henrissat, Bernard; Bairoch, Amos
  • Biochemical Journal, Vol. 316, Issue 2
  • DOI: 10.1042/bj3160695

Cloning, expression and characterization of a Family 48 exocellulase, Cel48A, from Thermobifida fusca: Thermobifida fusca exocellulase Cel48A
journal, August 2000

Nonequilibrium Equality for Free Energy Differences
journal, April 1997

CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software
journal, December 2009

  • Crowley, Michael F.; Williamson, Mark J.; Walker, Ross C.
  • International Journal of Quantum Chemistry, Vol. 109, Issue 15
  • DOI: 10.1002/qua.22372

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

Additive empirical force field for hexopyranose monosaccharides
journal, November 2008

  • Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh
  • Journal of Computational Chemistry, Vol. 29, Issue 15
  • DOI: 10.1002/jcc.21004

Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach
journal, November 1997

Ricin Toxin Contains at Least Three Galactose-Binding Sites Located in B Chain Subdomains 1α, 1β, and 2γ †
journal, January 1996

  • Frankel, Arthur E.; Burbage, Chris; Fu, Tao
  • Biochemistry, Vol. 35, Issue 47
  • DOI: 10.1021/bi960798s

CHARMM: The biomolecular simulation program
journal, July 2009

  • Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
  • Journal of Computational Chemistry, Vol. 30, Issue 10
  • DOI: 10.1002/jcc.21287

The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity
journal, October 2009

  • Zhang, Xiao-Zhou; Zhang, Zuoming; Zhu, Zhiguang
  • Applied Microbiology and Biotechnology, Vol. 86, Issue 2
  • DOI: 10.1007/s00253-009-2231-1

Identification of Two Functionally Different Classes of Exocellulases †
journal, January 1996

  • Barr, Brian K.; Hsieh, Yin-Liang; Ganem, Bruce
  • Biochemistry, Vol. 35, Issue 2
  • DOI: 10.1021/bi9520388

Free Energy Calculations with Non-Equilibrium Methods: Applications of the Jarzynski Relationship
journal, January 2006

  • Xiong, Hui; Crespo, Alejandro; Marti, Marcelo
  • Theoretical Chemistry Accounts, Vol. 116, Issue 1-3
  • DOI: 10.1007/s00214-005-0072-2

Isolation and properties of a major cellobiohydrolase from the cellulosome of Clostridium thermocellum.
journal, July 1991

A “fast growth” method of computing free energy differences
journal, April 2001

  • Hendrix, D. A.; Jarzynski, C.
  • The Journal of Chemical Physics, Vol. 114, Issue 14
  • DOI: 10.1063/1.1353552

An Introduction to the Bootstrap
book, May 1994

  • Efron, Bradley; Tibshirani, R. J.
  • Monographs on Statistics and Applied Probability
  • DOI: 10.1201/9780429246593
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Natural diversity of glycoside hydrolase family 48 exoglucanases: insights from structure
    journal, November 2017

    • Brunecky, Roman; Alahuhta, Markus; Sammond, Deanne W.
    • Biotechnology for Biofuels, Vol. 10, Issue 1
    • DOI: 10.1186/s13068-017-0951-5

    Determination of the native features of the exoglucanase Cel48S from Clostridium thermocellum
    journal, January 2018

      Sort by:
      [ × clear filter / sort ]

      Figures / Tables found in this record:

      Table I (p. 25)table
      Table II (p. 26)table
      Table III (p. 27)table
      Figure 1 (p. 28)figure
      Figure 2 (p. 29)figure
      Figure 3 (p. 30)figure
      Figure 4 (p. 31)figure
      Figure 5 (p. 32)figure
      Figure 6 (p. 33)figure
        [ × clear filter / sort ]
        Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.

        Similar Records in DOE PAGES and OSTI.GOV collections: