Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes

Bu, Lintao; Nimlos, Mark R.; Shirts, Michael R.; Stahlberg, Jerry; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

doi:10.1074/jbc.M112.365510

Title: Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes

Journal Article · Fri Jul 13 00:00:00 EDT 2012 · Journal of Biological Chemistry

DOI:https://doi.org/10.1074/jbc.M112.365510· OSTI ID:1050115

Bu, Lintao; Nimlos, Mark R.; Shirts, Michael R.; Stahlberg, Jerry; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

Cellulases hydrolyze {beta}-1,4 glycosidic linkages in cellulose, which are among the most prevalent and stable bonds in Nature. Cellulases comprise many glycoside hydrolase families and exist as processive or nonprocessive enzymes. Product inhibition negatively impacts cellulase action, but experimental measurements of product-binding constants vary significantly, and there is little consensus on the importance of this phenomenon. To provide molecular level insights into cellulase product inhibition, we examine the impact of product binding on processive and nonprocessive cellulases by calculating the binding free energy of cellobiose to the product sites of catalytic domains of processive and nonprocessive enzymes from glycoside hydrolase families 6 and 7. The results suggest that cellobiose binds to processive cellulases much more strongly than nonprocessive cellulases. We also predict that the presence of a cellodextrin bound in the reactant site of the catalytic domain, which is present during enzymatic catalysis, has no effect on product binding in nonprocessive cellulases, whereas it significantly increases product binding to processive cellulases. This difference in product binding correlates with hydrogen bonding between the substrate-side ligand and the cellobiose product in processive cellulase tunnels and the additional stabilization from the longer tunnel-forming loops. The hydrogen bonds between the substrate- and product-side ligands are disrupted by water in nonprocessive cellulase clefts, and the lack of long tunnel-forming loops results in lower affinity of the product ligand. These findings provide new insights into the large discrepancies reported for binding constants for cellulases and suggest that product inhibition will vary significantly based on the amount of productive binding for processive cellulases on cellulose.

Cite

Export

Save

Research Organization:: National Renewable Energy Lab. (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office

DOE Contract Number:: AC36-08GO28308

OSTI ID:: 1050115

Report Number(s):: NREL/JA-5100-55136; JBCHA3; TRN: US201218%%483

Journal Information:: Journal of Biological Chemistry, Vol. 287, Issue 29; ISSN 0021-9258

Country of Publication:: United States

Language:: English

References (56)

Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production Himmel, M. E.; Ding, S.-Y.; Johnson, D. K. Science, Vol. 315, Issue 5813, p. 804-807 https://doi.org/10.1126/science.1137016	journal	February 2007
Microbial Cellulose Utilization: Fundamentals and Biotechnology Lynd, L. R.; Weimer, P. J.; van Zyl, W. H. Microbiology and Molecular Biology Reviews, Vol. 66, Issue 3, p. 506-577 https://doi.org/10.1128/MMBR.66.3.506-577.2002	journal	September 2002
Reactor design for minimizing product inhibition during enzymatic lignocellulose hydrolysis: I. Significance and mechanism of cellobiose and glucose inhibition on cellulolytic enzymes Andrić, Pavle; Meyer, Anne S.; Jensen, Peter A. Biotechnology Advances, Vol. 28, Issue 3, p. 308-324 https://doi.org/10.1016/j.biotechadv.2010.01.003	journal	May 2010
Modeling cellulase kinetics on lignocellulosic substrates Bansal, Prabuddha; Hall, Mélanie; Realff, Matthew J. Biotechnology Advances, Vol. 27, Issue 6 https://doi.org/10.1016/j.biotechadv.2009.06.005	journal	November 2009
Kinetic dynamics in heterogeneous enzymatic hydrolysis of cellulose: an overview, an experimental study and mathematical modelling Gan, Q.; Allen, S. J.; Taylor, G. Process Biochemistry, Vol. 38, Issue 7 https://doi.org/10.1016/S0032-9592(02)00220-0	journal	February 2003
Factors affecting the enzymatic hydrolysis of cellulose in batch and continuous reactors: Computer simulation and experiment Gusakov, Alexander V.; Sinitsyn, Arkady P.; Klyosov, Anatole A. Biotechnology and Bioengineering, Vol. 29, Issue 7 https://doi.org/10.1002/bit.260290715	journal	May 1987
Discrimination Among Eight Modified Michaelis-Menten Kinetics Models of Cellulose Hydrolysis With a Large Range of Substrate/Enzyme Ratios: Inhibition by Cellobiose Bezerra, Rui M. F.; Dias, Albino A. Applied Biochemistry and Biotechnology, Vol. 112, Issue 3 https://doi.org/10.1385/ABAB:112:3:173	journal	January 2004
Enzymatic kinetic of cellulose hydrolysis: Inhibition by ethanol and cellobiose Bezerra, Rui M. F.; Dias, Albino A. Applied Biochemistry and Biotechnology, Vol. 126, Issue 1 https://doi.org/10.1007/s12010-005-0005-5	journal	July 2005
Inhibition of the Trichoderma reesei cellulases by cellobiose is strongly dependent on the nature of the substrate : Product Inhibition in Cellulose Hydrolysis Gruno, Marju; Väljamäe, Priit; Pettersson, Göran Biotechnology and Bioengineering, Vol. 86, Issue 5 https://doi.org/10.1002/bit.10838	journal	March 2004
Bioconversion of Cellulose into Ethanol by Nonisothermal Simultaneous Saccharification and Fermentation Oh, Kyeong-Keun; Kim, Seung-Wook; Jeong, Yong-Seob Applied Biochemistry and Biotechnology, Vol. 89, Issue 1 https://doi.org/10.1385/ABAB:89:1:15	journal	January 2000
Study of the enzymatic hydrolysis of cellulose for production of fuel ethanol by the simultaneous saccharification and fermentation process Philippidis, George P.; Smith, Tammy K.; Wyman, Charles E. Biotechnology and Bioengineering, Vol. 41, Issue 9, p. 846-853 https://doi.org/10.1002/bit.260410903	journal	April 1993
Kinetics of the enzymatic hydrolysis of cellulose Wald, Stephen; Wilke, Charles R.; Blanch, Harvey W. Biotechnology and Bioengineering, Vol. 26, Issue 3 https://doi.org/10.1002/bit.260260305	journal	March 1984
Cellulase kinetics as a function of cellulose pretreatment Bommarius, Andreas S.; Katona, Adrian; Cheben, Sean E. Metabolic Engineering, Vol. 10, Issue 6 https://doi.org/10.1016/j.ymben.2008.06.008	journal	November 2008
Applications of computational science for understanding enzymatic deconstruction of cellulose Beckham, Gregg T.; Bomble, Yannick J.; Bayer, Edward A. Current Opinion in Biotechnology, Vol. 22, Issue 2 https://doi.org/10.1016/j.copbio.2010.11.005	journal	April 2011
Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals Chundawat, Shishir P. S.; Beckham, Gregg T.; Himmel, Michael E. Annual Review of Chemical and Biomolecular Engineering, Vol. 2, Issue 1, p. 121-145 https://doi.org/10.1146/annurev-chembioeng-061010-114205	journal	July 2011
The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein Beckham, Gregg T.; Bomble, Yannick J.; Matthews, James F. Biophysical Journal, Vol. 99, Issue 11 https://doi.org/10.1016/j.bpj.2010.10.032	journal	December 2010
Identification of Amino Acids Responsible for Processivity in a Family 1 Carbohydrate-Binding Module from a Fungal Cellulase Beckham, Gregg T.; Matthews, James F.; Bomble, Yannick J. The Journal of Physical Chemistry B, Vol. 114, Issue 3 https://doi.org/10.1021/jp908810a	journal	January 2010
Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation Payne, Christina M.; Bomble, Yannick J.; Taylor, Courtney B. Journal of Biological Chemistry, Vol. 286, Issue 47 https://doi.org/10.1074/jbc.M111.297713	journal	September 2011
Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-binding Module Taylor, Courtney B.; Talib, M. Faiz; McCabe, Clare Journal of Biological Chemistry, Vol. 287, Issue 5 https://doi.org/10.1074/jbc.M111.270389	journal	December 2011
Molecular-Level Origins of Biomass Recalcitrance: Decrystallization Free Energies for Four Common Cellulose Polymorphs Beckham, Gregg T.; Matthews, James F.; Peters, Baron The Journal of Physical Chemistry B, Vol. 115, Issue 14 https://doi.org/10.1021/jp1106394	journal	April 2011
Decrystallization of Oligosaccharides from the Cellulose Iβ Surface with Molecular Simulation Payne, Christina M.; Himmel, Michael E.; Crowley, Michael F. The Journal of Physical Chemistry Letters, Vol. 2, Issue 13 https://doi.org/10.1021/jz2005122	journal	June 2011
Probing Carbohydrate Product Expulsion from a Processive Cellulase with Multiple Absolute Binding Free Energy Methods Bu, Lintao; Beckham, Gregg T.; Shirts, Michael R. Journal of Biological Chemistry, Vol. 286, Issue 20 https://doi.org/10.1074/jbc.M110.212076	journal	March 2011
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics Cantarel, B. L.; Coutinho, P. M.; Rancurel, C. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn663	journal	January 2009
Evaluation of Minimal Trichoderma reesei Cellulase Mixtures on Differently Pretreated Barley Straw Substrates Rosgaard, L.; Pedersen, S.; Langston, J. Biotechnology Progress, Vol. 23, Issue 6 https://doi.org/10.1021/bp070329p	journal	December 2007
Imaging the Enzymatic Digestion of Bacterial Cellulose Ribbons Reveals the Endo Character of the Cellobiohydrolase Cel6A from Humicola insolens and Its Mode of Synergy with Cellobiohydrolase Cel7A Boisset, C.; Fraschini, C.; Schulein, M. Applied and Environmental Microbiology, Vol. 66, Issue 4 https://doi.org/10.1128/AEM.66.4.1444-1452.2000	journal	April 2000
Undirectional degradation of valonia cellulose microcrystals subjected to cellulase action Chanzy, Henri; Henrissat, Bernard FEBS Letters, Vol. 184, Issue 2 https://doi.org/10.1016/0014-5793(85)80623-2	journal	May 1985
The action of 1,4-β-D-glucan cellobiohydrolase on Valonia cellulose microcrystals: An electron microscopic study Chanzy, Henri; Henrissat, Bernard; Vuong, Roger FEBS Letters, Vol. 153, Issue 1 https://doi.org/10.1016/0014-5793(83)80129-X	journal	March 1983
Enzymatic properties of cellulases from Humicola insolens Schülein, Martin Journal of Biotechnology, Vol. 57, Issue 1-3, p. 71-81 https://doi.org/10.1016/S0168-1656(97)00090-4	journal	September 1997
Structure and function of Humicola insolens family 6 cellulases: structure of the endoglucanase, Cel6B, at 1.6 Å resolution Davies, Gideon J.; Brzozowski, A. Marek; Dauter, Miroslawa Biochemical Journal, Vol. 348, Issue 1 https://doi.org/10.1042/0264-6021:3480201	journal	May 2000
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^† MacKerell, A. D.; Bashford, D.; Bellott, M. The Journal of Physical Chemistry B, Vol. 102, Issue 18 https://doi.org/10.1021/jp973084f	journal	April 1998
Force Field Influence on the Observation of π-Helical Protein Structures in Molecular Dynamics Simulations Feig, Michael; MacKerell,, Alexander D.; Brooks, Charles L. The Journal of Physical Chemistry B, Vol. 107, Issue 12 https://doi.org/10.1021/jp027293y	journal	March 2003
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations Mackerell, Alexander D.; Feig, Michael; Brooks, Charles L. Journal of Computational Chemistry, Vol. 25, Issue 11 https://doi.org/10.1002/jcc.20065	journal	August 2004
Improved Treatment of the Protein Backbone in Empirical Force Fields MacKerell, Alexander D.; Feig, Michael; Brooks, Charles L. Journal of the American Chemical Society, Vol. 126, Issue 3 https://doi.org/10.1021/ja036959e	journal	January 2004
Additive empirical force field for hexopyranose monosaccharides Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh Journal of Computational Chemistry, Vol. 29, Issue 15 https://doi.org/10.1002/jcc.21004	journal	November 2008
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses Guvench, Olgun; Hatcher, Elizabeth; Venable, Richard M. Journal of Chemical Theory and Computation, Vol. 5, Issue 9 https://doi.org/10.1021/ct900242e	journal	August 2009
CHARMM-GUI: A web-based graphical user interface for CHARMM Jo, Sunhwan; Kim, Taehoon; Iyer, Vidyashankara G. Journal of Computational Chemistry, Vol. 29, Issue 11 https://doi.org/10.1002/jcc.20945	journal	March 2008
A smooth particle mesh Ewald method Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L. The Journal of Chemical Physics, Vol. 103, Issue 19 https://doi.org/10.1063/1.470117	journal	November 1995
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C. Journal of Computational Physics, Vol. 23, Issue 3 https://doi.org/10.1016/0021-9991(77)90098-5	journal	March 1977
Canonical dynamics: Equilibrium phase-space distributions Hoover, William G. Physical Review A, Vol. 31, Issue 3 https://doi.org/10.1103/PhysRevA.31.1695	journal	March 1985
A unified formulation of the constant temperature molecular dynamics methods Nosé, Shuichi The Journal of Chemical Physics, Vol. 81, Issue 1 https://doi.org/10.1063/1.447334	journal	July 1984
CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software Crowley, Michael F.; Williamson, Mark J.; Walker, Ross C. International Journal of Quantum Chemistry, Vol. 109, Issue 15 https://doi.org/10.1002/qua.22372	journal	December 2009
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
Fast-growth thermodynamic integration: Error and efficiency analysis Hummer, Gerhard The Journal of Chemical Physics, Vol. 114, Issue 17 https://doi.org/10.1063/1.1363668	journal	May 2001
Free energy reconstruction from nonequilibrium single-molecule pulling experiments Hummer, G.; Szabo, A. Proceedings of the National Academy of Sciences, Vol. 98, Issue 7 https://doi.org/10.1073/pnas.071034098	journal	March 2001
Nonequilibrium Equality for Free Energy Differences Jarzynski, C. Physical Review Letters, Vol. 78, Issue 14 https://doi.org/10.1103/PhysRevLett.78.2690	journal	April 1997
Bootstrap Methods for Standard Errors, Confidence Intervals, and Other Measures of Statistical Accuracy Efron, B.; Tibshirani, R. Statistical Science, Vol. 1, Issue 1 https://doi.org/10.1214/ss/1177013815	journal	February 1986
Structural Basis for Ligand Binding and Processivity in Cellobiohydrolase Cel6A from Humicola insolens Varrot, Annabelle; Frandsen, Torben P.; von Ossowski, Ingemar Structure, Vol. 11, Issue 7 https://doi.org/10.1016/S0969-2126(03)00124-2	journal	July 2003
Distortion of a cellobio-derived isofagomine highlights the potential conformational itinerary of inverting β-glucosidasesElectronic supplementary information (ESI) available: details of data and structure quality for complex of cel6A with 1. See http://www.rsc.org/suppdata/cc/b3/b301592k/ Varrot, Annabelle; Macdonald, James; Stick, Robert V. Chemical Communications, Issue 8 https://doi.org/10.1039/b301592k	journal	March 2003
Structural Changes of the Active Site Tunnel of Humicola insolens Cellobiohydrolase, Cel6A, upon Oligosaccharide Binding ^† ^, ^‡ Varrot, Annabelle; Schülein, Martin; Davies, Gideon J. Biochemistry, Vol. 38, Issue 28 https://doi.org/10.1021/bi9903998	journal	July 1999
Determination of Product Inhibition of CBH1, CBH2, and EG1 Using a Novel Cellulase Activity Assay Du, Faye; Wolger, Erin; Wallace, Louise Applied Biochemistry and Biotechnology, Vol. 161, Issue 1-8 https://doi.org/10.1007/s12010-009-8796-4	journal	October 2009
Studies of the cellulolytic system of Trichoderma reesei QM 9414. Binding of small ligands to the 1,4-beta-glucan cellobiohydrolase II and influence of glucose on their affinity Tilbeurgh, Herman; Loontiens, Frank G.; Engelborgs, Yves European Journal of Biochemistry, Vol. 184, Issue 3 https://doi.org/10.1111/j.1432-1033.1989.tb15049.x	journal	October 1989
Fungal cellulase systems. Comparison of the specificities of the cellobiohydrolases isolated from Penicillium pinophilum and Trichoderma reesei Claeyssens, M.; Van Tilbeurgh, H.; Tomme, P. Biochemical Journal, Vol. 261, Issue 3 https://doi.org/10.1042/bj2610819	journal	August 1989
Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors: Cel7D/saccharide complex structures Ubhayasekera, Wimal; Muñoz, Inés G.; Vasella, Andrea FEBS Journal, Vol. 272, Issue 8 https://doi.org/10.1111/j.1742-4658.2005.04625.x	journal	March 2005
Traffic Jams Reduce Hydrolytic Efficiency of Cellulase on Cellulose Surface Igarashi, K.; Uchihashi, T.; Koivula, A. Science, Vol. 333, Issue 6047 https://doi.org/10.1126/science.1208386	journal	September 2011
Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis Jalak, Jürgen; Väljamäe, Priit Biotechnology and Bioengineering, Vol. 106, Issue 6 https://doi.org/10.1002/bit.22779	journal	April 2010

Similar Records

Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases

Journal Article · Thu May 21 00:00:00 EDT 2015 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry · OSTI ID:1050115

Vermaas, Josh V.; Crowley, Michael F.; Beckham, Gregg T.; +1 more

Single-molecule tracking reveals dual front door/back door inhibition of Cel7A cellulase by its product cellobiose

Journal Article · Mon Apr 22 00:00:00 EDT 2024 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1050115

Nong, Daguan; Haviland, Zachary K.; Zexer, Nerya; +5 more

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

Journal Article · Mon Feb 01 00:00:00 EST 2016 · Proteins · OSTI ID:1050115

Chen, Mo; Bu, Lintao; Alahuhta, Markus; +7 more

Related Subjects

09 BIOMASS FUELS
59 BASIC BIOLOGICAL SCIENCES
AFFINITY
BONDING
CATALYSIS
CELLOBIOSE
CELLULASE
CELLULOSE
COMPUTERS
ENZYMES
FREE ENERGY
GLYCOSIDES
HYDROGEN
HYDROLASES
SIMULATION
STABILIZATION
THERMODYNAMICS
WATER
cellulases
cellobiose
high product yields
enzymatic hydrolysis

Title: Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes

Citation Formats

References (56)

Similar Records

Related Subjects