1
|
Gomes M, Rondelez Y, Leibler L. Lessons from Biomass Valorization for Improving Plastic-Recycling Enzymes. Annu Rev Chem Biomol Eng 2022; 13:457-479. [PMID: 35378043 DOI: 10.1146/annurev-chembioeng-092120-091054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synthetic polymers such as plastics exhibit numerous advantageous properties that have made them essential components of our daily lives, with plastic production doubling every 15 years. The relatively low cost of petroleum-based polymers encourages their single use and overconsumption. Synthetic plastics are recalcitrant to biodegradation, and mismanagement of plastic waste leads to their accumulation in the ecosystem, resulting in a disastrous environmental footprint. Enzymes capable of depolymerizing plastics have been reported recently that may provide a starting point for eco-friendly plastic recycling routes. However, some questions remain about the mechanisms by which enzymes can digest insoluble solid substrates. We review the characterization and engineering of plastic-eating enzymes and provide some comparisons with the field of lignocellulosic biomass valorization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Margarida Gomes
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Yannick Rondelez
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Ludwik Leibler
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| |
Collapse
|
2
|
Kumar D, Murthy GS. Development and validation of a stochastic molecular model of cellulose hydrolysis by action of multiple cellulase enzymes. BIORESOUR BIOPROCESS 2017. [DOI: 10.1186/s40643-017-0184-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
3
|
Jeoh T, Cardona MJ, Karuna N, Mudinoor AR, Nill J. Mechanistic kinetic models of enzymatic cellulose hydrolysis-A review. Biotechnol Bioeng 2017; 114:1369-1385. [PMID: 28244589 DOI: 10.1002/bit.26277] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/10/2017] [Accepted: 02/22/2017] [Indexed: 01/05/2023]
Abstract
Bioconversion of lignocellulose forms the basis for renewable, advanced biofuels, and bioproducts. Mechanisms of hydrolysis of cellulose by cellulases have been actively studied for nearly 70 years with significant gains in understanding of the cellulolytic enzymes. Yet, a full mechanistic understanding of the hydrolysis reaction has been elusive. We present a review to highlight new insights gained since the most recent comprehensive review of cellulose hydrolysis kinetic models by Bansal et al. (2009) Biotechnol Adv 27:833-848. Recent models have taken a two-pronged approach to tackle the challenge of modeling the complex heterogeneous reaction-an enzyme-centric modeling approach centered on the molecularity of the cellulase-cellulose interactions to examine rate limiting elementary steps and a substrate-centric modeling approach aimed at capturing the limiting property of the insoluble cellulose substrate. Collectively, modeling results suggest that at the molecular-scale, how rapidly cellulases can bind productively (complexation) and release from cellulose (decomplexation) is limiting, while the overall hydrolysis rate is largely insensitive to the catalytic rate constant. The surface area of the insoluble substrate and the degrees of polymerization of the cellulose molecules in the reaction both limit initial hydrolysis rates only. Neither enzyme-centric models nor substrate-centric models can consistently capture hydrolysis time course at extended reaction times. Thus, questions of the true reaction limiting factors at extended reaction times and the role of complexation and decomplexation in rate limitation remain unresolved. Biotechnol. Bioeng. 2017;114: 1369-1385. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Tina Jeoh
- Biological and Agricultural Engineering, University of California, Davis, California
| | - Maria J Cardona
- Chemical Engineering, University of California, Davis, California.,Intel Corporation, Hillsboro, Oregon
| | - Nardrapee Karuna
- Biological and Agricultural Engineering, University of California, Davis, California.,Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Nakhon Pathom, Thailand
| | - Akshata R Mudinoor
- Biological and Agricultural Engineering, University of California, Davis, California
| | - Jennifer Nill
- Chemical Engineering, University of California, Davis, California
| |
Collapse
|
4
|
Karuna N, Jeoh T. The productive cellulase binding capacity of cellulosic substrates. Biotechnol Bioeng 2016; 114:533-542. [PMID: 27696345 DOI: 10.1002/bit.26193] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 01/18/2023]
Abstract
Cellulosic biomass is the most promising feedstock for renewable biofuel production; however, the mechanisms of the heterogeneous cellulose saccharification reaction are still unsolved. As cellulases need to bind isolated molecules of cellulose at the surface of insoluble cellulose fibrils or larger aggregated cellulose structures in order to hydrolyze glycosidic bonds, the "accessibility of cellulose to cellulases" is considered to be a reaction limiting property of cellulose. We have defined the accessibility of cellulose to cellulases as the productive binding capacity of cellulose, that is, the concentration of productive binding sites on cellulose that are accessible for binding and hydrolysis by cellulases. Productive cellulase binding to cellulose results in hydrolysis and can be quantified by measuring hydrolysis rates. In this study, we measured the productive Trichoderma reesei Cel7A (TrCel7A) binding capacity of five cellulosic substrates from different sources and processing histories. Swollen filter paper and bacterial cellulose had higher productive binding capacities of ∼6 µmol/g while filter paper, microcrystalline cellulose, and algal cellulose had lower productive binding capacities of ∼3 µmol/g. Swelling and regenerating filter paper using phosphoric acid increased the initial accessibility of the reducing ends to TrCel7A from 4 to 6 µmol/g. Moreover, this increase in initial productive binding capacity accounted in large part for the difference in the overall digestibility between filter paper and swollen filter paper. We further demonstrated that an understanding of how the productive binding capacity declines over the course of the hydrolysis reaction has the potential to predict overall saccharification time courses. Biotechnol. Bioeng. 2017;114: 533-542. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Nardrapee Karuna
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis 95616, California
| | - Tina Jeoh
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis 95616, California
| |
Collapse
|
5
|
Eibinger M, Zahel T, Ganner T, Plank H, Nidetzky B. Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:56. [PMID: 26962329 PMCID: PMC4784381 DOI: 10.1186/s13068-016-0463-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Enzymatic hydrolysis of cellulose involves the spatiotemporally correlated action of distinct polysaccharide chain cleaving activities confined to the surface of an insoluble substrate. Because cellulases differ in preference for attacking crystalline compared to amorphous cellulose, the spatial distribution of structural order across the cellulose surface imposes additional constraints on the dynamic interplay between the enzymes. Reconstruction of total system behavior from single-molecule activity parameters is a longstanding key goal in the field. RESULTS We have developed a stochastic, cellular automata-based modeling approach to describe degradation of cellulosic material by a cellulase system at single-molecule resolution. Substrate morphology was modeled to represent the amorphous and crystalline phases as well as the different spatial orientations of the polysaccharide chains. The enzyme system model consisted of an internally chain-cleaving endoglucanase (EG) as well as two processively acting, reducing and non-reducing chain end-cleaving cellobiohydrolases (CBHs). Substrate preference (amorphous: EG, CBH II; crystalline: CBH I) and characteristic frequencies for chain cleavage, processive movement, and dissociation were assigned from biochemical data. Once adsorbed, enzymes were allowed to reach surface-exposed substrate sites through "random-walk" lateral diffusion or processive motion. Simulations revealed that slow dissociation of processive enzymes at obstacles obstructing further movement resulted in local jamming of the cellulases, with consequent delay in the degradation of the surface area affected. Exploiting validation against evidence from atomic force microscopy imaging as a unique opportunity opened up by the modeling approach, we show that spatiotemporal characteristics of cellulose surface degradation by the system of synergizing cellulases were reproduced quantitatively at the nanometer resolution of the experimental data. This in turn gave useful prediction of the soluble sugar release rate. CONCLUSIONS Salient dynamic features of cellulose surface degradation by different cellulases acting in synergy were reproduced in simulations in good agreement with evidence from high-resolution visualization experiments. Due to the single-molecule resolution of the modeling approach, the utility of the presented model lies not only in predicting system behavior but also in elucidating inherently complex (e.g., stochastic) phenomena involved in enzymatic cellulose degradation. Thus, it creates synergy with experiment to advance the mechanistic understanding for improved application.
Collapse
Affiliation(s)
- Manuel Eibinger
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Thomas Zahel
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Thomas Ganner
- />Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- />Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- />Graz Centre for Electron Microscopy, Steyrergasse 17, 8010 Graz, Austria
| | - Bernd Nidetzky
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
- />Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| |
Collapse
|
6
|
Huron M, Hudebine D, Lopes Ferreira N, Lachenal D. Mechanistic modeling of enzymatic hydrolysis of cellulose integrating substrate morphology and cocktail composition. Biotechnol Bioeng 2015; 113:1011-23. [PMID: 26524470 DOI: 10.1002/bit.25873] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/20/2015] [Accepted: 10/26/2015] [Indexed: 11/12/2022]
Abstract
A mechanistic model of enzymatic hydrolysis taking into account the morphology of the cellulosic particles and its evolution with time was developed. The individual behavior of the main enzymes involved in the reaction (cellobiohydrolases, endoglucanases, and β-glucosidases), as well as synergy effects, were also included. A large panel of experimental tests was done to fit and validate the model. This database included different enzymes mixtures and operating conditions and allowed to determine and compare with accuracy the adsorption and kinetic parameters of the different enzymes. Model predictions on short hydrolysis times were very satisfactory. On longer times, a deactivation constant was added to represent the hydrolysis slowdown. The model also allowed to predict the impact of enzymes ratios and initial substrate parameters (chain length distribution, polymerization degree) on hydrolysis, and to follow the evolution of these parameters with time. This model revealed general trends on the impact of cellulose morphology on hydrolysis. It is a useful tool to better understand the mechanisms involved in enzymatic hydrolysis of cellulose and to determine optimal cellulolytic cocktails for process design.
Collapse
Affiliation(s)
- Maïté Huron
- IFP Energies Nouvelles, Rond-point de l'échangeur de Solaize - BP 3, 69360 Solaize, France
| | - Damien Hudebine
- IFP Energies Nouvelles, Rond-point de l'échangeur de Solaize - BP 3, 69360 Solaize, France.
| | | | - Dominique Lachenal
- Grenoble INP-Pagora, 461 rue de la Papeterie BP65, Saint Martin d'Hères Cedex, France
| |
Collapse
|
7
|
Nag A, Sprague MA, Griggs AJ, Lischeske JJ, Stickel JJ, Mittal A, Wang W, Johnson DK. Parameter determination and validation for a mechanistic model of the enzymatic saccharification of cellulose-Iβ. Biotechnol Prog 2015; 31:1237-48. [PMID: 26081044 DOI: 10.1002/btpr.2122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/08/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Ambarish Nag
- Computational Science Center; National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401
| | - Michael A. Sprague
- Computational Science Center; National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401
| | - Andrew J. Griggs
- National Bioenergy Center; National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401
| | - James J. Lischeske
- National Bioenergy Center; National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401
| | - Jonathan J. Stickel
- National Bioenergy Center; National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401
| | - Ashutosh Mittal
- Biosciences Center; National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401
| | - Wei Wang
- Biosciences Center; National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401
| | - David K. Johnson
- Biosciences Center; National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401
| |
Collapse
|
8
|
Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| |
Collapse
|
9
|
Zhang Y, Xu B, Zhou W. On a novel mechanistic model for simultaneous enzymatic hydrolysis of cellulose and hemicellulose considering morphology. Biotechnol Bioeng 2014; 111:1767-81. [DOI: 10.1002/bit.25244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 02/07/2014] [Accepted: 03/19/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Yang Zhang
- Department of Chemical Engineering; Michigan Technological University; Houghton Michigan 49931
| | - Bingqian Xu
- Engineering and Nanoscale Science and Engineering Center; University of Georgia; Athens Georgia 30602
| | - Wen Zhou
- Department of Chemical Engineering; Michigan Technological University; Houghton Michigan 49931
| |
Collapse
|
10
|
Eibinger M, Bubner P, Ganner T, Plank H, Nidetzky B. Surface structural dynamics of enzymatic cellulose degradation, revealed by combined kinetic and atomic force microscopy studies. FEBS J 2013; 281:275-90. [DOI: 10.1111/febs.12594] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/18/2013] [Accepted: 10/21/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Manuel Eibinger
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology; Austria
| | - Patricia Bubner
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology; Austria
| | - Thomas Ganner
- Institute for Electron Microscopy and Fine Structure Research; Graz University of Technology; Austria
- Center for Electron Microscopy; Graz University of Technology; Austria
| | - Harald Plank
- Institute for Electron Microscopy and Fine Structure Research; Graz University of Technology; Austria
- Center for Electron Microscopy; Graz University of Technology; Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology; Austria
| |
Collapse
|
11
|
Kumar D, Murthy GS. Stochastic molecular model of enzymatic hydrolysis of cellulose for ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:63. [PMID: 23638989 PMCID: PMC3664589 DOI: 10.1186/1754-6834-6-63] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 04/29/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND During cellulosic ethanol production, cellulose hydrolysis is achieved by synergistic action of cellulase enzyme complex consisting of multiple enzymes with different mode of actions. Enzymatic hydrolysis of cellulose is one of the bottlenecks in the commercialization of the process due to low hydrolysis rates and high cost of enzymes. A robust hydrolysis model that can predict hydrolysis profile under various scenarios can act as an important forecasting tool to improve the hydrolysis process. However, multiple factors affecting hydrolysis: cellulose structure and complex enzyme-substrate interactions during hydrolysis make it diffucult to develop mathematical kinetic models that can simulate hydrolysis in presence of multiple enzymes with high fidelity. In this study, a comprehensive hydrolysis model based on stochastic molecular modeling approch in which each hydrolysis event is translated into a discrete event is presented. The model captures the structural features of cellulose, enzyme properties (mode of actions, synergism, inhibition), and most importantly dynamic morphological changes in the substrate that directly affect the enzyme-substrate interactions during hydrolysis. RESULTS Cellulose was modeled as a group of microfibrils consisting of elementary fibrils bundles, where each elementary fibril was represented as a three dimensional matrix of glucose molecules. Hydrolysis of cellulose was simulated based on Monte Carlo simulation technique. Cellulose hydrolysis results predicted by model simulations agree well with the experimental data from literature. Coefficients of determination for model predictions and experimental values were in the range of 0.75 to 0.96 for Avicel hydrolysis by CBH I action. Model was able to simulate the synergistic action of multiple enzymes during hydrolysis. The model simulations captured the important experimental observations: effect of structural properties, enzyme inhibition and enzyme loadings on the hydrolysis and degree of synergism among enzymes. CONCLUSIONS The model was effective in capturing the dynamic behavior of cellulose hydrolysis during action of individual as well as multiple cellulases. Simulations were in qualitative and quantitative agreement with experimental data. Several experimentally observed phenomena were simulated without the need for any additional assumptions or parameter changes and confirmed the validity of using the stochastic molecular modeling approach to quantitatively and qualitatively describe the cellulose hydrolysis.
Collapse
Affiliation(s)
- Deepak Kumar
- Biological and Ecological Engineering, Oregon State University, Corvallis, USA
| | - Ganti S Murthy
- Biological and Ecological Engineering, Oregon State University, Corvallis, USA
| |
Collapse
|
12
|
Bubner P, Plank H, Nidetzky B. Visualizing cellulase activity. Biotechnol Bioeng 2013; 110:1529-49. [DOI: 10.1002/bit.24884] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/08/2013] [Accepted: 02/22/2013] [Indexed: 11/08/2022]
|
13
|
Ganner T, Bubner P, Eibinger M, Mayrhofer C, Plank H, Nidetzky B. Dissecting and reconstructing synergism: in situ visualization of cooperativity among cellulases. J Biol Chem 2012; 287:43215-22. [PMID: 23118223 PMCID: PMC3527909 DOI: 10.1074/jbc.m112.419952] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulose is the most abundant biopolymer and a major reservoir of fixed carbon on earth. Comprehension of the elusive mechanism of its enzymatic degradation represents a fundamental problem at the interface of biology, biotechnology, and materials science. The interdependence of cellulose disintegration and hydrolysis and the synergistic interplay among cellulases is yet poorly understood. Here we report evidence from in situ atomic force microscopy (AFM) that delineates degradation of a polymorphic cellulose substrate as a dynamic cycle of alternating exposure and removal of crystalline fibers. Direct observation shows that chain-end-cleaving cellobiohydrolases (CBH I, CBH II) and an internally chain-cleaving endoglucanase (EG), the major components of cellulase systems, take on distinct roles: EG and CBH II make the cellulose surface accessible for CBH I by removing amorphous-unordered substrate areas, thus exposing otherwise embedded crystalline-ordered nanofibrils of the cellulose. Subsequently, these fibrils are degraded efficiently by CBH I, thereby uncovering new amorphous areas. Without prior action of EG and CBH II, CBH I was poorly active on the cellulosic substrate. This leads to the conclusion that synergism among cellulases is morphology-dependent and governed by the cooperativity between enzymes degrading amorphous regions and those targeting primarily crystalline regions. The surface-disrupting activity of cellulases therefore strongly depends on mesoscopic structural features of the substrate: size and packing of crystalline fibers are key determinants of the overall efficiency of cellulose degradation.
Collapse
Affiliation(s)
- Thomas Ganner
- Institute for Electron Microscopy and Fine Structure Research, Graz University of Technology, Steyrergasse 17, A-8010 Graz, Austria
| | | | | | | | | | | |
Collapse
|
14
|
Asztalos A, Daniels M, Sethi A, Shen T, Langan P, Redondo A, Gnanakaran S. A coarse-grained model for synergistic action of multiple enzymes on cellulose. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:55. [PMID: 22853643 PMCID: PMC3475064 DOI: 10.1186/1754-6834-5-55] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 06/21/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. RESULTS We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. CONCLUSIONS Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails. This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.
Collapse
Affiliation(s)
- Andrea Asztalos
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Department of Physics, University of Notre Dame, Notre Dame, IN, 46556, USA
- Present Address: Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Marcus Daniels
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Anurag Sethi
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Tongye Shen
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Present Address: UT-ORNL, Center for Molecular Biophysics and Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Paul Langan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Present Address: Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Antonio Redondo
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | | |
Collapse
|
15
|
Marana SR. Structural and mechanistic fundamentals for designing of cellulases. Comput Struct Biotechnol J 2012; 2:e201209006. [PMID: 24688647 PMCID: PMC3962180 DOI: 10.5936/csbj.201209006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/20/2012] [Accepted: 09/23/2012] [Indexed: 11/22/2022] Open
Affiliation(s)
- Sandro R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, São Paulo, 05513-970, SP, Brazil
| |
Collapse
|
16
|
Griggs AJ, Stickel JJ, Lischeske JJ. A mechanistic model for enzymatic saccharification of cellulose using continuous distribution kinetics II: Cooperative enzyme action, solution kinetics, and product inhibition. Biotechnol Bioeng 2011; 109:676-85. [DOI: 10.1002/bit.23354] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 09/16/2011] [Accepted: 09/26/2011] [Indexed: 11/10/2022]
|
17
|
Griggs AJ, Stickel JJ, Lischeske JJ. A mechanistic model for enzymatic saccharification of cellulose using continuous distribution kinetics I: Depolymerization by EGI and CBHI. Biotechnol Bioeng 2011; 109:665-75. [DOI: 10.1002/bit.23355] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 09/16/2011] [Accepted: 09/26/2011] [Indexed: 11/07/2022]
|