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Ma B, Wang R, Chen B, Liu W, Zhou S, Li X, Gong J, Shang S, Li Y, Xu D, Tan Z. Insights into the effect of protein glycosylation on carbohydrate substrate binding. Int J Biol Macromol 2023; 235:123833. [PMID: 36870654 DOI: 10.1016/j.ijbiomac.2023.123833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
The role of glycosylation in the binding of glycoproteins to carbohydrate substrates has not been well understood. The present study addresses this knowledge gap by elucidating the links between the glycosylation patterns of a model glycoprotein, a Family 1 carbohydrate-binding module (TrCBM1), and the thermodynamic and structural properties of its binding to different carbohydrate substrates using isothermal titration calorimetry and computational simulation. The variations in glycosylation patterns cause a gradual transition of the binding to soluble cellohexaose from an entropy-driven process to an enthalpy-driven one, a trend closely correlated with the glycan-induced shift of the predominant binding force from hydrophobic interactions to hydrogen bonding. However, when binding to a large surface of solid cellulose, glycans on TrCBM1 have a more dispersed distribution and thus have less adverse impact on the hydrophobic interaction forces, leading to overall improved binding. Unexpectedly, our simulation results also suggest an evolutionary role of O-mannosylation in transforming the substrate binding features of TrCBM1 from those of type A CBMs to those of type B CBMs. Taken together, these findings provide new fundamental insights into the molecular basis of the role of glycosylation in protein-carbohydrate interactions and are expected to better facilitate further studies in this area.
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Affiliation(s)
- Bo Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Sichuan 610064, China
| | - Baoquan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenqiang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Sen Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xue Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinyuan Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shiying Shang
- Center of Pharmaceutical Technology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yaohao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Sichuan 610064, China.
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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2
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Sprenger K, Roeters SJ, Mauri S, Mertig R, Nishiyama Y, Pfaendtner J, Weidner T. Direct Evidence for Aligned Binding of Cellulase Enzymes to Cellulose Surfaces. J Phys Chem Lett 2021; 12:10684-10688. [PMID: 34709817 DOI: 10.1021/acs.jpclett.1c02757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The conversion of biomass into green fuels and chemicals is of great societal interest. Engineers have been designing new cellulase enzymes for the breakdown of otherwise insoluble cellulose materials. A barrier to the rational design of new enzymes has been our lack of a molecular picture of how cellulase binding occurs. A critical factor is the attachment via the enzyme's carbohydrate binding module (CBM). To elucidate the structural and mechanistic details of cellulase adsorption, we have combined experimental data from sum frequency generation spectroscopy with molecular dynamics simulations to probe the equilibrium structure and surface alignment of a 14-residue peptide mimicking the CBM. The data show that binding is driven by hydrogen bonding and that tyrosine side chains within the CBM align the cellulase with the registry of the cellulose surface. Such an alignment is favorable for the translocation and effective cellulose breakdown and is therefore likely an important parameter for the design of novel enzymes.
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Affiliation(s)
- Kayla Sprenger
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Steven J Roeters
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Sergio Mauri
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Rolf Mertig
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98192, United States
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98192, United States
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3
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Akram F, Akram R, Ikram Ul Haq, Nawaz A, Jabbar Z, Ahmed Z. Biotechnological Eminence of Chitinases: A Focus on Thermophilic Enzyme Sources, Production Strategies and Prominent Applications. Protein Pept Lett 2021; 28:1009-1022. [PMID: 33602064 DOI: 10.2174/0929866528666210218215359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/24/2020] [Accepted: 01/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Chitin, the second most abundant polysaccharide in nature, is a constantly valuable and renewable raw material after cellulose. Due to advancement in technology, industrial interest has grown to take advantage of the chitin. OBJECTIVE Now, biomass is being treated with diverse microbial enzymes or cells for the production of desired products under best industrial conditions. Glycosidic bonds in chitin structure are degraded by chitinase enzymes, which are characterized into number of glycoside hydrolase (GHs) families. METHODS Thermophilic microorganisms are remarkable sources of industrially important thermostable enzymes, having ability to survive harsh industrial processing conditions. Thermostable chitinases have an edge over mesophilic chitinases as they can hydrolyse the substrate at relatively high temperatures and exhibit decreased viscosity, significantly reduced contamination risk, thermal and chemical stability and increased solubility. Various methods are employed to purify the enzyme and increase its yield by optimizing various parameters such as temperature, pH, agitation, and by investigating the effect of different chemicals and metal ions etc. Results: Thermostable chitinase enzymes show high specific activity at elevated temperature which distinguish them from mesophiles. Genetic engineering can be used for further improvement of natural chitinases, and unlimited potential for the production of thermophilic chitinases has been highlighted due to advancement in synthetic biological techniques. Thermostable chitinases are then used in different fields such as bioremediation, medicine, agriculture and pharmaceuticals. CONCLUSION This review will provide information about chitinases, biotechnological potential of thermostable enzyme and the methods by which they are being produced and optimized for several industrial applications. Some of the applications of thermostable chitinases have also been briefly described.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Rabia Akram
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Ali Nawaz
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Zuriat Jabbar
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
| | - Zeeshan Ahmed
- Institute of Industrial Biotechnology, GC University, Lahore-54000, . Pakistan
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4
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Wu Z, Beltran-Villegas DJ, Jayaraman A. Development of a New Coarse-Grained Model to Simulate Assembly of Cellulose Chains Due to Hydrogen Bonding. J Chem Theory Comput 2020; 16:4599-4614. [DOI: 10.1021/acs.jctc.0c00225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Daniel J. Beltran-Villegas
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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5
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Baig KS. Interaction of enzymes with lignocellulosic materials: causes, mechanism and influencing factors. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00310-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AbstractFor the production of biofuel (bioethanol), enzymatic adsorption onto a lignocellulosic biomass surface is a prior condition for the enzymatic hydrolysis process to occur. Lignocellulosic substances are mainly composed of cellulose, hemicellulose and lignin. The polysaccharide matrix (cellulose and hemicellulose) is capable of producing bioethanol. Therefore, lignin is removed or its concentration is reduced from the adsorption substrates by pretreatments. Selected enzymes are used for the production of reducing sugars from cellulosic materials, which in turn are converted to bioethanol. Adsorption of enzymes onto the substrate surface is a complicated process. A large number of research have been performed on the adsorption process, but little has been done to understand the mechanism of adsorption process. This article reviews the mechanisms of adsorption of enzymes onto the biomass surfaces. A conceptual adsorption mechanism is presented which will fill the gaps in literature and help researchers and industry to use adsorption more efficiently. The process of enzymatic adsorption starts with the reciprocal interplay of enzymes and substrates and ends with the establishment of molecular and cellular binding. The kinetics of an enzymatic reaction is almost the same as that of a characteristic chemical catalytic reaction. The influencing factors discussed in detail are: surface characteristics of the participating materials, the environmental factors, such as the associated flow conditions, temperature, concentration, etc. Pretreatment of lignocellulosic materials and optimum range of shear force and temperature for getting better results of adsorption are recommended.
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6
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Wang R, Xu D. Molecular dynamics investigations of oligosaccharides recognized by family 16 and 22 carbohydrate binding modules. Phys Chem Chem Phys 2019; 21:21485-21496. [PMID: 31535114 DOI: 10.1039/c9cp04673a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As a non-catalytic domain, carbohydrate binding modules (CBMs) are often considered to play some key roles in the degradation and recognition of polysaccharides catalyzed by cellulases. In this work, we investigated the recognition dynamics of cello- or xylo-saccharides by two typical CBMs (CBM16-1 and CBM22-2), which are grouped into Type B CBMs. By combining extensive molecular dynamics, principle component analysis, and binding free energy calculations, we constructed several complex models of the two CBMs in both complex cello- and xylo-oligosaccharides. The corresponding substrate recognition affinity and critical residues having significant contributions were systematically investigated. The residues containing aromatic side chain groups were shown to contribute significantly to substrate binding. The calculated binding free energies were in fairly good agreement with the experimental measurements with the absolute mean error of 0.69 kcal mol-1. The overall electrostatic interactions were shown to have negative effects on substrate recognition. Further metadynamics simulations revealed the substrate dissociation process.
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Affiliation(s)
- Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China. and Research Center for Materials Genome Engineering, Sichuan University, Chengdu, Sichuan 610065, P. R. China
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7
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Weber J, Petrović D, Strodel B, Smits SHJ, Kolkenbrock S, Leggewie C, Jaeger KE. Interaction of carbohydrate-binding modules with poly(ethylene terephthalate). Appl Microbiol Biotechnol 2019; 103:4801-4812. [PMID: 30993383 PMCID: PMC6536475 DOI: 10.1007/s00253-019-09760-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 01/26/2023]
Abstract
Poly(ethylene terephthalate) (PET) is one of the most widely applied synthetic polymers, but its hydrophobicity is challenging for many industrial applications. Biotechnological modification of PET surface can be achieved by PET hydrolyzing cutinases. In order to increase the adsorption towards their unnatural substrate, the enzymes are fused to carbohydrate-binding modules (CBMs) leading to enhanced activity. In this study, we identified novel PET binding CBMs and characterized the CBM-PET interplay. We developed a semi-quantitative method to detect CBMs bound to PET films. Screening of eight CBMs from diverse families for PET binding revealed one CBM that possesses a high affinity towards PET. Molecular dynamics (MD) simulations of the CBM-PET interface revealed tryptophan residues forming an aromatic triad on the peptide surface. Their interaction with phenyl rings of PET is stabilized by additional hydrogen bonds formed between amino acids close to the aromatic triad. Furthermore, the ratio of hydrophobic to polar contacts at the interface was identified as an important feature determining the strength of PET binding of CBMs. The interaction of CBM tryptophan residues with PET was confirmed experimentally by tryptophan quenching measurements after addition of PET nanoparticles to CBM. Our findings are useful for engineering PET hydrolyzing enzymes and may also find applications in functionalization of PET.
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Affiliation(s)
- Joanna Weber
- evoxx technologies GmbH, Alfred-Nobel-Str. 10, D-40789, Monheim am Rhein, Germany
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany
- Bayer AG, Friedrich-Ebert-Straße 475, 42117, Wuppertal, Germany
| | - Dušan Petrović
- Institute of Complex Systems ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstraße 1, D-40225, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| | - Stephan Kolkenbrock
- evoxx technologies GmbH, Alfred-Nobel-Str. 10, D-40789, Monheim am Rhein, Germany
- Altona Diagnostics GmbH, Mörkenstr. 12, 22767, Hamburg, Germany
| | - Christian Leggewie
- evoxx technologies GmbH, Alfred-Nobel-Str. 10, D-40789, Monheim am Rhein, Germany.
- Erber Enzymes GmbH, Otto-Hahn-Straße 15, 44227, Dortmund, Germany.
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany.
- Institute of Molecular Enzyme Technology, Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany.
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8
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Carbohydrate binding modules enhance cellulose enzymatic hydrolysis by increasing access of cellulases to the substrate. Carbohydr Polym 2019; 211:57-68. [DOI: 10.1016/j.carbpol.2019.01.108] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 11/22/2022]
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9
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Li P, Zhang C, Xu D. Molecular dynamics investigations of cello-oligosaccharide recognition by Cel9G-CBM3c from Clostridium cellulovorans. Phys Chem Chem Phys 2018; 20:5235-5245. [PMID: 29399685 DOI: 10.1039/c7cp07175b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The processive mechanism of cellulases against cellulose represents one of the key mechanisms in the conversion of biomass. A reliable model of substrate binding in a multidomain cellulase is a prerequisite for fully understanding this mechanism. In this study, the specificity of the recognition of the polysaccharide by the multidomain endoglucanase Cel9G from Clostridium cellulovorans was investigated by molecular dynamics simulations. Aromatic ring-containing residues were found to be critical for stabilizing the substrate. The calculated subtotal contributions of polar residues close to the active site, e.g., D58, E244, R315 and D420, also have some critical functions in substrate binding. Unlike other members of the carbohydrate-binding module family, CBM3c alone is shown not to bind cellulose very well, which is also consistent with experimental conclusions.
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Affiliation(s)
- Penghui Li
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
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10
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Wang Z, Jönsson LJ. Comparison of catalytically non-productive adsorption of fungal proteins to lignins and pseudo-lignin using isobaric mass tagging. BIORESOURCE TECHNOLOGY 2018; 268:393-401. [PMID: 30099290 DOI: 10.1016/j.biortech.2018.07.149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/28/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Catalytically non-productive adsorption of fungal enzymes to pseudo-lignin (PL) was compared to adsorption to lignin preparations derived from different sources (SL, spruce; BL, birch; OL, beech) using different methods [steam pretreatment/enzymatic saccharification (SL, BL) and organosolv processing (OL)]. The protein adsorption to the SL was more extensive than the adsorption to the hardwood lignins, which was relatively similar to the adsorption to the PL. The adsorption patterns of 13 individual proteins were studied using isobaric mass tagging with TMTsixplex reagent and LC-MS/MS analysis. The results suggest that, on an average, adsorption of proteins equipped with carbohydrate-binding modules, such as the cellulases CBHI, EGII, and EGIV, was less dependent on the quality of the lignin/PL than adsorption of other proteins, such as β-Xyl, Xyn-1, and Xyn-2, which are involved in xylan degradation.
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Affiliation(s)
- Zhao Wang
- Department of Chemistry, KBC Chemical-Biological Centre, Umeå University, SE-901 87 Umeå, Sweden
| | - Leif J Jönsson
- Department of Chemistry, KBC Chemical-Biological Centre, Umeå University, SE-901 87 Umeå, Sweden.
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11
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Basit A, Liu J, Rahim K, Jiang W, Lou H. Thermophilic xylanases: from bench to bottle. Crit Rev Biotechnol 2018; 38:989-1002. [DOI: 10.1080/07388551.2018.1425662] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Abdul Basit
- Beijing Advanced Innovation Center for Food Nutrition and Human Health and State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Junquan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health and State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kashif Rahim
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wei Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health and State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huiqiang Lou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health and State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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12
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Jaiyong P, Bryce RA. Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet. Phys Chem Chem Phys 2017; 19:15346-15355. [DOI: 10.1039/c7cp02160g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adsorption of carbohydrates on graphene has the potential to improve graphene dispersibility in water. Here we assess the ability of DFTB-based and NDDO-based quantum chemical methods to model β-cyclodextrin conformations and interactions with graphene.
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Affiliation(s)
- Panichakorn Jaiyong
- Division of Pharmacy and Optometry
- School of Health Sciences
- Faculty of Biology
- Medicine and Health
- University of Manchester
| | - Richard A. Bryce
- Division of Pharmacy and Optometry
- School of Health Sciences
- Faculty of Biology
- Medicine and Health
- University of Manchester
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13
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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
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14
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Carbohydrate-binding modules of fungal cellulases: occurrence in nature, function, and relevance in industrial biomass conversion. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:103-65. [PMID: 24767427 DOI: 10.1016/b978-0-12-800260-5.00004-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this review, the present knowledge on the occurrence of cellulases, with a special emphasis on the presence of carbohydrate-binding modules (CBMs) in various fungal strains, has been summarized. The importance of efficient fungal cellulases is growing due to their potential uses in biorefinery processes where lignocellulosic biomasses are converted to platform sugars and further to biofuels and chemicals. Most secreted cellulases studied in detail have a bimodular structure containing an active core domain attached to a CBM. CBMs are traditionally been considered as essential parts in cellulases, especially in cellobiohydrolases. However, presently available genome data indicate that many cellulases lack the binding domains in cellulose-degrading organisms. Recent data also demonstrate that CBMs are not necessary for the action of cellulases and they solely increase the concentration of enzymes on the substrate surfaces. On the other hand, in practical industrial processes where high substrate concentrations with low amounts of water are employed, the enzymes have been shown to act equally efficiently with and without CBM. Furthermore, available kinetic data show that enzymes without CBMs can desorb more readily from the often lignaceous substrates, that is, they are not stuck on the substrates and are thus available for new actions. In this review, the available data on the natural habitats of different wood-degrading organisms (with emphasis on the amount of water present during wood degradation) and occurrence of cellulose-binding domains in their genome have been assessed in order to identify evolutionary advantages for the development of CBM-less cellulases in nature.
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15
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Zhang M, Wang B, Xu B. Measurements of single molecular affinity interactions between carbohydrate-binding modules and crystalline cellulose fibrils. Phys Chem Chem Phys 2013; 15:6508-15. [PMID: 23532050 DOI: 10.1039/c3cp51072g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Combining atomic force microscopy (AFM) recognition imaging and single molecule dynamic force spectroscopy (SMDFS), we studied the single molecule affinity interactions between the carbohydrate-binding module (CBM) and plant cell wall cellulose using the CBM3a (from Clostridium thermocellum) and CBM2a (from Cellvibrio japonicus) functionalized AFM tips. The binding efficiencies of the CBMs to the cellulose were determined by the binding areas on the crystalline cellulose fibrils surface using the recognition imaging. Several dynamic and kinetic parameters, such as the reconstructed free energy change, energy barrier and bond lifetime constant, were also obtained based on the measured single molecule unbinding forces, which are used to illuminate the affinity of the CBMs binding to the natural and single cellulose surface from a totally different aspect. It was found that CBM3a has a little higher binding efficiency and affinity than CBM2a to both natural and extracted cellulose surfaces and both the CBMs have higher affinities to the natural cell wall cellulose compared to the extracted single cellulose. The in-depth understanding of the binding mechanisms of the CBM-cellulose interactions of this study may pave the way for more efficient plant cell wall degradation and eventually facilitate biofuel production.
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Affiliation(s)
- Mengmeng Zhang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, GA 30602, USA
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16
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Zhao L, Meng K, Bai Y, Shi P, Huang H, Luo H, Wang Y, Yang P, Song W, Yao B. Two family 11 xylanases from Achaetomium sp. Xz-8 with high catalytic efficiency and application potentials in the brewing industry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:6880-6889. [PMID: 23790084 DOI: 10.1021/jf4001296] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This study identified two family-11 xylanase genes (xynC81 and xynC83) in Achaetomium sp. Xz-8, a thermophilic strain from a desert area with substantial xylanase activity, and successfully expressed them in Pichia pastoris . Their deduced amino acid sequences showed the highest identity of ≤90% to known fungal xylanases and of ≤62% with each other. The purified recombinant xylanases showed optimal activities at pH 5.5 and 60-65 °C and exhibited stability over pH 5.0-10.0 and temperatures at 55 °C and below. XynC81 had high catalytic efficiency (6082 mL/s/mg), and XynC83 was favorable for xylooligosaccharide production. Under simulated mashing conditions, combination of XynC83 and a commercial β-glucanase improved the filtration rate by 34.76%, which is much better than that of Novozymes Ultraflo (20.71%). XynC81 and XynC83 had a synergistic effect on viscosity reduction (7.08%), which is comparable with that of Ultraflo (8.47%). Thus, XynC81 and XynC83 represent good candidates for application in the brewing industry.
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Affiliation(s)
- Liang Zhao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
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17
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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]
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18
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Zhao Z, Shklyaev OE, Nili A, Mohamed MNA, Kubicki JD, Crespi VH, Zhong L. Cellulose Microfibril Twist, Mechanics, and Implication for Cellulose Biosynthesis. J Phys Chem A 2013; 117:2580-9. [DOI: 10.1021/jp3089929] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhen Zhao
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
| | - Oleg E. Shklyaev
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Departments
of Physics, Chemistry, and Materials Science and Engineering, The Pennsylvania State University, State College, Pennsylvania
16801, United States
| | - Abdolmajid Nili
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Departments
of Physics, Chemistry, and Materials Science and Engineering, The Pennsylvania State University, State College, Pennsylvania
16801, United States
| | - Mohamed Naseer Ali Mohamed
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Department of Geosciences, Pennsylvania State University, State College, Pennsylvania 16801,
United States
| | - James D. Kubicki
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Department of Geosciences, Pennsylvania State University, State College, Pennsylvania 16801,
United States
| | - Vincent H. Crespi
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Departments
of Physics, Chemistry, and Materials Science and Engineering, The Pennsylvania State University, State College, Pennsylvania
16801, United States
| | - Linghao Zhong
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Department
of Chemistry, Pennsylvania State University, Mont Alto, Pennsylvania 17237, United States
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19
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Chauve M, Barre L, Tapin-Lingua S, Silva Perez DD, Decottignies D, Perez S, Ferreira NL. Evolution and impact of cellulose architecture during enzymatic hydrolysis by fungal cellulases. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.412146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Introduction of a unique tryptophan residue into various positions of Bacillus licheniformis DnaK. Int J Biol Macromol 2012; 52:231-43. [PMID: 23085489 DOI: 10.1016/j.ijbiomac.2012.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/08/2012] [Accepted: 10/10/2012] [Indexed: 11/22/2022]
Abstract
Site-directed mutagenesis together with biochemical and biophysical techniques were used to probe effects of single-tryptophan-incorporated mutations on a bacterial molecular chaperone, Bacillus licheniformis DnaK (BlDnaK). Specifically, five phenylalanine residues (Phe(120), Phe(174), Phe(186), Phe(378) and Phe(396)) of BlDnaK were individually replaced by single tryptophans, thus creating site-specific probes for the fluorescence analysis of the protein. The steady-state ATPase activity for BlDnaK, F120W, F174W, F186W, F378W, and F396W was determined to be 76.01, 52.82, 25.32, 53.31, 58.84, and 47.53 nmol Pi/min/mg, respectively. Complementation test revealed that the single mutation at codons 120, 186, and 378 of the dnaK gene still allowed an Escherichia coli dnaK756-Ts strain to grow at a stringent temperature of 44°C. Simultaneous addition of co-chaperones and NR-peptide did not synergistically stimulate the ATPase activity of F174W and F396W, and these two proteins were unable to assist the refolding of GdnHCl-denatured luciferase. The heat-induced denaturation of all variants could be fitted adequately to a three-state model, in agreement with the observation for the wild-type protein. By CD spectral analysis, GdnHCl-induced unfolding transition for BlDnaK was 1.51 M corresponding to ΔG(N-U) of 1.69 kcal/mol; however, the transitions for mutant proteins were 1.07-1.55 M equivalent to ΔG(N-U) of 0.94-2.93 kcal/mol. The emission maximum of single-tryptophan-incorporated variants was in the range of 333.2-335.8 nm. Acrylamide quenching analysis showed that the mutant proteins had a dynamic quenching constant of 3.0-4.2 M(-1). Taken together, these results suggest that the molecular properties of BlDnaK have been significantly changed upon the individual replacement of selected phenylalanine residues by tryptophan.
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21
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Chi MC, Chen YY, Lo HF, Lin LL. Experimental evidence for the involvement of amino acid residue Glu398 in the autocatalytic processing of Bacillus licheniformis γ-glutamyltranspeptidase. FEBS Open Bio 2012; 2:298-304. [PMID: 23772362 PMCID: PMC3678132 DOI: 10.1016/j.fob.2012.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 09/25/2012] [Accepted: 09/25/2012] [Indexed: 11/18/2022] Open
Abstract
The role of glutamate 398 in the autocatalytic processing of Bacillus licheniformis γ-glutamyltranspeptidase (BlGGT) was explored by site-directed mutagenesis. This glutamate was substituted by either alanine, aspartate, arginine or glutamine and the expressed mutant enzymes were purified to apparent homogeneity with metal-affinity chromatography. SDS–PAGE analysis showed that E398A, E398D and E398K were unable to process themselves into a large and a small subunit. However, E398Q was not only able to process itself, but also had a catalytic activity comparable to that of BlGGT. As compared with the wild-type enzyme, no significant change in circular dichroism spectra was observed for the mutant proteins. Thermal unfolding of BlGGT, E398A, E398D, E398K and E398Q followed the two-state unfolding process with a transition point (Tm) of 47.7–69.4 °C. Tryptophan fluorescence spectra of the mutant enzymes were different from the wild-type protein in terms of fluorescence intensity. Native BlGGT started to unfold beyond ∼1.92 M guanidine hydrochloride (GdnHCl) and reached an unfolded intermediate, [GdnHCl]0.5, N–U, at 3.07 M equivalent to free energy change (ΔGN−UH2O) of 14.53 kcal/mol for the N → U process, whereas the denaturation midpoints for the mutant enzymes were 1.31–2.99 M equivalent to ΔGN−UH2O of 3.29–12.05 kcal/mol. Taken together, these results strongly suggest that the explored glutamate residue is indeed important for the autocatalytic processing of BlGGT.
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Affiliation(s)
- Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, Taiwan
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22
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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.
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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
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23
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Mori T, Chikayama E, Tsuboi Y, Ishida N, Shisa N, Noritake Y, Moriya S, Kikuchi J. Exploring the conformational space of amorphous cellulose using NMR chemical shifts. Carbohydr Polym 2012; 90:1197-203. [PMID: 22939331 DOI: 10.1016/j.carbpol.2012.06.027] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 06/06/2012] [Accepted: 06/11/2012] [Indexed: 12/20/2022]
Abstract
(13)C-labeled amorphous cellulose and (13)C NMR chemical shifts by 2D (13)C-(13)C correlation spectroscopy were obtained in the regenerated solid-state from ionic liquids. On the basis of the assigned chemical shifts, combined with information from molecular dynamics and quantum chemistry computer simulations a twisted structure for amorphous cellulose is proposed exposing more hydrophilic surface than that of extended crystalline cellulose.
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Affiliation(s)
- Tetsuya Mori
- Biotechnology Laboratory, Toyota Central R&D Laboratories, Inc., 41-1, Nagakute 480-1192, Japan.
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24
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Segato F, Damasio ARL, Gonçalves TA, Murakami MT, Squina FM, Polizeli M, Mort AJ, Prade RA. Two structurally discrete GH7-cellobiohydrolases compete for the same cellulosic substrate fiber. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:21. [PMID: 22494694 PMCID: PMC3431977 DOI: 10.1186/1754-6834-5-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 03/30/2012] [Indexed: 05/14/2023]
Abstract
BACKGROUND Cellulose consisting of arrays of linear beta-1,4 linked glucans, is the most abundant carbon-containing polymer present in biomass. Recalcitrance of crystalline cellulose towards enzymatic degradation is widely reported and is the result of intra- and inter-molecular hydrogen bonds within and among the linear glucans. Cellobiohydrolases are enzymes that attack crystalline cellulose. Here we report on two forms of glycosyl hydrolase family 7 cellobiohydrolases common to all Aspergillii that attack Avicel, cotton cellulose and other forms of crystalline cellulose. RESULTS Cellobiohydrolases Cbh1 and CelD have similar catalytic domains but only Cbh1 contains a carbohydrate-binding domain (CBD) that binds to cellulose. Structural superpositioning of Cbh1 and CelD on the Talaromyces emersonii Cel7A 3-dimensional structure, identifies the typical tunnel-like catalytic active site while Cbh1 shows an additional loop that partially obstructs the substrate-fitting channel. CelD does not have a CBD and shows a four amino acid residue deletion on the tunnel-obstructing loop providing a continuous opening in the absence of a CBD. Cbh1 and CelD are catalytically functional and while specific activity against Avicel is 7.7 and 0.5 U.mg prot-1, respectively specific activity on pNPC is virtually identical. Cbh1 is slightly more stable to thermal inactivation compared to CelD and is much less sensitive to glucose inhibition suggesting that an open tunnel configuration, or absence of a CBD, alters the way the catalytic domain interacts with the substrate. Cbh1 and CelD enzyme mixtures on crystalline cellulosic substrates show a strong combinatorial effort response for mixtures where Cbh1 is present in 2:1 or 4:1 molar excess. When CelD was overrepresented the combinatorial effort could only be partially overcome. CelD appears to bind and hydrolyze only loose cellulosic chains while Cbh1 is capable of opening new cellulosic substrate molecules away from the cellulosic fiber. CONCLUSION Cellobiohydrolases both with and without a CBD occur in most fungal genomes where both enzymes are secreted, and likely participate in cellulose degradation. The fact that only Cbh1 binds to the substrate and in combination with CelD exhibits strong synergy only when Cbh1 is present in excess, suggests that Cbh1 unties enough chains from cellulose fibers, thus enabling processive access of CelD.
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Affiliation(s)
- Fernando Segato
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais, Campinas, Sao Paulo, Brazil
| | - André R L Damasio
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
- Department of Biochemistry, Ribeirão Preto School of Medicine, Ribeirão Preto, Sao Paulo, Brazil
| | - Thiago Augusto Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais, Campinas, Sao Paulo, Brazil
| | - Mario T Murakami
- Laboratório Nacional de Biociências (LNBio), Campinas, Sao Paulo, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais, Campinas, Sao Paulo, Brazil
| | | | - Andrew J Mort
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Rolf A Prade
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais, Campinas, Sao Paulo, Brazil
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Abstract
Although it has a deceptively simple primary structure, the collective organization of bulk cellulose, particularly as it exists in cellulose fibers in the cell walls of living plants and other organisms, is quite diverse and complex. While some experimental techniques, such as vibrational spectroscopy and diffraction from partially crystalline samples, are able to provide insights into the organization of bulk cellulose, its intrinsic complexity has left many questions still unanswered. For this reason, additional probes of cellulose structure would be highly desirable. With the continuing advances in computer power through massive parallelization, and the steady progress in computer codes and force fields for modeling carbohydrate systems, molecular mechanics simulations have become an attractive means of studying cellulosic systems at the atomic and molecular level. The coming decade will almost certainly see remarkable advances in the understanding of cellulose using such simulations.
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26
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Barnett CB, Wilkinson KA, Naidoo KJ. Molecular Details from Computational Reaction Dynamics for the Cellobiohydrolase I Glycosylation Reaction. J Am Chem Soc 2011; 133:19474-82. [DOI: 10.1021/ja206842j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher B. Barnett
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Karl A. Wilkinson
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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27
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Lee YC, Lin DT, Ong PL, Chen HL, Lo HF, Lin LL. Contribution of conserved Glu255 and Cys289 residues to catalytic activity of recombinant aldehyde dehydrogenase from Bacillus licheniformis. BIOCHEMISTRY. BIOKHIMIIA 2011; 76:1233-1241. [PMID: 22117550 DOI: 10.1134/s0006297911110058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Based on the sequence homology, we have modeled the three-dimensional structure of Bacillus licheniformis aldehyde dehydrogenase (BlALDH) and identified two different residues, Glu255 and Cys289, that might be responsible for the catalytic function of the enzyme. The role of these residues was further investigated by site-directed mutagenesis and biophysical analysis. The expressed parental and mutant proteins were purified by nickel-chelate chromatography, and their molecular masses were determined to be approximately 53 kDa by SDS-PAGE. As compared with the parental BlALDH, a dramatic decrease or even complete loss of the dehydrogenase activity was observed for the mutant enzymes. Structural analysis showed that the intrinsic fluorescence and circular dichroism spectra of the mutant proteins were similar to the parental enzyme, but most of the variants exhibited a different sensitivity towards thermal- and guanidine hydrochloride-induced denaturation. These observations indicate that residues Glu255 and Cys289 play an important role in the dehydrogenase activity of BlALDH, and the rigidity of the enzyme has been changed as a consequence of the mutations.
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Affiliation(s)
- Yen-Chung Lee
- Department of Bioagricultural Science, National Chiayi University, Chiayi City, Taiwan
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28
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Warden AC, Little BA, Haritos VS. A cellular automaton model of crystalline cellulose hydrolysis by cellulases. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:39. [PMID: 22005054 PMCID: PMC3214134 DOI: 10.1186/1754-6834-4-39] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 10/17/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Cellulose from plant biomass is an abundant, renewable material which could be a major feedstock for low emissions transport fuels such as cellulosic ethanol. Cellulase enzymes that break down cellulose into fermentable sugars are composed of different types - cellobiohydrolases I and II, endoglucanase and β-glucosidase - with separate functions. They form a complex interacting network between themselves, soluble hydrolysis product molecules, solution and solid phase substrates and inhibitors. There have been many models proposed for enzymatic saccharification however none have yet employed a cellular automaton approach, which allows important phenomena, such as enzyme crowding on the surface of solid substrates, denaturation and substrate inhibition, to be considered in the model. RESULTS The Cellulase 4D model was developed de novo taking into account the size and composition of the substrate and surface-acting enzymes were ascribed behaviors based on their movements, catalytic activities and rates, affinity for, and potential for crowding of, the cellulose surface, substrates and inhibitors, and denaturation rates. A basic case modeled on literature-derived parameters obtained from Trichoderma reesei cellulases resulted in cellulose hydrolysis curves that closely matched curves obtained from published experimental data. Scenarios were tested in the model, which included variation of enzyme loadings, adsorption strengths of surface acting enzymes and reaction periods, and the effect on saccharide production over time was assessed. The model simulations indicated an optimal enzyme loading of between 0.5 and 2 of the base case concentrations where a balance was obtained between enzyme crowding on the cellulose crystal, and that the affinities of enzymes for the cellulose surface had a large effect on cellulose hydrolysis. In addition, improvements to the cellobiohydrolase I activity period substantially improved overall glucose production. CONCLUSIONS Cellulase 4D simulates the enzymatic hydrolysis of cellulose to glucose by surface and solution phase-acting enzymes and accounts for complex phenomena that have previously not been included in cellulose hydrolysis models. The model is intended as a tool for industry, researchers and educators alike to explore options for enzyme engineering and process development and to test hypotheses regarding cellulase mechanisms.
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Affiliation(s)
- Andrew C Warden
- CSIRO Energy Transformed Flagship and CSIRO Ecosystems Sciences, PO Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - Bryce A Little
- CSIRO Livestock Industries, FD McMaster Laboratory, Armidale, New South Wales 2350, Australia
- CSIRO Livestock Industries, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Victoria S Haritos
- CSIRO Energy Transformed Flagship and CSIRO Ecosystems Sciences, PO Box 1700, Canberra, Australian Capital Territory 2601, Australia
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29
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Zeng M, Ximenes E, Ladisch MR, Mosier NS, Vermerris W, Huang CP, Sherman DM. Tissue-specific biomass recalcitrance in corn stover pretreated with liquid hot-water: SEM imaging (part 2). Biotechnol Bioeng 2011; 109:398-404. [PMID: 21928340 DOI: 10.1002/bit.23335] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 08/30/2011] [Accepted: 09/06/2011] [Indexed: 11/06/2022]
Abstract
In the first part of our work, we combined compositional analysis, pretreatment and enzyme hydrolysis for fractionated pith, rind, and leaf tissues from a hybrid stay-green corn, in order to identify the role of structural characteristics on enzyme hydrolysis of cell walls. Hydrolysis experiments coupled with chemical analysis of the different fractions of corn stover showed significant differences in cell wall structure before and after liquid hot water pretreatment. The extent of enzyme hydrolysis followed the sequence rind < leaves < pith with 90% conversion of cellulose to glucose in 24 h in the best cases. Since similar lignin contents remained after liquid hot water pretreatment of leaves, rind, and pith, our results indicated that the amount of lignin alone is not sufficient to explain the different enzymatic hydrolysis characteristics of the fractions. While the role of structural characteristics on enzyme hydrolysis of cell walls is measured as described in part I, the SEM images presented in this part II of our work show that sugar yields from enzymatic hydrolysis of corn fractions correlate with changes in plant cell wall structure both before and after liquid hot water pretreatment.
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Affiliation(s)
- Meijuan Zeng
- Laboratory of Renewable Resources Engineering, Potter Engineering Center, Purdue University, 500 Central Drive, West Lafayette, Indiana 47907-2022, USA
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30
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Challenges of the utilization of wood polymers: how can they be overcome? Appl Microbiol Biotechnol 2011; 91:1525-36. [DOI: 10.1007/s00253-011-3350-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 04/30/2011] [Accepted: 05/01/2011] [Indexed: 01/05/2023]
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31
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Chundawat SP, Beckham GT, Himmel ME, Dale BE. Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals. Annu Rev Chem Biomol Eng 2011; 2:121-45. [PMID: 22432613 DOI: 10.1146/annurev-chembioeng-061010-114205] [Citation(s) in RCA: 463] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shishir P.S. Chundawat
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824;
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401
- National Advanced Biofuels Consortium, National Renewable Energy Laboratory, Golden, Colorado 80401
- Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado 80401
- Renewable and Sustainable Energy Institute, Boulder, Colorado 80309
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401;
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Bruce E. Dale
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824;
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824
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32
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The impact of Trichoderma reesei Cel7A carbohydrate binding domain mutations on its binding to a cellulose surface: a molecular dynamics free energy study. J Mol Model 2011; 18:1355-64. [DOI: 10.1007/s00894-011-1167-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/27/2011] [Indexed: 10/18/2022]
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33
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Chundawat SPS, Bellesia G, Uppugundla N, da Costa Sousa L, Gao D, Cheh AM, Agarwal UP, Bianchetti CM, Phillips GN, Langan P, Balan V, Gnanakaran S, Dale BE. Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate. J Am Chem Soc 2011; 133:11163-74. [DOI: 10.1021/ja2011115] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | - Albert M. Cheh
- Departments of Environmental Science and Chemistry, American University, Washington, D.C. 20016, United States
| | - Umesh P. Agarwal
- Forest Product Laboratory, USDA Forest Service, Madison, Wisconsin 53726, United States
| | - Christopher M. Bianchetti
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - George N. Phillips
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
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34
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Abstract
Cellulose is an abundant and renewable biopolymer that can be used for biofuel generation; however, structural entrapment with other cell wall components hinders enzyme-substrate interactions, a key bottleneck for ethanol production. Biomass is routinely subjected to treatments that facilitate cellulase-cellulose contacts. Cellulases and glucosidases act by hydrolyzing glycosidic bonds of linear glucose β-1,4-linked polymers, producing glucose. Here we describe eight high-temperature-operating cellulases (TCel enzymes) identified from a survey of thermobacterial and archaeal genomes. Three TCel enzymes preferentially hydrolyzed soluble cellulose, while two preferred insoluble cellulose such as cotton linters and filter paper. TCel enzymes had temperature optima ranging from 85°C to 102°C. TCel enzymes were stable, retaining 80% of initial activity after 120 h at 85°C. Two modes of cellulose breakdown, i.e., with endo- and exo-acting glucanases, were detected, and with two-enzyme combinations at 85°C, synergistic cellulase activity was observed for some enzyme combinations.
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35
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Bu L, Beckham GT, Shirts MR, Nimlos MR, Adney WS, Himmel ME, Crowley MF. Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods. J Biol Chem 2011; 286:18161-9. [PMID: 21454590 PMCID: PMC3093888 DOI: 10.1074/jbc.m110.212076] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/04/2011] [Indexed: 11/17/2022] Open
Abstract
Understanding the enzymatic mechanism that cellulases employ to degrade cellulose is critical to efforts to efficiently utilize plant biomass as a sustainable energy resource. A key component of cellulase action on cellulose is product inhibition from monosaccharide and disaccharides in the product site of cellulase tunnel. The absolute binding free energy of cellobiose and glucose to the product site of the catalytic tunnel of the Family 7 cellobiohydrolase (Cel7A) of Trichoderma reesei (Hypocrea jecorina) was calculated using two different approaches: steered molecular dynamics (SMD) simulations and alchemical free energy perturbation molecular dynamics (FEP/MD) simulations. For the SMD approach, three methods based on Jarzynski's equality were used to construct the potential of mean force from multiple pulling trajectories. The calculated binding free energies, -14.4 kcal/mol using SMD and -11.2 kcal/mol using FEP/MD, are in good qualitative agreement. Analysis of the SMD pulling trajectories suggests that several protein residues (Arg-251, Asp-259, Asp-262, Trp-376, and Tyr-381) play key roles in cellobiose and glucose binding to the catalytic tunnel. Five mutations (R251A, D259A, D262A, W376A, and Y381A) were made computationally to measure the changes in free energy during the product expulsion process. The absolute binding free energies of cellobiose to the catalytic tunnel of these five mutants are -13.1, -6.0, -11.5, -7.5, and -8.8 kcal/mol, respectively. The results demonstrated that all of the mutants tested can lower the binding free energy of cellobiose, which provides potential applications in engineering the enzyme to accelerate the product expulsion process and improve the efficiency of biomass conversion.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA.
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36
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Sugar-binding sites on the surface of the carbohydrate-binding module of CBH I from Trichoderma reesei. Carbohydr Res 2011; 346:839-46. [DOI: 10.1016/j.carres.2011.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 01/17/2011] [Accepted: 01/19/2011] [Indexed: 11/22/2022]
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37
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Beckham GT, Bomble YJ, Matthews JF, Taylor CB, Resch MG, Yarbrough JM, Decker SR, Bu L, Zhao X, McCabe C, Wohlert J, Bergenstråhle M, Brady JW, Adney WS, Himmel ME, Crowley MF. The O-glycosylated linker from the Trichoderma reesei Family 7 cellulase is a flexible, disordered protein. Biophys J 2011; 99:3773-81. [PMID: 21112302 DOI: 10.1016/j.bpj.2010.10.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022] Open
Abstract
Fungi and bacteria secrete glycoprotein cocktails to deconstruct cellulose. Cellulose-degrading enzymes (cellulases) are often modular, with catalytic domains for cellulose hydrolysis and carbohydrate-binding modules connected by linkers rich in serine and threonine with O-glycosylation. Few studies have probed the role that the linker and O-glycans play in catalysis. Since different expression and growth conditions produce different glycosylation patterns that affect enzyme activity, the structure-function relationships that glycosylation imparts to linkers are relevant for understanding cellulase mechanisms. Here, the linker of the Trichoderma reesei Family 7 cellobiohydrolase (Cel7A) is examined by simulation. Our results suggest that the Cel7A linker is an intrinsically disordered protein with and without glycosylation. Contrary to the predominant view, the O-glycosylation does not change the stiffness of the linker, as measured by the relative fluctuations in the end-to-end distance; rather, it provides a 16 Å extension, thus expanding the operating range of Cel7A. We explain observations from previous biochemical experiments in the light of results obtained here, and compare the Cel7A linker with linkers from other cellulases with sequence-based tools to predict disorder. This preliminary screen indicates that linkers from Family 7 enzymes from other genera and other cellulases within T. reesei may not be as disordered, warranting further study.
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Affiliation(s)
- Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado, USA
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38
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Wohlert J, Berglund LA. A Coarse-Grained Model for Molecular Dynamics Simulations of Native Cellulose. J Chem Theory Comput 2011. [DOI: 10.1021/ct100489z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jakob Wohlert
- Wallenberg Wood Science Center, Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Lars A. Berglund
- Wallenberg Wood Science Center, Royal Institute of Technology, SE-10044 Stockholm, Sweden
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39
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Batista PR, de Souza Costa MG, Pascutti PG, Bisch PM, de Souza W. High temperatures enhance cooperative motions between CBM and catalytic domains of a thermostable cellulase: mechanism insights from essential dynamics. Phys Chem Chem Phys 2011; 13:13709-20. [DOI: 10.1039/c0cp02697b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Applications of computational science for understanding enzymatic deconstruction of cellulose. Curr Opin Biotechnol 2010; 22:231-8. [PMID: 21168322 DOI: 10.1016/j.copbio.2010.11.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 11/07/2010] [Indexed: 10/18/2022]
Abstract
Understanding the molecular-level mechanisms that enzymes employ to deconstruct plant cell walls is a fundamental scientific challenge with significant ramifications for renewable fuel production from biomass. In nature, bacteria and fungi use enzyme cocktails that include processive and non-processive cellulases and hemicellulases to convert cellulose and hemicellulose to soluble sugars. Catalyzed by an accelerated biofuels R&D portfolio, there is now a wealth of new structural and experimental insights related to cellulases and the structure of plant cell walls. From this background, computational approaches commonly used in other fields are now poised to offer insights complementary to experiments designed to probe mechanisms of plant cell wall deconstruction. Here we outline the current status of computational approaches for a collection of critical problems in cellulose deconstruction. We discuss path sampling methods to measure rates of elementary steps of enzyme action, coarse-grained modeling for understanding macromolecular, cellulosomal complexes, methods to screen for enzyme improvements, and studies of cellulose at the molecular level. Overall, simulation is a complementary tool to understand carbohydrate-active enzymes and plant cell walls, which will enable industrial processes for the production of advanced, renewable fuels.
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41
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Meso-Scale Modeling of Polysaccharides in Plant Cell Walls: An Application to Translation of CBMs on the Cellulose Surface. ACTA ACUST UNITED AC 2010. [DOI: 10.1021/bk-2010-1052.ch005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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42
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Kalluri UC, Keller M. Bioenergy research: a new paradigm in multidisciplinary research. J R Soc Interface 2010; 7:1391-401. [PMID: 20542958 PMCID: PMC3227023 DOI: 10.1098/rsif.2009.0564] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 05/10/2010] [Indexed: 12/28/2022] Open
Abstract
The field of biology is becoming increasingly interdisciplinary and cross-cutting. This changing research atmosphere is creating the way for a new kind of enquiry that while building upon the traditional research establishment is providing a new multidisciplinary framework to more effectively address scientific grand challenges. Using the US Department of Energy sponsored BioEnergy Science Center as an example, we highlight how impactful breakthroughs in biofuel science can be achieved within a large cross-disciplinary team environment. Such transformational insights are key to furthering our understanding and in generating models, theories and processes that can be used to overcome recalcitrance of biomass for sustainable biofuel production. Multidisciplinary approaches have an increasingly greater role to play in meeting rising demands for food, fibre, energy, clean environment and good health. Discoveries achieved by diverse minds and cross-applications of tools and analytical approaches have tremendous potential to fill existing knowledge gaps, clear roadblocks and facilitate translation of basic sciences discoveries as solutions towards addressing some of the most pressing global issues.
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Affiliation(s)
- Udaya C. Kalluri
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- BESC BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Martin Keller
- Biological and Environmental Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- BESC BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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43
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Probing the catalytically essential residues of a recombinant dipeptidyl carboxypeptidase from Escherichia coli. Biologia (Bratisl) 2010. [DOI: 10.2478/s11756-010-0040-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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44
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Yui T, Shiiba H, Tsutsumi Y, Hayashi S, Miyata T, Hirata F. Systematic docking study of the carbohydrate binding module protein of Cel7A with the cellulose Ialpha crystal model. J Phys Chem B 2010; 114:49-58. [PMID: 19928978 DOI: 10.1021/jp908249r] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A computer docking study has been carried out on the crystal surfaces of cellulose Ialpha crystal models for the carbohydrate binding module (CBM) protein of the cellobiohydrolase Cel7A produced by Trichoderma reesei. Binding free energy maps between the CBM and the crystal surface were obtained by calculating the noncovalent interactions and the solvation free energy at grid points covering the area of the unit cell dimensions at the crystal surface. The potential maps obtained from grid searches of the hydrophobic (110) crystal surface exhibited two distinct potential wells. These reflected the 2-fold helical symmetry of the cellulose chain and had lower binding energies at the minimum positions than those for the hydrophilic (100) and (010) crystal surfaces. The CBM-cellulose crystal complex models derived from the minimum positions were then subjected to molecular dynamics (MD) simulation under an explicit solvent system. The (110) complex models exhibited larger affinities at the interface than the (100) and (010) ones. The CBM was more stably bound to the (110) surface when it was placed in an antiparallel orientation with respect to the cellulose fiber axis. In the solvated dynamics state, the curved (110) surface resulting from the fiber twist somewhat assisted a complementary fit with the CBM at the interface. In addition to the conventional Generalized Born (GB) method, the three-dimensional reference interaction site model (3D-RISM) theory was adopted to assess a solvent effect for the solvated MD trajectories. Large exothermic values for the noncovalent interactions appeared correlated to and were mostly compensated by endothermic values for the solvation free energy. These gave total binding free energies of -13 to -28 kcal/mol. Results also suggested that the hydrogen bonding scheme was not essential for substrate specificity.
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Affiliation(s)
- Toshifumi Yui
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, 1-1 Nishi, Gakuen Kibanadai, Miyazaki 889-2192, Japan.
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Beckham GT, Matthews JF, Bomble YJ, Bu L, Adney WS, Himmel ME, Nimlos MR, Crowley MF. Identification of Amino Acids Responsible for Processivity in a Family 1 Carbohydrate-Binding Module from a Fungal Cellulase. J Phys Chem B 2010; 114:1447-53. [DOI: 10.1021/jp908810a] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - James F. Matthews
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Yannick J. Bomble
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - William S. Adney
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael E. Himmel
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Mark R. Nimlos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael F. Crowley
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
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46
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Song Y, Gao L, Li L, Zheng Q. Influence of gliadins on rheology of methylcellulose in 70% (v/v) aqueous ethanol. Food Hydrocoll 2010. [DOI: 10.1016/j.foodhyd.2009.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Bu L, Beckham GT, Crowley MF, Chang CH, Matthews JF, Bomble YJ, Adney WS, Himmel ME, Nimlos MR. The energy landscape for the interaction of the family 1 carbohydrate-binding module and the cellulose surface is altered by hydrolyzed glycosidic bonds. J Phys Chem B 2009; 113:10994-1002. [PMID: 19594145 DOI: 10.1021/jp904003z] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A multiscale simulation model is used to construct potential and free energy surfaces for the carbohydrate-binding module [CBM] from an industrially important cellulase, Trichoderma reesei cellobiohydrolase I, on the hydrophobic face of a coarse-grained cellulose Ibeta polymorph. We predict from computation that the CBM alone exhibits regions of stability on the hydrophobic face of cellulose every 5 and 10 A, corresponding to a glucose unit and a cellobiose unit, respectively. In addition, we predict a new role for the CBM: specifically, that in the presence of hydrolyzed cellulose chain ends, the CBM exerts a thermodynamic driving force to translate away from the free cellulose chain ends. This suggests that the CBM is not only required for binding to cellulose, as has been known for two decades, but also that it has evolved to both assist the enzyme in recognizing a cellulose chain end and exert a driving force on the enzyme during processive hydrolysis of cellulose.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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48
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Zhong L, Matthews JF, Hansen PI, Crowley MF, Cleary JM, Walker RC, Nimlos MR, Brooks CL, Adney WS, Himmel ME, Brady JW. Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Ibeta: the enzyme-substrate complex. Carbohydr Res 2009; 344:1984-92. [PMID: 19699474 DOI: 10.1016/j.carres.2009.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2008] [Revised: 07/13/2009] [Accepted: 07/14/2009] [Indexed: 11/29/2022]
Abstract
Cellobiohydrolases are the dominant components of the commercially relevant Trichoderma reesei cellulase system. Although natural cellulases can totally hydrolyze crystalline cellulose to soluble sugars, the current enzyme loadings and long digestion times required render these enzymes less than cost effective for biomass conversion processes. It is clear that cellobiohydrolases must be improved via protein engineering to reduce processing costs. To better understand cellobiohydrolase function, new simulations have been conducted using charmm of cellobiohydrolase I (CBH I) from T.reesei interacting with a model segment (cellodextrin) of a cellulose microfibril in which one chain from the substrate has been placed into the active site tunnel mimicking the hypothesized configuration prior to final substrate docking (i.e., the +1 and +2 sites are unoccupied), which is also the structure following a catalytic bond scission. No tendency was found for the protein to dissociate from or translate along the substrate surface during this initial simulation, nor to align with the direction of the cellulose chains. However, a tendency for the decrystallized cellodextrin to partially re-anneal into the cellulose surface hints that the arbitrary starting configuration selected was not ideal.
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Affiliation(s)
- Linghao Zhong
- Department of Food Science, Cornell University, Ithaca, NY 14853, United States
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49
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50
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Abstract
The development of sustainable, low-carbon, liquid fuels from cellulosic biomass will require advances in many areas of science and engineering. This review describes the major topics of enquiry concerning cellulosic biofuels with an emphasis on those areas of research and development that include research problems of interest to plant biologists.
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Affiliation(s)
- Andrew Carroll
- Department of Biology, Stanford University, Stanford, California 94305, USA.
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