1
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Kuch NJ, Kutschke ME, Parker A, Bingman CA, Fox BG. Contribution of calcium ligands in substrate binding and product release in the Acetovibrio thermocellus glycoside hydrolase family 9 cellulase CelR. J Biol Chem 2023; 299:104655. [PMID: 36990218 PMCID: PMC10149213 DOI: 10.1016/j.jbc.2023.104655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Enzymatic deconstruction of lignocellulosic biomass is crucial to establishment of the renewable biofuel and bioproduct economy. Better understanding of these enzymes, including their catalytic and binding domains, and other features offer potential avenues for improvement. Glycoside hydrolase family 9 (GH9) enzymes are attractive targets because they have members that exhibit exo- and endo-cellulolytic activity, processivity of reaction, and thermostability. This study examines a GH9 from Acetovibrio thermocellus ATCC 27405, AtCelR containing a catalytic domain and a carbohydrate binding module (CBM3c). Crystal structures of the enzyme without substrate, bound to cellohexaose (substrate) or cellobiose (product), show the positioning of ligands to calcium and adjacent residues in the catalytic domain that may contribute to substrate binding and facilitate product release. We also investigated the properties of the enzyme engineered to contain an additional carbohydrate binding module (CBM3a). Relative to the catalytic domain alone, CBM3a gave improved binding for Avicel (a crystalline form of cellulose), and catalytic efficiency (kcat/KM) was improved 40× with both CBM3c and CBM3a present. However, because of the molecular weight added by CBM3a, the specific activity of the engineered enzyme was not increased relative to the native construct consisting of only the catalytic and CBM3c domains. This work provides new insight into a potential role of the conserved calcium in the catalytic domain and identifies contributions and limitations of domain engineering for AtCelR and perhaps other GH9 enzymes.
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Affiliation(s)
- Nathaniel J Kuch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mark E Kutschke
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alex Parker
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Dane County Youth Apprenticeship Program, Dane County School Consortium, Monona, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Collaborative Crystallography Core, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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2
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The interplay between lytic polysaccharide monooxygenases and glycoside hydrolases. Essays Biochem 2023; 67:551-559. [PMID: 36876880 DOI: 10.1042/ebc20220156] [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: 10/20/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 03/07/2023]
Abstract
In nature, enzymatic degradation of recalcitrant polysaccharides such as chitin and cellulose takes place by a synergistic interaction between glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The two different families of carbohydrate-active enzymes use two different mechanisms when breaking glycosidic bonds between sugar moieties. GHs employ a hydrolytic activity and LPMOs are oxidative. Consequently, the topologies of the active sites differ dramatically. GHs have tunnels or clefts lined with a sheet of aromatic amino acid residues accommodating single polymer chains being threaded into the active site. LPMOs are adapted to bind to the flat crystalline surfaces of chitin and cellulose. It is believed that the LPMO oxidative mechanism provides new chain ends that the GHs can attach to and degrade, often in a processive manner. Indeed, there are many reports of synergies as well as rate enhancements when LPMOs are applied in concert with GHs. Still, these enhancements vary in magnitude with respect to the nature of the GH and the LPMO. Moreover, impediment of GH catalysis is also observed. In the present review, we discuss central works where the interplay between LPMOs and GHs has been studied and comment on future challenges to be addressed to fully use the potential of this interplay to improve enzymatic polysaccharide degradation.
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3
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Li P, Wang X, Zhang C, Xu D. Processive binding mechanism of Cel9G from Clostridium cellulovorans: molecular dynamics and free energy landscape investigations. Phys Chem Chem Phys 2023; 25:646-657. [DOI: 10.1039/d2cp04830b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The processive binding mechanism of cellulose by Cel9G from C. cellulovorans was investigated by MD and metadynamics simulations.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Chunchun Zhang
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
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4
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Haataja T, Gado JE, Nutt A, Anderson NT, Nilsson M, Momeni MH, Isaksson R, Väljamäe P, Johansson G, Payne CM, Ståhlberg J. Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non-productive binding: insights from crystal structures and MD simulation. FEBS J 2023; 290:379-399. [PMID: 35997626 PMCID: PMC10087753 DOI: 10.1111/febs.16602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/30/2022] [Accepted: 08/17/2022] [Indexed: 02/05/2023]
Abstract
Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) (EC3.2.1.176) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p-nitrophenyl-β-d-cellobioside (pNPC), p-nitrophenyl-β-d-lactoside (pNPL) and methylumbelliferyl-β-d-cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o-nitrophenyl-β-d-cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium. Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non-productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non-productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates (kcat ) than TrCel7A, but higher Michaelis-Menten (KM ) constants as well. Furthermore, oNPC turned out to be useful as an active-site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.
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Affiliation(s)
- Topi Haataja
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Japheth E Gado
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA.,Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Anu Nutt
- Department of Chemistry, Uppsala University, Sweden.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Nolan T Anderson
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Mikael Nilsson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Majid Haddad Momeni
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roland Isaksson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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5
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Zangiabadi M, Zhao Y. Synergistic Hydrolysis of Cellulose by a Blend of Cellulase-Mimicking Polymeric Nanoparticle Catalysts. J Am Chem Soc 2022; 144:17110-17119. [PMID: 36069714 PMCID: PMC10183977 DOI: 10.1021/jacs.2c06848] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzyme-like catalysts by design have been a long sought-after goal of chemists but difficult to realize due to the challenges in the construction of multifunctionalized active sites with accurately positioned catalytic groups for complex substrates. Hydrolysis of cellulose is a key step in biomass utilization and requires multiple enzymes to work in concert to overcome the difficulty associated with hydrolyzing the recalcitrant substrate. We here report methods to construct synthetic versions of these enzymes through covalent molecular imprinting and strategic postmodification of the imprinted sites. The synthetic catalysts cleave a cellulose chain endolytically at multiple positions or exolytically from the nonreducing end by one or three glucose units at a time, all using the dicarboxylic acid motif found in natural cellulases. By mimicking the endocellulase, exocellulase, and β-glucosidase, the synthetic catalysts hydrolyze cellulose in a synergistic manner, with an activity at 90 °C in pH 6.5 buffer more than doubled that of Aspergillus niger cellulase at pH 5 and 37 °C and 44% of that of a commercial cellulase blend (from Novozyme). As robust cross-linked polymeric nanoparticles, the synthetic catalysts showed little changes in activity after preheating at 90 °C for 3 days and could be reused, maintaining 76% of activity after 10 reaction cycles.
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Affiliation(s)
- Milad Zangiabadi
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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6
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Arnling Bååth J, Jensen K, Borch K, Westh P, Kari J. Sabatier Principle for Rationalizing Enzymatic Hydrolysis of a Synthetic Polyester. JACS AU 2022; 2:1223-1231. [PMID: 35647598 PMCID: PMC9131473 DOI: 10.1021/jacsau.2c00204] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 05/04/2023]
Abstract
Interfacial enzyme reactions are common in Nature and in industrial settings, including the enzymatic deconstruction of poly(ethylene terephthalate) (PET) waste. Kinetic descriptions of PET hydrolases are necessary for both comparative analyses, discussions of structure-function relations and rational optimization of technical processes. We investigated whether the Sabatier principle could be used for this purpose. Specifically, we compared the kinetics of two well-known PET hydrolases, leaf-branch compost cutinase (LCC) and a cutinase from the bacterium Thermobifida fusca (TfC), when adding different concentrations of the surfactant cetyltrimethylammonium bromide (CTAB). We found that CTAB consistently lowered the strength of enzyme-PET interactions, while its effect on enzymatic turnover was strongly biphasic. Thus, at gradually increasing CTAB concentrations, turnover was initially promoted and subsequently suppressed. This correlation with maximal turnover at an intermediate binding strength was in accordance with the Sabatier principle. One consequence of these results was that both enzymes had too strong intrinsic interaction with PET for optimal turnover, especially TfC, which showed a 20-fold improvement of k cat at the maximum. LCC on the other hand had an intrinsic substrate affinity closer to the Sabatier optimum, and the turnover rate was 5-fold improved at weakened substrate binding. Our results showed that the Sabatier principle may indeed rationalize enzymatic PET degradation and support process optimization. Finally, we suggest that future discovery efforts should consider enzymes with weakened substrate binding because strong adsorption seems to limit their catalytic performance.
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Affiliation(s)
- Jenny Arnling Bååth
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, Kgs. Lyngby DK-2800, Denmark
| | - Kenneth Jensen
- Novozymes
A/S, Biologiens Vej 2, Kgs. Lyngby DK-2800, Denmark
| | - Kim Borch
- Novozymes
A/S, Biologiens Vej 2, Kgs. Lyngby DK-2800, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, Kgs. Lyngby DK-2800, Denmark
- . Phone: +45 45 25 26 41
| | - Jeppe Kari
- Department
of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000, Denmark
- . Phone: +45 46 74 27 20
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7
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Gado JE, Harrison BE, Sandgren M, Ståhlberg J, Beckham GT, Payne CM. Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases. J Biol Chem 2021; 297:100931. [PMID: 34216620 PMCID: PMC8329511 DOI: 10.1016/j.jbc.2021.100931] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 06/18/2021] [Accepted: 06/29/2021] [Indexed: 11/28/2022] Open
Abstract
Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These enzymes are often bimodular, including a catalytic domain and carbohydrate-binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able to discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our machine learning results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.
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Affiliation(s)
- Japheth E Gado
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, USA; Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Brent E Harrison
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, USA.
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8
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Kari J, Molina GA, Schaller KS, Schiano-di-Cola C, Christensen SJ, Badino SF, Sørensen TH, Røjel NS, Keller MB, Sørensen NR, Kolaczkowski B, Olsen JP, Krogh KBRM, Jensen K, Cavaleiro AM, Peters GHJ, Spodsberg N, Borch K, Westh P. Physical constraints and functional plasticity of cellulases. Nat Commun 2021; 12:3847. [PMID: 34158485 PMCID: PMC8219668 DOI: 10.1038/s41467-021-24075-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Enzyme reactions, both in Nature and technical applications, commonly occur at the interface of immiscible phases. Nevertheless, stringent descriptions of interfacial enzyme catalysis remain sparse, and this is partly due to a shortage of coherent experimental data to guide and assess such work. In this work, we produced and kinetically characterized 83 cellulases, which revealed a conspicuous linear free energy relationship (LFER) between the substrate binding strength and the activation barrier. The scaling occurred despite the investigated enzymes being structurally and mechanistically diverse. We suggest that the scaling reflects basic physical restrictions of the hydrolytic process and that evolutionary selection has condensed cellulase phenotypes near the line. One consequence of the LFER is that the activity of a cellulase can be estimated from its substrate binding strength, irrespectively of structural and mechanistic details, and this appears promising for in silico selection and design within this industrially important group of enzymes.
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Affiliation(s)
- Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gustavo A Molina
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kay S Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Corinna Schiano-di-Cola
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stefan J Christensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Silke F Badino
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nanna S Røjel
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Malene B Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Nanna Rolsted Sørensen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Bartlomiej Kolaczkowski
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | | | | | | | | | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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9
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Li X, Zangiabadi M, Zhao Y. Molecularly Imprinted Synthetic Glucosidase for the Hydrolysis of Cellulose in Aqueous and Nonaqueous Solutions. J Am Chem Soc 2021; 143:5172-5181. [DOI: 10.1021/jacs.1c01352] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaowei Li
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Milad Zangiabadi
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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10
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Chundawat SPS, Nemmaru B, Hackl M, Brady SK, Hilton MA, Johnson MM, Chang S, Lang MJ, Huh H, Lee SH, Yarbrough JM, López CA, Gnanakaran S. Molecular origins of reduced activity and binding commitment of processive cellulases and associated carbohydrate-binding proteins to cellulose III. J Biol Chem 2021; 296:100431. [PMID: 33610545 PMCID: PMC8010709 DOI: 10.1016/j.jbc.2021.100431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 11/30/2022] Open
Abstract
Efficient enzymatic saccharification of cellulosic biomass into fermentable sugars can enable production of bioproducts like ethanol. Native crystalline cellulose, or cellulose I, is inefficiently processed via enzymatic hydrolysis but can be converted into the structurally distinct cellulose III allomorph that is processed via cellulase cocktails derived from Trichoderma reesei up to 20-fold faster. However, characterization of individual cellulases from T. reesei, like the processive exocellulase Cel7A, shows reduced binding and activity at low enzyme loadings toward cellulose III. To clarify this discrepancy, we monitored the single-molecule initial binding commitment and subsequent processive motility of Cel7A enzymes and associated carbohydrate-binding modules (CBMs) on cellulose using optical tweezers force spectroscopy. We confirmed a 48% lower initial binding commitment and 32% slower processive motility of Cel7A on cellulose III, which we hypothesized derives from reduced binding affinity of the Cel7A binding domain CBM1. Classical CBM–cellulose pull-down assays, depending on the adsorption model fitted, predicted between 1.2- and 7-fold reduction in CBM1 binding affinity for cellulose III. Force spectroscopy measurements of CBM1–cellulose interactions, along with molecular dynamics simulations, indicated that previous interpretations of classical binding assay results using multisite adsorption models may have complicated analysis, and instead suggest simpler single-site models should be used. These findings were corroborated by binding analysis of other type-A CBMs (CBM2a, CBM3a, CBM5, CBM10, and CBM64) on both cellulose allomorphs. Finally, we discuss how complementary analytical tools are critical to gain insight into the complex mechanisms of insoluble polysaccharides hydrolysis by cellulolytic enzymes and associated carbohydrate-binding proteins.
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Affiliation(s)
- Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
| | - Bhargava Nemmaru
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Markus Hackl
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sonia K Brady
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Mark A Hilton
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Madeline M Johnson
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Sungrok Chang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Hyun Huh
- Department of Physics and Astronomy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sang-Hyuk Lee
- Department of Physics and Astronomy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - John M Yarbrough
- Biosciences Center, National Renewable Energy Lab, Golden, Colorado, USA
| | - Cesar A López
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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11
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Schaller KS, Kari J, Molina GA, Tidemand KD, Borch K, Peters GHJ, Westh P. Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach. ACS OMEGA 2021; 6:1547-1555. [PMID: 33490814 PMCID: PMC7818601 DOI: 10.1021/acsomega.0c05361] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/24/2020] [Indexed: 05/21/2023]
Abstract
While heterogeneous enzyme reactions play an essential role in both nature and green industries, computational predictions of their catalytic properties remain scarce. Recent experimental work demonstrated the applicability of the Sabatier principle for heterogeneous biocatalysis. This provides a simple relationship between binding strength and the catalytic rate and potentially opens a new way for inexpensive computational determination of kinetic parameters. However, broader implementation of this approach will require fast and reliable prediction of binding free energies of complex two-phase systems, and computational procedures for this are still elusive. Here, we propose a new framework for the assessment of the binding strengths of multidomain proteins, in general, and interfacial enzymes, in particular, based on an extended linear interaction energy (LIE) method. This two-domain LIE (2D-LIE) approach was successfully applied to predict binding and activation free energies of a diverse set of cellulases and resulted in robust models with high accuracy. Overall, our method provides a fast computational screening tool for cellulases that have not been experimentally characterized, and we posit that it may also be applicable to other heterogeneously acting biocatalysts.
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Affiliation(s)
- Kay S. Schaller
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Jeppe Kari
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Gustavo A. Molina
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes
A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | - Günther H. J. Peters
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- . Phone: +45 45 25 26 41
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12
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Liu Z, Li J, Jie C, Wu B, Hao N. A multifunctional α-amylase BSGH13 from Bacillus subtilis BS-5 possessing endoglucanase and xylanase activities. Int J Biol Macromol 2021; 171:166-176. [PMID: 33421464 DOI: 10.1016/j.ijbiomac.2021.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/25/2020] [Accepted: 01/01/2021] [Indexed: 10/22/2022]
Abstract
Exploring new multifunctional enzymes and understanding the mechanisms of catalytic promiscuity will be of enormous industrial and academic values. In the present study, we reported the discovery and characterization of a multifunctional enzyme BSGH13 from Bacillus subtilis BS-5. Remarkably, BSGH13 possessed α-amylase, endoglucanase, and xylanase activities. To our knowledge, this was the first report on an amylase from Bacillus species having additional endoglucanase and xylanase activities. Subsequently, we analyzed the effects of aromatic residues substitution at each site of the active site architecture on ligand-binding affinity and catalytic specificity of BSGH13 by a combination of virtual mutation and site-directed mutagenesis approaches. Our results indicated that the introduction of aromatic amino acids Phe or Trp at the positions L182 and L183 altered the local interaction network of BSGH13 towards different substrates, thus changing the multifunctional properties of BSGH13. Moreover, we provided an expanded perspective on studies of multifunctional enzymes.
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Affiliation(s)
- Zhaoxing Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, 639 Longmian avenue, Nanjing 211198, Jiangsu, China
| | - Chen Jie
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China.
| | - Ning Hao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China.
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13
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Zou G, Bao D, Wang Y, Zhou S, Xiao M, Yang Z, Wang Y, Zhou Z. Alleviating product inhibition of Trichoderma reesei cellulase complex with a product-activated mushroom endoglucanase. BIORESOURCE TECHNOLOGY 2021; 319:124119. [PMID: 32957048 DOI: 10.1016/j.biortech.2020.124119] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Product inhibition of cellulase is a challenging issue in industrial processes. Here, we introduced a product-activated mushroom cellulase, PaCel3A from Polyporus arcularius, into Trichoderma reesei. The filter paper activity, carboxymethyl cellulase activity, and saccharification efficiency (substrate: pretreated rice straw, PRS) of transformants increased significantly with this enzyme (by 18.4-26.8%, 13.8-22.8%, and 17.0%, respectively). A mutant of PaCel3A, PaCel3AM, obtained based on B-factor analysis, saturated mutagenesis, and residual activity assay, showed improved thermostability. The PRS saccharification efficiency using the cellulase complex from T. reesei transformants overexpressing pacel3am increased by 56.4%-63.0%. In addition, the T. reesei cellulase complex obtained by adding the purified recombinant PaCel3AM from T. reesei (rCel3aM-tr) to hydrolyze PRS resulted in increased reducing sugar yields at all sampling points, outperforming the cellulase complexes without rCel3aM-tr. These results suggest that introducing product-activated cellulase genes is a simple and feasible method to alleviate the product inhibition of cellulase.
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Affiliation(s)
- Gen Zou
- Shanghai Key Laboratory of Agricultural Genetics and Breeding; Institute of Edible Fungi, Shanghai Academy of Agriculture Science, 1000 Jinqi Rd, Fengxian 201403, Shanghai, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai 200032, China.
| | - Dapeng Bao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding; Institute of Edible Fungi, Shanghai Academy of Agriculture Science, 1000 Jinqi Rd, Fengxian 201403, Shanghai, China.
| | - Ying Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding; Institute of Edible Fungi, Shanghai Academy of Agriculture Science, 1000 Jinqi Rd, Fengxian 201403, Shanghai, China
| | - Sichi Zhou
- Shanghai Key Laboratory of Agricultural Genetics and Breeding; Institute of Edible Fungi, Shanghai Academy of Agriculture Science, 1000 Jinqi Rd, Fengxian 201403, Shanghai, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai 200032, China.
| | - Zhanshan Yang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding; Institute of Edible Fungi, Shanghai Academy of Agriculture Science, 1000 Jinqi Rd, Fengxian 201403, Shanghai, China
| | - Yinmei Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai 200032, China.
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai 200032, China.
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14
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Lv K, Shao W, Pedroso MM, Peng J, Wu B, Li J, He B, Schenk G. Enhancing the catalytic activity of a GH5 processive endoglucanase from Bacillus subtilis BS-5 by site-directed mutagenesis. Int J Biol Macromol 2020; 168:442-452. [PMID: 33310097 DOI: 10.1016/j.ijbiomac.2020.12.060] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022]
Abstract
Processive endoglucanases possess both endo- and exoglucanase activity, making them attractive discovery and engineering targets. Here, a processive endoglucanase EG5C-1 from Bacillus subtilis was employed as the starting point for enzyme engineering. Referring to the complex structure information of EG5C-1 and cellohexaose, the amino acid residues in the active site architecture were identified and subjected to alanine scanning mutagenesis. The residues were chosen for a saturation mutagenesis since their variants showed similar activities to EG5C-1. Variants D70Q and S235W showed increased activity towards the substrates CMC and Avicel, an increase was further enhanced in D70Q/S235W double mutant, which displayed a 2.1- and 1.7-fold improvement in the hydrolytic activity towards CMC and Avicel, respectively. In addition, kinetic measurements showed that double mutant had higher substrate affinity (Km) and a significantly higher catalytic efficiency (kcat/Km). The binding isotherms of wild-type EG5C-1 and double mutant D70Q/S235W suggested that the binding capability of EG5C-1 for the insoluble substrate was weaker than that of D70Q/S235W. Molecular dynamics simulations suggested that the collaborative substitutions of D70Q and S235W altered the hydrogen bonding network within the active site architecture and introduced new hydrogen bonds between the enzyme and cellohexaose, thus enhancing both substrate affinity and catalytic efficiency.
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Affiliation(s)
- Kemin Lv
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Wenyu Shao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jiayu Peng
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China.
| | - Jiahuang Li
- School of Life Science, Nanjing University, Nanjing 210023, Jiangsu, China.
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
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15
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Nakamura A, Ishiwata D, Visootsat A, Uchiyama T, Mizutani K, Kaneko S, Murata T, Igarashi K, Iino R. Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases. J Biol Chem 2020; 295:14606-14617. [PMID: 32816991 PMCID: PMC7586223 DOI: 10.1074/jbc.ra120.014792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
Cellobiohydrolases directly convert crystalline cellulose into cellobiose and are of biotechnological interest to achieve efficient biomass utilization. As a result, much research in the field has focused on identifying cellobiohydrolases that are very fast. Cellobiohydrolase A from the bacterium Cellulomonas fimi (CfCel6B) and cellobiohydrolase II from the fungus Trichoderma reesei (TrCel6A) have similar catalytic domains (CDs) and show similar hydrolytic activity. However, TrCel6A and CfCel6B have different cellulose-binding domains (CBDs) and linkers: TrCel6A has a glycosylated peptide linker, whereas CfCel6B's linker consists of three fibronectin type 3 domains. We previously found that TrCel6A's linker plays an important role in increasing the binding rate constant to crystalline cellulose. However, it was not clear whether CfCel6B's linker has similar function. Here we analyze kinetic parameters of CfCel6B using single-molecule fluorescence imaging to compare CfCel6B and TrCel6A. We find that CBD is important for initial binding of CfCel6B, but the contribution of the linker to the binding rate constant or to the dissociation rate constant is minor. The crystal structure of the CfCel6B CD showed longer loops at the entrance and exit of the substrate-binding tunnel compared with TrCel6A CD, which results in higher processivity. Furthermore, CfCel6B CD showed not only fast surface diffusion but also slow processive movement, which is not observed in TrCel6A CD. Combined with the results of a phylogenetic tree analysis, we propose that bacterial cellobiohydrolases are designed to degrade crystalline cellulose using high-affinity CBD and high-processivity CD.
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Affiliation(s)
- Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Shizuoka, Shizuoka, Japan.
| | - Daiki Ishiwata
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Akasit Visootsat
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Taku Uchiyama
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Kenji Mizutani
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan
| | - Satoshi Kaneko
- Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Ryota Iino
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
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16
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Patel M, Patel HM, Dave S. Determination of bioethanol production potential from lignocellulosic biomass using novel Cel-5m isolated from cow rumen metagenome. Int J Biol Macromol 2020; 153:1099-1106. [DOI: 10.1016/j.ijbiomac.2019.10.240] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/13/2019] [Accepted: 10/25/2019] [Indexed: 11/17/2022]
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17
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Sørlie M, Horn SJ, Vaaje-Kolstad G, Eijsink VG. Using chitosan to understand chitinases and the role of processivity in the degradation of recalcitrant polysaccharides. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Abstract
Extracellular polysaccharides and glycoproteins of pathogenic bacteria assist in adherence, autoaggregation, biofilm formation, and host immune system evasion. As a result, considerable research in the field of glycobiology is dedicated to study the composition and function of glycans associated with virulence, as well as the enzymes involved in their biosynthesis with the aim to identify novel antibiotic targets. Especially, insights into the enzyme mechanism, substrate binding, and transition-state structures are valuable as a starting point for rational inhibitor design. An intriguing aspect of enzymes that generate or process polysaccharides and glycoproteins is the level of processivity. The existence of enzymatic processivity reflects the need for regulation of the final glycan/glycoprotein length and structure, depending on the role they perform. In this Review, we describe the currently reported examples of various processive enzymes involved in polymerization and transfer of sugar moieties, predominantly in bacterial pathogens, with a focus on the biochemical methods, to showcase the importance of studying processivity for understanding the mechanism.
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Affiliation(s)
- Liubov Yakovlieva
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Marthe T. C. Walvoort
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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19
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Kołaczkowski BM, Schaller KS, Sørensen TH, Peters GHJ, Jensen K, Krogh KBRM, Westh P. Removal of N-linked glycans in cellobiohydrolase Cel7A from Trichoderma reesei reveals higher activity and binding affinity on crystalline cellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:136. [PMID: 32782472 PMCID: PMC7412794 DOI: 10.1186/s13068-020-01779-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/29/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cellobiohydrolase from glycoside hydrolase family 7 is a major component of commercial enzymatic mixtures for lignocellulosic biomass degradation. For many years, Trichoderma reesei Cel7A (TrCel7A) has served as a model to understand structure-function relationships of processive cellobiohydrolases. The architecture of TrCel7A includes an N-glycosylated catalytic domain, which is connected to a carbohydrate-binding module through a flexible, O-glycosylated linker. Depending on the fungal expression host, glycosylation can vary not only in glycoforms, but also in site occupancy, leading to a complex pattern of glycans, which can affect the enzyme's stability and kinetics. RESULTS Two expression hosts, Aspergillus oryzae and Trichoderma reesei, were utilized to successfully express wild-types TrCel7A (WT Ao and WT Tr ) and the triple N-glycosylation site deficient mutants TrCel7A N45Q, N270Q, N384Q (ΔN-glyc Ao and ΔN-glyc Tr ). Also, we expressed single N-glycosylation site deficient mutants TrCel7A (N45Q Ao , N270Q Ao , N384Q Ao ). The TrCel7A enzymes were studied by steady-state kinetics under both substrate- and enzyme-saturating conditions using different cellulosic substrates. The Michaelis constant (K M ) was consistently found to be lowered for the variants with reduced N-glycosylation content, and for the triple deficient mutants, it was less than half of the WTs' value on some substrates. The ability of the enzyme to combine productively with sites on the cellulose surface followed a similar pattern on all tested substrates. Thus, site density (number of sites per gram cellulose) was 30-60% higher for the single deficient variants compared to the WT, and about twofold larger for the triple deficient enzyme. Molecular dynamic simulation of the N-glycan mutants TrCel7A revealed higher number of contacts between CD and cellulose crystal upon removal of glycans at position N45 and N384. CONCLUSIONS The kinetic changes of TrCel7A imposed by removal of N-linked glycans reflected modifications of substrate accessibility. The presence of N-glycans with extended structures increased K M and decreased attack site density of TrCel7A likely due to steric hindrance effect and distance between the enzyme and the cellulose surface, preventing the enzyme from achieving optimal conformation. This knowledge could be applied to modify enzyme glycosylation to engineer enzyme with higher activity on the insoluble substrates.
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Affiliation(s)
| | - Kay S. Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kgs. Lyngby, Denmark
| | | | - Günther H. J. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kgs. Lyngby, Denmark
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20
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Hamre AG, Sørlie M. Kinetic relationships with processivity in Serratia marcescens family 18 glycoside hydrolases. Biochem Biophys Res Commun 2020; 521:120-124. [PMID: 31629467 DOI: 10.1016/j.bbrc.2019.10.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022]
Abstract
In nature, recalcitrant polysaccharides such as chitin and cellulose are degraded by glycoside hydrolases (GH) that act synergistically through different modes of action including attack from reducing-end and nonreducing-end (exo-mode) and random (endo-mode) on single polysaccharide chains. Both modes can be combined with a processive mechanism where the GH remain bound to the polysaccharide to perform multiple catalytic steps before dissociation into the solution. In this work, we have determined association rate constants and their activation paramaters for three co-evolved GHs from Serratia marcescens (SmChiA, SmChiB, and SmChiC) with an oligomeric substrate. Interestingly, we observe a positive correlation between the association rate constants and processive ability for the GHs. Previously, a positive correlation has been observed between substrate binding affinity and processive ability. SmChiA with highest processive ability of the three GHs bind with a kon of 11.5 ± 0.2 μM-1s-1, which is five-fold and 130-fold faster than SmChiB (less processive) and SmChiC (nonprocessive), respectively.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway.
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21
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Crystal Structure of a GH3 β-Glucosidase from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2019; 20:ijms20235962. [PMID: 31783503 PMCID: PMC6929035 DOI: 10.3390/ijms20235962] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 11/17/2022] Open
Abstract
Beta-glucosidases (β-glucosidases) have attracted considerable attention in recent years for use in various biotechnological applications. They are also essential enzymes for lignocellulose degradation in biofuel production. However, cost-effective biomass conversion requires the use of highly efficient enzymes. Thus, the search for new enzymes as better alternatives of the currently available enzyme preparations is highly important. Thermophilic fungi are nowadays considered as a promising source of enzymes with improved stability. Here, the crystal structure of a family GH3 β-glucosidase from the thermophilic fungus Chaetomium thermophilum (CtBGL) was determined at a resolution of 2.99 Å. The structure showed the three-domain architecture found in other β-glucosidases with variations in loops and linker regions. The active site catalytic residues in CtBGL were identified as Asp287 (nucleophile) and Glu517 (acid/base). Structural comparison of CtBGL with Protein Data Bank (PDB)-deposited structures revealed variations among glycosylated Asn residues. The enzyme displayed moderate glycosylation compared to other GH3 family β-glucosidases with similar structure. A new glycosylation site at position Asn504 was identified in CtBGL. Moreover, comparison with respect to several thermostability parameters suggested that glycosylation and charged residues involved in electrostatic interactions may contribute to the stability of the enzyme at elevated temperatures. The reported CtBGL structure provides additional insights into the family GH3 enzymes and could offer new ideas for further improvements in β-glucosidases for more efficient use in biotechnological applications regarding cellulose degradation.
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Abstract
Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.
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23
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Jana S, Hamre AG, Eijsink VGH, Sørlie M, Payne CM. Polar residues lining the binding cleft of a Serratia marcescens family 18 chitinase position the substrate for attack and stabilize associative interactions. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1657600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Anne Grethe Hamre
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
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24
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A biochemical comparison of fungal GH6 cellobiohydrolases. Biochem J 2019; 476:2157-2172. [DOI: 10.1042/bcj20190185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 02/02/2023]
Abstract
AbstractCellobiohydrolases (CBHs) from glycoside hydrolase family 6 (GH6) make up an important part of the secretome in many cellulolytic fungi. They are also of technical interest, particularly because they are part of the enzyme cocktails that are used for the industrial breakdown of lignocellulosic biomass. Nevertheless, functional studies of GH6 CBHs are scarce and focused on a few model enzymes. To elucidate functional breadth among GH6 CBHs, we conducted a comparative biochemical study of seven GH6 CBHs originating from fungi living in different habitats, in addition to one enzyme variant. The enzyme sequences were investigated by phylogenetic analyses to ensure that they were not closely related phylogenetically. The selected enzymes were all heterologously expressed in Aspergillus oryzae, purified and thoroughly characterized biochemically. This approach allowed direct comparisons of functional data, and the results revealed substantial variability. For example, the adsorption capacity on cellulose spanned two orders of magnitude and kinetic parameters, derived from two independent steady-state methods also varied significantly. While the different functional parameters covered wide ranges, they were not independent since they changed in parallel between two poles. One pole was characterized by strong substrate interactions, high adsorption capacity and low turnover number while the other showed weak substrate interactions, poor adsorption and high turnover. The investigated enzymes essentially defined a continuum between these two opposites, and this scaling of functional parameters raises interesting questions regarding functional plasticity and evolution of GH6 CBHs.
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25
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Jiang W. Accelerating Convergence of Free Energy Computations with Hamiltonian Simulated Annealing of Solvent (HSAS). J Chem Theory Comput 2019; 15:2179-2186. [PMID: 30821969 DOI: 10.1021/acs.jctc.8b01147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Coupling between binding of a ligand to a receptor and the displacement of a number of bound water molecules is a common event in molecular recognition processes. When the binding site is deeply buried and the exchange of water molecules with the bulk region is difficult to sample, the convergence and accuracy in free energy calculations can be severely compromised. Traditionally, Grand Canonical Monte Carlo (GCMC) based methods have been used to accelerate equilibration of water-at the expense, however, of lengthy trials before a molecular dynamics (MD) simulation. In this paper, a user-friendly and cost-efficient method, Hamiltonian simulated annealing of solvent in combination with λ-exchange of free energy perturbation (FEP) is proposed to accelerate the sampling of water molecules in free energy calculations. As an illustrative example with reliable data from previous GCMC simulations, absolute binding affinity of camphor to cytochrome P450 was calculated. The simulated hydration state change in the buried binding pocket quantitatively agrees with GCMC simulations. It is shown that the new protocol significantly accelerates sampling of water in a buried binding pocket and the convergence of free energy, with negligible setup and computing costs compared to GCMC methods.
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Affiliation(s)
- Wei Jiang
- Computational Science Division , Argonne National Laboratory , 9700 South Cass Avenue, Building 240 , Argonne , Illinois 60439 , United States
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26
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Hamre AG, Kaupang A, Payne CM, Väljamäe P, Sørlie M. Thermodynamic Signatures of Substrate Binding for Three Thermobifida fusca Cellulases with Different Modes of Action. Biochemistry 2019; 58:1648-1659. [PMID: 30785271 DOI: 10.1021/acs.biochem.9b00014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzymatic breakdown of recalcitrant polysaccharides is achieved by synergistic enzyme cocktails of glycoside hydrolases (GHs) and accessory enzymes. Many GHs are processive, meaning that they stay bound to the substrate between subsequent catalytic interactions. Cellulases are GHs that catalyze the hydrolysis of cellulose [β-1,4-linked glucose (Glc)]. Here, we have determined the relative subsite binding affinity for a glucose moiety as well as the thermodynamic signatures for (Glc)6 binding to three of the seven cellulases produced by the bacterium Thermobifida fusca. TfCel48A is exo-processive, TfCel9A endo-processive, and TfCel5A endo-nonprocessive. Initial hydrolysis of (Glc)5 and (Glc)6 was performed in H218O enabling the incorporation of an 18O atom at the new reducing end anomeric carbon. A matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of the products reveals the intensity ratios of otherwise identical 18O- and 16O-containing products to provide insight into how the substrate is placed during productive binding. The two processive cellulases have significant binding affinity in subsites where products dissociate during processive hydrolysis, aligned with a need to have a pushing potential to remove obstacles on the substrate. Moreover, we observed a correlation between processive ability and favorable binding free energy, as previously postulated. Upon ligand binding, the largest contribution to the binding free energy is desolvation for all three cellulases as determined by isothermal titration calorimetry. The two endo-active cellulases show a more favorable solvation entropy change compared to the exo-active cellulase, while the two processive cellulases have less favorable changes in binding enthalpy compared to the nonprocessive TfCel5A.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science , Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
| | - Anita Kaupang
- Department of Chemistry, Biotechnology and Food Science , Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering , University of Kentucky , 177 F. Paul Anderson Tower , Lexington , Kentucky 40506 , United States
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology , University of Tartu , 50090 Tartu , Estonia
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science , Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
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Madhuprakash J, Dalhus B, Vaaje-Kolstad G, Sakuda S, Podile AR, Eijsink VGH, Sørlie M. Structural and Thermodynamic Signatures of Ligand Binding to the Enigmatic Chitinase D of Serratia proteamaculans. J Phys Chem B 2019; 123:2270-2279. [PMID: 30789732 DOI: 10.1021/acs.jpcb.8b11448] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Gram-negative bacteria Serratia marcescens and Serratia proteamaculans have efficient chitinolytic machineries that degrade chitin into N-acetylglucosamine (GlcNAc), which is used as a carbon and energy source. The enzymatic degradation of chitin in these bacteria occurs through the synergistic action of glycoside hydrolases (GHs) that have complementary activities; an endo-acting GH (ChiC) making random scissions on the polysaccharide chains and two exo-acting GHs mainly targeting single reducing (ChiA) and nonreducing (ChiB) chain ends. Both bacteria produce low amounts of a fourth GH18 (ChiD) with an unclear role in chitin degradation. Here, we have determined the thermodynamic signatures for binding of (GlcNAc)6 and the inhibitor allosamidin to SpChiD as well as the crystal structure of SpChiD in complex with allosamidin. The binding free energies for the two ligands are similar (Δ Gr° = -8.9 ± 0.1 and -8.4 ± 0.1 kcal/mol, respectively) with clear enthalpic penalties (Δ Hr° = 3.2 ± 0.1 and 1.8 ± 0.1 kcal/mol, respectively). Binding of (GlcNAc)6 is dominated by solvation entropy change (- TΔ Ssolv° = -17.4 ± 0.4 kcal/mol) and the conformational entropy change dominates for allosamidin binding (- TΔ Sconf° = -9.0 ± 0.2 kcal/mol). These signatures as well as the interactions with allosamidin are very similar to those of SmChiB suggesting that both enzymes are nonreducing end-specific.
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Affiliation(s)
- Jogi Madhuprakash
- Department of Chemistry, Biotechnology and Food Science , NMBU-Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway.,Department of Plant Sciences, School of Life Sciences , University of Hyderabad , Gachibowli, 500046 Hyderabad , India
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine , University of Oslo , P.O. Box 4950, Nydalen, N-0424 Oslo , Norway.,Department of Microbiology, Clinic for Laboratory Medicine , Oslo University Hospital, Rikshospitalet , P.O. Box 4950, Nydalen, N-0424 Oslo , Norway
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science , NMBU-Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
| | - Shohei Sakuda
- Department of Applied Biological Chemistry , University of Tokyo , Bunkyo-Ku, 113 Tokyo , Japan
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences , University of Hyderabad , Gachibowli, 500046 Hyderabad , India
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science , NMBU-Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science , NMBU-Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås , Norway
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28
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Gesteira TF, Coulson-Thomas VJ. Structural basis of oligosaccharide processing by glycosaminoglycan sulfotransferases. Glycobiology 2019; 28:885-897. [PMID: 29878110 DOI: 10.1093/glycob/cwy055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/06/2018] [Indexed: 02/04/2023] Open
Abstract
Heparan sulfate (HS) is a sulfated polysaccharide that plays a key role in morphogenesis, physiology and pathogenesis. The biosynthesis of HS takes place in the Golgi apparatus by a group of enzymes that polymerize, epimerize and sulfate the sugar chain. This biosynthetic process introduces varying degrees of sulfate substitution, which are tightly regulated and directly dictate binding specificity to different cytokines, morphogens and growth factors. Here, we report the use of molecular dynamics simulations to investigate the dynamics of substrate recognition of two glycosaminoglycan (GAG) sulfotransferases, N-deacetylase-N-sulfotransferase and 2-O-sulfotransferase to the HS chain during the biosynthetic process. We performed multiple simulations of the binding of the sulfotransferase domains to both the HS oligosaccharide substrate and sulfate donor, 3'-phosphoadenosine-5'-phosphosulfate. Analysis of extended simulations provide detailed and useful insights into the atomic interactions that are at work during oligosaccharide processing. The fast information matching method was used to detect the enzyme global dynamics and to predict the pairwise contact of residues responsible for GAG-enzyme binding and unbinding. The correlation between HS displacement and the location of the modified GAG chain were calculated, indicating a possible route for HS and heparin during sulfotransferase processing. Our data also show sulfotransferases contain a conserved interspaced positively charged amino acid residues that form a patch which controls the protein-GAG binding equilibrium. Together, our findings provide further understanding on the fine-tuned complex mechanism of GAG biosynthesis. Our findings can also be extrapolated to other systems for calculating rates of protein-GAG binding.
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Affiliation(s)
- Tarsis F Gesteira
- College of Optometry, University of Houston, 4901 Calhoun Rd, Houston, TX, USA.,Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio,100 - 6o andar, 04044-020 São Paulo, SP, Brazil
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29
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Geronimo I, Ntarima P, Piens K, Gudmundsson M, Hansson H, Sandgren M, Payne CM. Kinetic and molecular dynamics study of inhibition and transglycosylation in Hypocrea jecorina family 3 β-glucosidases. J Biol Chem 2019; 294:3169-3180. [PMID: 30602567 DOI: 10.1074/jbc.ra118.007027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Indexed: 01/09/2023] Open
Abstract
β-Glucosidases enhance enzymatic biomass conversion by relieving cellobiose inhibition of endoglucanases and cellobiohydrolases. However, the susceptibility of these enzymes to inhibition and transglycosylation at high glucose or cellobiose concentrations severely limits their activity and, consequently, the overall efficiency of enzyme mixtures. We determined the impact of these two processes on the hydrolytic activity of the industrially relevant family 3 β-glucosidases from Hypocrea jecorina, HjCel3A and HjCel3B, and investigated the underlying molecular mechanisms through kinetic studies, binding free energy calculations, and molecular dynamics (MD) simulations. HjCel3B had a 7-fold higher specificity for cellobiose than HjCel3A but greater tendency for glucose inhibition. Energy decomposition analysis indicated that cellobiose has relatively weak electrostatic interactions with binding site residues, allowing it to be easily displaced by glucose and free to inhibit other hydrolytic enzymes. HjCel3A is, thus, preferable as an industrial β-glucosidase despite its lower activity caused by transglycosylation. This competing pathway to hydrolysis arises from binding of glucose or cellobiose at the product site after formation of the glycosyl-enzyme intermediate. MD simulations revealed that binding is facilitated by hydrophobic interactions with Trp-37, Phe-260, and Tyr-443. Targeting these aromatic residues for mutation to reduce substrate affinity at the product site would therefore potentially mitigate transglycosidic activity. Engineering improved variants of HjCel3A and other structurally similar β-glucosidases would have a significant economic effect on enzymatic biomass conversion in terms of yield and production cost as the process can be consequently conducted at higher substrate loadings.
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Affiliation(s)
- Inacrist Geronimo
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046
| | - Patricia Ntarima
- the Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium, and
| | - Kathleen Piens
- the Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium, and
| | - Mikael Gudmundsson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Christina M Payne
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, .,the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
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30
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Kognole AA, Payne CM. Cellulose-specific Type B carbohydrate binding modules: understanding oligomeric and non-crystalline substrate recognition mechanisms. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:319. [PMID: 30519283 PMCID: PMC6267901 DOI: 10.1186/s13068-018-1321-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/22/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Effective enzymatic degradation of crystalline polysaccharides requires a synergistic cocktail of hydrolytic enzymes tailored to the wide-ranging degree of substrate crystallinity. To accomplish this type of targeted carbohydrate recognition, nature produces multi-modular enzymes, having at least one catalytic domain appended to one or more carbohydrate binding modules (CBMs). The Type B CBM categorization encompasses several families (i.e., protein folds) of CBMs that are generally thought to selectively bind oligomeric polysaccharides; however, a subset of cellulose-specific CBM families (17 and 28) appear to bind non-crystalline cellulose more tightly than oligomers and in a manner that discriminates between surface topology. RESULTS To provide insight into this unexplained phenomenon, we investigated the molecular-level origins of oligomeric and non-crystalline carbohydrate recognition in cellulose-specific Type B CBMs using molecular dynamics (MD) simulation and free energy calculations. Examining two CBMs from three different families (4, 17, and 28), we describe how protein-ligand dynamics contribute to observed variations in binding affinity of oligomers within the same CBM family. Comparisons across the three CBM families identified factors leading to modified functionality prohibiting competitive binding, despite similarity in sequence and specificity. Using free energy perturbation with Hamiltonian replica exchange MD, we also examined the hypothesis that the open topology of the binding grooves in families 17 and 28 necessitates tight binding of an oligomer, while the more confined family 4 binding groove does not require the same degree of tight binding. Finally, we elucidated the mechanisms of non-crystalline carbohydrate recognition by modeling CBMs complexed with a partially decrystallized cellulose substrate. Molecular simulation provided structural and dynamic data for direct comparison to oligomeric modes of carbohydrate recognition, and umbrella sampling MD was used to determine ligand binding free energy. Comparing both protein-carbohydrate interactions and ligand binding free energies, which were in good agreement with experimental values, we confirmed the hypothesis that family 17 and 28 CBMs bind non-crystalline cellulose and oligomers with different affinities (i.e., high and low). CONCLUSIONS Our study provides an unprecedented level of insight into the complex solid and soluble carbohydrate substrate recognition mechanisms of Type B CBMs, the findings of which hold considerable promise for enhancing lignocellulosic biomass conversion technology and development of plant cell wall probes.
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Affiliation(s)
- Abhishek A. Kognole
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F Paul Anderson Tower, Lexington, KY 40506 USA
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F Paul Anderson Tower, Lexington, KY 40506 USA
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31
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Jiang W, Thirman J, Jo S, Roux B. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis. J Phys Chem B 2018; 122:9435-9442. [PMID: 30253098 DOI: 10.1021/acs.jpcb.8b03277] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free-energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559-2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a preidentified "solute" and a second one via the introduction of flattening torsional free-energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of p-xylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. The tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free-energy computations.
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Affiliation(s)
- Wei Jiang
- Computational Science Division , Argonne National Laboratory , 9700 South Cass Avenue, Building 240 , Argonne , Illinois 60439 , United States
| | - Jonathan Thirman
- Computational Science Division , Argonne National Laboratory , 9700 South Cass Avenue, Building 240 , Argonne , Illinois 60439 , United States
| | - Sunhwan Jo
- Computational Science Division , Argonne National Laboratory , 9700 South Cass Avenue, Building 240 , Argonne , Illinois 60439 , United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science , University of Chicago , 929 57th Street , Chicago , Illinois 60637 , United States
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32
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Nakamura A, Okazaki KI, Furuta T, Sakurai M, Iino R. Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin. Nat Commun 2018; 9:3814. [PMID: 30232340 PMCID: PMC6145945 DOI: 10.1038/s41467-018-06362-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/29/2018] [Indexed: 12/02/2022] Open
Abstract
Processive chitinase is a linear molecular motor which moves on the surface of crystalline chitin driven by processive hydrolysis of single chitin chain. Here, we analyse the mechanism underlying unidirectional movement of Serratia marcescens chitinase A (SmChiA) using high-precision single-molecule imaging, X-ray crystallography, and all-atom molecular dynamics simulation. SmChiA shows fast unidirectional movement of ~50 nm s-1 with 1 nm forward and backward steps, consistent with the length of reaction product chitobiose. Analysis of the kinetic isotope effect reveals fast substrate-assisted catalysis with time constant of ~3 ms. Decrystallization of the single chitin chain from crystal surface is the rate-limiting step of movement with time constant of ~17 ms, achieved by binding free energy at the product-binding site of SmChiA. Our results demonstrate that SmChiA operates as a burnt-bridge Brownian ratchet wherein the Brownian motion along the single chitin chain is rectified forward by substrate-assisted catalysis.
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Grants
- JP15H06898 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP17K18429 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP17H05899 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP16H00789 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP16H00858 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP17K19213 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP18H05424 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP15H04366 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 01311805 MEXT | National Institutes of Natural Sciences (NINS)
- J281002 MEXT | National Institutes of Natural Sciences (NINS)
- Advanced Technology Institute Research Grants (RG2709)
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Affiliation(s)
- Akihiko Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, 444-8787, Okazaki, Aichi, Japan.
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, 240-0193, Japan.
| | - Kei-Ichi Okazaki
- Institute for Molecular Science, National Institutes of Natural Sciences, 444-8787, Okazaki, Aichi, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, 444-8787, Okazaki, Aichi, Japan.
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, 240-0193, Japan.
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33
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Zhai R, Hu J, Saddler JN. The inhibition of hemicellulosic sugars on cellulose hydrolysis are highly dependant on the cellulase productive binding, processivity, and substrate surface charges. BIORESOURCE TECHNOLOGY 2018; 258:79-87. [PMID: 29524690 DOI: 10.1016/j.biortech.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/02/2017] [Accepted: 12/04/2017] [Indexed: 05/24/2023]
Abstract
In this study, the influence of major hemicellulosic sugars (mannose and xylose) on cellulose hydrolysis and major enzyme activities were evaluated by using both commercial enzyme cocktail and purified cellulase monocomponents over a "library" of cellulosic substrates. Surprisingly, the results showed that unlike glucose, mannose/xylose did not inhibit individual cellulase activities but significantly decreased their hydrolytic performance on cellulose substrates. When various enzyme-substrate interactions (e.g. adsorption/desorption, productive binding, and processive moving) were evaluated, it appeared that these hemicellulosic sugars significantly reduced the productive binding and processivity of Cel7A, which in turn limited cellulase hydrolytic efficacy. Among a range of major cellulose characteristics (e.g. crystallinity, degree of polymerization, accessibility, and surface charges), the acid group content of the cellulosic substrates seemed to be the main driver that determined the extent of hemicellulosic sugar inhibition. Our results provided new insights for better understanding the sugar inhibition mechanisms of cellulose hydrolysis.
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Affiliation(s)
- Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada
| | - Jinguang Hu
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada.
| | - Jack N Saddler
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada
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34
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Zhang KD, Li W, Wang YF, Zheng YL, Tan FC, Ma XQ, Yao LS, Bayer EA, Wang LS, Li FL. Processive Degradation of Crystalline Cellulose by a Multimodular Endoglucanase via a Wirewalking Mode. Biomacromolecules 2018; 19:1686-1696. [DOI: 10.1021/acs.biomac.8b00340] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kun-Di Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People’s Republic of China
| | - Wen Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People’s Republic of China
| | - Ye-Fei Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
| | - Yan-Lin Zheng
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, People’s Republic of China
| | - Fang-Cheng Tan
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
| | - Xiao-Qing Ma
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, People’s Republic of China
| | - Li-Shan Yao
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lu-Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People’s Republic of China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, People’s Republic of China
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35
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Wu B, Zheng S, Pedroso MM, Guddat LW, Chang S, He B, Schenk G. Processivity and enzymatic mechanism of a multifunctional family 5 endoglucanase from Bacillus subtilis BS-5 with potential applications in the saccharification of cellulosic substrates. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:20. [PMID: 29422948 PMCID: PMC5787917 DOI: 10.1186/s13068-018-1022-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/11/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Presently, enzymes still constitute a major part of the cost of biofuel production from lignocellulosic biomass. Processive endoglucanases, which possess both endoglucanase and exoglucanase activity, have the potential to reduce the costs of biomass saccharification when used together with commercial cellulases. Therefore, the exploration of new processive endoglucanases has attracted much attention with a view to accelerating the industrialization of biofuels and biochemicals. RESULTS The endoglucanase EG5C and its truncated form EG5C-1 from Bacillus subtilis BS-5 were expressed and characterized. EG5C was a typical endoglucanase, comprised of a family 5 catalytic domain and family 3 carbohydrate-binding domain, and which had high activity toward soluble cellulosic substrates, but low activity toward insoluble cellulosic substrates. Importantly, the truncated form EG5C-1 was a processive endoglucanase that hydrolyzed not only carboxymethyl cellulose (CMC), but also insoluble cellulosic substrates. The hydrolytic activities of EG5C-1 towards CMC, phosphoric acid-swollen cellulose (PASC), p-nitrophenyl-β-d-cellobioside, filter paper and Avicel are 4170, 700, 2550, 405 and 320 U/μmol, respectively. These data demonstrated that EG5C-1 had higher activity ratio of exoglucanase to endoglucanase than other known processive endoglucanases. When PASC was degraded by EG5C-1, the ratio of soluble to insoluble reducing sugars was about 3.7 after 3 h of incubation with cellobiose and cellotriose as the main products. Importantly, EG5C-1 alone was able to hydrolyze filter paper and PASC. At 5% substrate concentration and 10 FPU/g PASC enzyme loading, the saccharification yield was 76.5% after 60 h of incubation. Replacement of a phenylalanine residue (F238) by an alanine at the entrance/exit of the substrate binding cleft significantly reduces the ability of EG5C-1 to degrade filter paper and Avicel, but this mutation has little impact on CMCase activity. The processivity of this mutant was also greatly reduced while its cellulose binding ability was markedly enhanced. CONCLUSIONS The processive endoglucanase EG5C-1 from B. subtilis BS-5 exhibits excellent properties that render it a suitable candidate for use in biofuel and biochemical production from lignocellulosic biomass. In addition, our studies also provide useful information for research on enzyme processivity at the molecular level.
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Affiliation(s)
- Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
- China Jiangsu National Synergetic Innovation Center for Advanced Materials, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Shan Zheng
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
| | - Siyuan Chang
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Bingfang He
- China Jiangsu National Synergetic Innovation Center for Advanced Materials, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816 Jiangsu China
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072 Australia
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36
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Badino SF, Kari J, Christensen SJ, Borch K, Westh P. Direct kinetic comparison of the two cellobiohydrolases Cel6A and Cel7A from Hypocrea jecorina. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1739-1745. [DOI: 10.1016/j.bbapap.2017.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/25/2017] [Accepted: 08/14/2017] [Indexed: 01/17/2023]
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37
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Alanine substitution in cellobiohydrolase provides new insights into substrate threading. Sci Rep 2017; 7:16320. [PMID: 29176588 PMCID: PMC5701224 DOI: 10.1038/s41598-017-16434-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/13/2017] [Indexed: 12/14/2022] Open
Abstract
The glycoside hydrolase family 7 (GH7) member cellobiohydrolase (CBH) is a key enzyme that degrades crystalline cellulose, an important structural component of plant cell walls. As GH7 CBH is a major component in the enzyme mixture used to degrade biomass into fermentable glucose in biorefineries, enhancing its catalytic activity will significantly impact development in this field. GH7 CBH possesses a catalytic tunnel through which cellulose substrates are threaded and hydrolysed. Despite numerous studies dissecting this processive mechanism, the role of amino acid residues in the tunnel remains not fully understood. Herein, we examined the respective contributions of nine amino acid residues in the catalytic tunnel of GH7 CBH from Talaromyces cellulolyticus by substitution with alanine. As a result, N62A and K203A mutants were found to possess significantly higher cellulase activities than wild type. Molecular dynamics simulations showed that the N62 residue interacted strongly with the cellulose substrate, impeding threading, while the N62A mutant allowed cellulose to proceed more smoothly. Furthermore, the W63 residue was observed to facilitate twisting of the cellulose substrate in our simulations. This study helps elucidate cellulose threading and provides insight into biomass hydrolysis.
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38
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Wu X, Tian Z, Jiang X, Zhang Q, Wang L. Enhancement in catalytic activity of Aspergillus niger XynB by selective site-directed mutagenesis of active site amino acids. Appl Microbiol Biotechnol 2017; 102:249-260. [DOI: 10.1007/s00253-017-8607-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 01/25/2023]
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Goedegebuur F, Dankmeyer L, Gualfetti P, Karkehabadi S, Hansson H, Jana S, Huynh V, Kelemen BR, Kruithof P, Larenas EA, Teunissen PJM, Ståhlberg J, Payne CM, Mitchinson C, Sandgren M. Improving the thermal stability of cellobiohydrolase Cel7A from Hypocrea jecorina by directed evolution. J Biol Chem 2017; 292:17418-17430. [PMID: 28860192 DOI: 10.1074/jbc.m117.803270] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/24/2017] [Indexed: 11/06/2022] Open
Abstract
Secreted mixtures of Hypocrea jecorina cellulases are able to efficiently degrade cellulosic biomass to fermentable sugars at large, commercially relevant scales. H. jecorina Cel7A, cellobiohydrolase I, from glycoside hydrolase family 7, is the workhorse enzyme of the process. However, the thermal stability of Cel7A limits its use to processes where temperatures are no higher than 50 °C. Enhanced thermal stability is desirable to enable the use of higher processing temperatures and to improve the economic feasibility of industrial biomass conversion. Here, we enhanced the thermal stability of Cel7A through directed evolution. Sites with increased thermal stability properties were combined, and a Cel7A variant (FCA398) was obtained, which exhibited a 10.4 °C increase in Tm and a 44-fold greater half-life compared with the wild-type enzyme. This Cel7A variant contains 18 mutated sites and is active under application conditions up to at least 75 °C. The X-ray crystal structure of the catalytic domain was determined at 2.1 Å resolution and showed that the effects of the mutations are local and do not introduce major backbone conformational changes. Molecular dynamics simulations revealed that the catalytic domain of wild-type Cel7A and the FCA398 variant exhibit similar behavior at 300 K, whereas at elevated temperature (475 and 525 K), the FCA398 variant fluctuates less and maintains more native contacts over time. Combining the structural and dynamic investigations, rationales were developed for the stabilizing effect at many of the mutated sites.
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Affiliation(s)
- Frits Goedegebuur
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands,
| | - Lydia Dankmeyer
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands
| | | | - Saeid Karkehabadi
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Henrik Hansson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Suvamay Jana
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Vicky Huynh
- DuPont Industrial Biosciences, Palo Alto, California 94304
| | | | - Paulien Kruithof
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands
| | | | | | - Jerry Ståhlberg
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Christina M Payne
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | | | - Mats Sandgren
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
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Kuusk S, Sørlie M, Väljamäe P. Human Chitotriosidase Is an Endo-Processive Enzyme. PLoS One 2017; 12:e0171042. [PMID: 28129403 PMCID: PMC5271402 DOI: 10.1371/journal.pone.0171042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/13/2017] [Indexed: 01/17/2023] Open
Abstract
Human chitotriosidase (HCHT) is involved in immune response to chitin-containing pathogens in humans. The enzyme is able to degrade chitooligosaccharides as well as crystalline chitin. The catalytic domain of HCHT is connected to the carbohydrate binding module (CBM) through a flexible hinge region. In humans, two active isoforms of HCHT are found-the full length enzyme and its truncated version lacking CBM and the hinge region. The active site architecture of HCHT is reminiscent to that of the reducing-end exo-acting processive chitinase ChiA from bacterium Serratia marcescens (SmChiA). However, the presence of flexible hinge region and occurrence of two active isoforms are reminiscent to that of non-processive endo-chitinase from S. marcescens, SmChiC. Although the studies on soluble chitin derivatives suggest the endo-character of HCHT, the mode of action of the enzyme on crystalline chitin is not known. Here, we made a thorough characterization of HCHT in terms of the mode of action, processivity, binding, and rate constants for the catalysis and dissociation using α-chitin as substrate. HCHT efficiently released the end-label from reducing-end labelled chitin and had also high probability (95%) of endo-mode initiation of processive run. These results qualify HCHT as an endo-processive enzyme. Processivity and the rate constant of dissociation of HCHT were found to be in-between those, characteristic to processive exo-enzymes, like SmChiA and randomly acting non-processive endo-enzymes, like SmChiC. Apart from increasing the affinity for chitin, CBM had no major effect on kinetic properties of HCHT.
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Affiliation(s)
- Silja Kuusk
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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41
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Kognole AA, Payne CM. Inhibition of Mammalian Glycoprotein YKL-40: IDENTIFICATION OF THE PHYSIOLOGICAL LIGAND. J Biol Chem 2017; 292:2624-2636. [PMID: 28053085 DOI: 10.1074/jbc.m116.764985] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/22/2016] [Indexed: 12/21/2022] Open
Abstract
YKL-40 is a mammalian glycoprotein associated with progression, severity, and prognosis of chronic inflammatory diseases and a multitude of cancers. Despite this well documented association, identification of the lectin's physiological ligand and, accordingly, biological function has proven experimentally difficult. YKL-40 has been shown to bind chito-oligosaccharides; however, the production of chitin by the human body has not yet been documented. Possible alternative ligands include proteoglycans, polysaccharides, and fibers like collagen, all of which makeup the extracellular matrix. It is likely that YKL-40 is interacting with these alternative polysaccharides or proteins within the body, extending its function to cell biological roles such as mediating cellular receptors and cell adhesion and migration. Here, we consider the feasibility of polysaccharides, including cello-oligosaccharides, hyaluronan, heparan sulfate, heparin, and chondroitin sulfate, and collagen-like peptides as physiological ligands for YKL-40. We use molecular dynamics simulations to resolve the molecular level recognition mechanisms and calculate the free energy of binding the hypothesized ligands to YKL-40, addressing thermodynamic preference relative to chito-oligosaccharides. Our results suggest that chitohexaose and hyaluronan preferentially bind to YKL-40 over collagen, and hyaluronan is likely the preferred physiological ligand, because the negatively charged hyaluronan shows enhanced affinity for YKL-40 over neutral chitohexaose. Collagen binds in two locations at the YKL-40 surface, potentially related to a role in fibrillar formation. Finally, heparin non-specifically binds at the YKL-40 surface, as predicted from structural studies. Overall, YKL-40 likely binds many natural ligands in vivo, but its concurrence with physical maladies may be related to associated increases in hyaluronan.
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Affiliation(s)
- Abhishek A Kognole
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Christina M Payne
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
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42
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Kari J, Kont R, Borch K, Buskov S, Olsen JP, Cruyz-Bagger N, Väljamäe P, Westh P. Anomeric Selectivity and Product Profile of a Processive Cellulase. Biochemistry 2016; 56:167-178. [PMID: 28026938 DOI: 10.1021/acs.biochem.6b00636] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellobiohydrolases (CBHs) make up an important group of enzymes for both natural carbon cycling and industrial deconstruction of lignocellulosic biomass. The consecutive hydrolysis of one cellulose strand relies on an intricate pattern of enzyme-substrate interactions in the long, tunnel-shaped binding site of the CBH. In this work, we have investigated the initial complexation mode with cellulose of the most thoroughly studied CBH, Cel7A from Hypocrea jecorina (HjCel7A). We found that HjCel7A predominantly produces glucose when it initiates a processive run on insoluble microcrystalline cellulose, confirming the validity of an even and odd product ratio as an estimate of processivity. Moreover, the glucose released from cellulose was predominantly α-glucose. A link between the initial binding mode of the enzyme and the reducing end configuration was investigated by inhibition studies with the two anomers of cellobiose. A clear preference for β-cellobiose in product binding site +2 was observed for HjCel7A, but not the homologous endoglucanase, HjCe7B. Possible relationships between this anomeric preference in the product site and the prevalence of odd-numbered initial-cut products are discussed, and a correlation between processivity and anomer selectivity is proposed.
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Affiliation(s)
- Jeppe Kari
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | - Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Kim Borch
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Steen Buskov
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Johan Pelck Olsen
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | | | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Peter Westh
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
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43
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Kont R, Kari J, Borch K, Westh P, Väljamäe P. Inter-domain Synergism Is Required for Efficient Feeding of Cellulose Chain into Active Site of Cellobiohydrolase Cel7A. J Biol Chem 2016; 291:26013-26023. [PMID: 27780868 DOI: 10.1074/jbc.m116.756007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/21/2016] [Indexed: 01/27/2023] Open
Abstract
Structural polysaccharides like cellulose and chitin are abundant and their enzymatic degradation to soluble sugars is an important route in green chemistry. Processive glycoside hydrolases (GHs), like cellobiohydrolase Cel7A of Trichoderma reesei (TrCel7A) are key components of efficient enzyme systems. TrCel7A consists of a catalytic domain (CD) and a smaller carbohydrate-binding module (CBM) connected through the glycosylated linker peptide. A tunnel-shaped active site rests in the CD and contains 10 glucose unit binding sites. The active site of TrCel7A is lined with four Trp residues with two of them, Trp-40 and Trp-38, in the substrate binding sites near the tunnel entrance. Although addressed in numerous studies the elucidation of the role of CBM and active site aromatics has been obscured by a complex multistep mechanism of processive GHs. Here we studied the role of the CBM-linker and Trp-38 of TrCel7A with respect to binding affinity, on- and off-rates, processivity, and synergism with endoglucanase. The CBM-linker increased the on-rate and substrate affinity of the enzyme. The Trp-38 to Ala substitution resulted in increased off-rates and decreased processivity. The effect of the Trp-38 to Ala substitution on on-rates was strongly dependent on the presence of the CBM-linker. This compensation between CBM-linker and Trp-38 indicates synergism between CBM-linker and CD in feeding the cellulose chain into the active site. The inter-domain synergism was pre-requisite for the efficient degradation of cellulose in the presence of endoglucanase.
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Affiliation(s)
- Riin Kont
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Jeppe Kari
- the Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark, and
| | - Kim Borch
- Novozymes A/S, Bagsværd DK-2880, Denmark
| | - Peter Westh
- the Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark, and
| | - Priit Väljamäe
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia,
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44
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Mayes HB, Knott BC, Crowley MF, Broadbelt LJ, Ståhlberg J, Beckham GT. Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases. Chem Sci 2016; 7:5955-5968. [PMID: 30155195 PMCID: PMC6091422 DOI: 10.1039/c6sc00571c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/29/2016] [Indexed: 12/16/2022] Open
Abstract
In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase (TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleaving the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2SO ring configuration as it reaches its binding site. This work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.
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Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Brandon C Knott
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Michael F Crowley
- Biosciences Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology , Swedish University of Agricultural Sciences , SE-75007 , Uppsala , Sweden .
| | - Gregg T Beckham
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
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45
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Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. Sci Rep 2016; 6:23605. [PMID: 27009476 PMCID: PMC4806347 DOI: 10.1038/srep23605] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/09/2016] [Indexed: 02/02/2023] Open
Abstract
Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.
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46
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Wang Y, Zhang S, Song X, Yao L. Cellulose chain binding free energy drives the processive move of cellulases on the cellulose surface. Biotechnol Bioeng 2016; 113:1873-80. [DOI: 10.1002/bit.25970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/17/2016] [Accepted: 02/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Shujun Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Xiangfei Song
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
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47
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Jana S, Hamre AG, Wildberger P, Holen MM, Eijsink VGH, Beckham GT, Sørlie M, Payne CM. Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases. J Phys Chem B 2016; 120:1236-49. [PMID: 26824449 DOI: 10.1021/acs.jpcb.5b12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microorganisms use a host of enzymes, including processive glycoside hydrolases, to deconstruct recalcitrant polysaccharides to sugars. Processive glycoside hydrolases closely associate with polymer chains and repeatedly cleave glycosidic linkages without dissociating from the crystalline surface after each hydrolytic step; they are typically the most abundant enzymes in both natural secretomes and industrial cocktails by virtue of their significant hydrolytic potential. The ubiquity of aromatic residues lining the enzyme catalytic tunnels and clefts is a notable feature of processive glycoside hydrolases. We hypothesized that these aromatic residues have uniquely defined roles, such as substrate chain acquisition and binding in the catalytic tunnel, that are defined by their local environment and position relative to the substrate and the catalytic center. Here, we investigated this hypothesis with variants of Serratia marcescens family 18 processive chitinases ChiA and ChiB. We applied molecular simulation and free energy calculations to assess active site dynamics and ligand binding free energies. Isothermal titration calorimetry provided further insight into enthalpic and entropic contributions to ligand binding free energy. Thus, the roles of six aromatic residues, Trp-167, Trp-275, and Phe-396 in ChiA, and Trp-97, Trp-220, and Phe-190 in ChiB, have been examined. We observed that point mutation of the tryptophan residues to alanine results in unfavorable changes in the free energy of binding relative to wild-type. The most drastic effects were observed for residues positioned at the "entrances" of the deep substrate-binding clefts and known to be important for processivity. Interestingly, phenylalanine mutations in ChiA and ChiB had little to no effect on chito-oligomer binding, in accordance with the limited effects of their removal on chitinase functionality.
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Affiliation(s)
- Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
| | - Anne Grethe Hamre
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Patricia Wildberger
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Matilde Mengkrog Holen
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
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48
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Jin T, Yu H, Huang XF. Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B. Sci Rep 2016; 6:20766. [PMID: 26865097 PMCID: PMC4749975 DOI: 10.1038/srep20766] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/04/2016] [Indexed: 12/31/2022] Open
Abstract
Protein Tyrosine Phosphatase 1B (PTP1B) has been recognized as a promising therapeutic target for treating obesity, diabetes, and certain cancers for over a decade. Previous drug design has focused on inhibitors targeting the active site of PTP1B. However, this has not been successful because the active site is positively charged and conserved among the protein tyrosine phosphatases. Therefore, it is important to develop PTP1B inhibitors with alternative inhibitory strategies. Using computational studies including molecular docking, molecular dynamics simulations, and binding free energy calculations, we found that lupane triterpenes selectively inhibited PTP1B by targeting its more hydrophobic and less conserved allosteric site. These findings were verified using two enzymatic assays. Furthermore, the cell culture studies showed that lupeol and betulinic acid inhibited the PTP1B activity stimulated by TNFα in neurons. Our study indicates that lupane triterpenes are selective PTP1B allosteric inhibitors with significant potential for treating those diseases with elevated PTP1B activity.
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Affiliation(s)
- Tiantian Jin
- Centre for Translational Neuroscience, School of Medicine, University of Wollongong, and Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW 2522, Australia
| | - Haibo Yu
- School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Xu-Feng Huang
- Centre for Translational Neuroscience, School of Medicine, University of Wollongong, and Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW 2522, Australia
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49
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Amore A, Ciesielski PN, Lin CY, Salvachúa D, Sànchez i Nogué V. Development of Lignocellulosic Biorefinery Technologies: Recent Advances and Current Challenges. Aust J Chem 2016. [DOI: 10.1071/ch16022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent developments of the biorefinery concept are described within this review, which focuses on the efforts required to make the lignocellulosic biorefinery a sustainable and economically viable reality. Despite the major research and development endeavours directed towards this goal over the past several decades, the integrated production of biofuel and other bio-based products still needs to be optimized from both technical and economical perspectives. This review will highlight recent progress towards the optimization of the major biorefinery processes, including biomass pretreatment and fractionation, saccharification of sugars, and conversion of sugars and lignin into fuels and chemical precursors. In addition, advances in genetic modification of biomass structure and composition for the purpose of enhancing the efficacy of conversion processes, which is emerging as a powerful tool for tailoring biomass fated for the biorefinery, will be overviewed. The continual improvement of these processes and their integration in the format of a modern biorefinery is paving the way for a sustainable bio-economy which will displace large portions of petroleum-derived fuels and chemicals with renewable substitutes.
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50
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Hamre AG, Jana S, Reppert NK, Payne CM, Sørlie M. Processivity, Substrate Positioning, and Binding: The Role of Polar Residues in a Family 18 Glycoside Hydrolase. Biochemistry 2015; 54:7292-306. [PMID: 26503416 DOI: 10.1021/acs.biochem.5b00830] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzymatic degradation of recalcitrant polysaccharides such as cellulose (β-1,4-linked glucose) and chitin (β-1,4-linked N-acetylglucosamine) by glycoside hydrolases (GHs) is of significant biological and economical importance. In nature, depolymerization is primarily accomplished by processive GHs, which remain attached to the substrate between subsequent hydrolytic reactions. Recent computational efforts have suggested that the processive ability of a GH is directly linked to the ligand binding free energy. The contribution of individual aromatic residues in the active site of these enzymes has been extensively studied. In this study, we offer the first experimental evidence confirming correlation of binding free energy and degree of processivity and evidence that polar residues are essential for maintaining processive ability. Exchanging Thr(276) with Ala in substrate binding subsite -2 in the processive ChiA of Serratia marcescens results in a decrease in both the enthalpy (2.6 and 3.8 kcal/mol) and free energy (0.5 and 2.2 kcal/mol) for the binding to the substrate (GlcNAc)6 and the inhibitor allosamidin, respectively, compared to that of the wild type. Moreover, the initial apparent processivity as measured by [(GlcNAc)2]/[GlcNAc] ratios (17.1 ± 0.4) and chitin degradation efficiency (20%) are greatly reduced for ChiA-T276A versus those of the wild type (30.1 ± 1.5 and 75%, respectively). Mutation of Arg(172) to Ala reduces the level of recognition and positioning of the substrate into the active site. Molecular dynamics simulations indicate ChiA-R172A behaves like the wild type, but the dynamics of ChiA-T276A are greatly influenced by mutation, which is reflective of their influence on processivity.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
| | - Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Nicole K Reppert
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
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