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Nolte RJM, Elemans JAAW. Artificial Processive Catalytic Systems. Chemistry 2024; 30:e202304230. [PMID: 38314967 DOI: 10.1002/chem.202304230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Processive catalysts remain attached to a substrate and perform multiple rounds of catalysis. They are abundant in nature. This review highlights artificial processive catalytic systems, which can be divided into (A) catalytic rings that move along a polymer chain, (B) catalytic pores that hold polymer chains and decompose them, (C) catalysts that remain attached to and move around a cyclic substrate via supramolecular interactions, and (D) anchored catalysts that remain in contact with a substrate via multiple catalytic interactions (see frontispiece).
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Affiliation(s)
- Roeland J M Nolte
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 125, 6525AJ, Nijmegen, The, Netherlands
| | - Johannes A A W Elemans
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 125, 6525AJ, Nijmegen, The, Netherlands
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2
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Zajki-Zechmeister K, Eibinger M, Kaira GS, Nidetzky B. Mechanochemical Coupling of Catalysis and Motion in a Cellulose-Degrading Multienzyme Nanomachine. ACS Catal 2024; 14:2656-2663. [PMID: 38384941 PMCID: PMC10877591 DOI: 10.1021/acscatal.3c05653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/13/2024] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Abstract
The cellulosome is a megadalton-size protein complex that functions as a biological nanomachine of cellulosic fiber degradation. We show that the cellulosome behaves as a Brownian ratchet that rectifies protein motions on the cellulose surface into a propulsion mechanism by coupling to the hydrolysis of cellulose chains. Movement on cellulose fibrils is unidirectional and results from "macromolecular crawl" composed of dynamic switches between elongated and compact spatial arrangements of enzyme subunits. Deletion of the main exocellulase Cel48S eliminates conformational bias for aligning the subunits to the long fibril axis, which we reveal as crucial for optimum coupling between directional movement and substrate degradation. Implications of the cellulosome acting as a mechanochemical motor suggest a distinct mechanism of enzymatic machinery in the deconstruction of cellulose assemblies.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
| | - Gaurav Singh Kaira
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, Graz 8010, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, Graz 8010, Austria
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3
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Nousi A, Molina GA, Schiano-di-Cola C, Sørensen TH, Borch K, Pedersen JN, Westh P, Marie R. Impact of Synergy Partner Cel7B on Cel7A Binding Rates: Insights from Single-Molecule Data. J Phys Chem B 2024; 128:635-647. [PMID: 38227769 PMCID: PMC10824242 DOI: 10.1021/acs.jpcb.3c05697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Enzymatic degradation of cellulosic biomass is a well-established route for the sustainable production of biofuels, chemicals, and materials. A strategy employed by nature and industry to achieve an efficient degradation of cellulose is that cellobiohydrolases (or exocellulases), such as Cel7A, work synergistically with endoglucanases, such as Cel7B, to achieve the complete degradation of cellulose. However, a complete mechanistic understanding of this exo-endo synergy is still lacking. Here, we used single-molecule fluorescence microscopy to quantify the binding kinetics of Cel7A on cellulose when it is acting alone on the cellulose fibrils and in the presence of its synergy partner, the endoglucanase Cel7B. To this end, we used a fluorescently tagged Cel7A and studied its binding in the presence of the unlabeled Cel7B. This provided the single-molecule data necessary for the estimation of the rate constants of association kON and dissociation kOFF of Cel7A for the substrate. We show that the presence of Cel7B does not impact the dissociation rate constant, kOFF. But, the association rate of Cel7A decreases by a factor of 2 when Cel7B is present at a molar proportion of 10:1. This ratio has previously been shown to lead to synergy. This decrease in association rate is observed in a wide range of total enzyme concentrations, from sub nM to μM concentrations. This decrease in kON is consistent with the formation of cellulase clusters recently observed by others using atomic force microscopy.
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Affiliation(s)
- Aimilia Nousi
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gustavo Avelar Molina
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | | | - Kim Borch
- Novozymes
A/S, Krogshøjvej
36, 2880 Bagsværd, Denmark
| | - Jonas N. Pedersen
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
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4
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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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Effect of multimodularity and spatial organization of glycoside hydrolases on catalysis. Essays Biochem 2023; 67:629-638. [PMID: 36866571 DOI: 10.1042/ebc20220167] [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: 11/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 03/04/2023]
Abstract
The wide diversity among the carbohydrate-active enzymes (CAZymes) reflects the equally broad versatility in terms of composition and chemicals bonds found in the plant cell wall polymers on which they are active. This diversity is also expressed through the various strategies developed to circumvent the recalcitrance of these substrates to biological degradation. Glycoside hydrolases (GHs) are the most abundant of the CAZymes and are expressed as isolated catalytic modules or in association with carbohydrate-binding module (CBM), acting in synergism within complex arrays of enzymes. This multimodularity can be even more complex. The cellulosome presents a scaffold protein immobilized to the outer membrane of some microorganisms on which enzymes are grafted to prevent their dispersion and increase catalytic synergism. In polysaccharide utilization loci (PUL), GHs are also distributed across the membranes of some bacteria to co-ordinate the deconstruction of polysaccharides and the internalization of metabolizable carbohydrates. Although the study and characterization of these enzymatic activities need to take into account the entirety of this complex organization-in particular because of the dynamics involved in it-technical problems limit the present study to isolated enzymes. However, these enzymatic complexes also have a spatiotemporal organization, whose still neglected aspect must be considered. In the present review, the different levels of multimodularity that can occur in GHs will be reviewed, from its simplest forms to the most complex. In addition, attempts to characterize or study the effect on catalytic activity of the spatial organization within GHs will be addressed.
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Chaudhari YB, Várnai A, Sørlie M, Horn SJ, Eijsink VGH. Engineering cellulases for conversion of lignocellulosic biomass. Protein Eng Des Sel 2023; 36:gzad002. [PMID: 36892404 PMCID: PMC10394125 DOI: 10.1093/protein/gzad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023] Open
Abstract
Lignocellulosic biomass is a renewable source of energy, chemicals and materials. Many applications of this resource require the depolymerization of one or more of its polymeric constituents. Efficient enzymatic depolymerization of cellulose to glucose by cellulases and accessory enzymes such as lytic polysaccharide monooxygenases is a prerequisite for economically viable exploitation of this biomass. Microbes produce a remarkably diverse range of cellulases, which consist of glycoside hydrolase (GH) catalytic domains and, although not in all cases, substrate-binding carbohydrate-binding modules (CBMs). As enzymes are a considerable cost factor, there is great interest in finding or engineering improved and robust cellulases, with higher activity and stability, easy expression, and minimal product inhibition. This review addresses relevant engineering targets for cellulases, discusses a few notable cellulase engineering studies of the past decades and provides an overview of recent work in the field.
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Affiliation(s)
- Yogesh B Chaudhari
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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