1
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Sorgenfrei FA, Sloan JJ, Weissensteiner F, Zechner M, Mehner NA, Ellinghaus TL, Schachtschabel D, Seemayer S, Kroutil W. Solvent concentration at 50% protein unfolding may reform enzyme stability ranking and process window identification. Nat Commun 2024; 15:5420. [PMID: 38926341 PMCID: PMC11208486 DOI: 10.1038/s41467-024-49774-0] [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: 07/19/2023] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
As water miscible organic co-solvents are often required for enzyme reactions to improve e.g., the solubility of the substrate in the aqueous medium, an enzyme is required which displays high stability in the presence of this co-solvent. Consequently, it is of utmost importance to identify the most suitable enzyme or the appropriate reaction conditions. Until now, the melting temperature is used in general as a measure for stability of enzymes. The experiments here show, that the melting temperature does not correlate to the activity observed in the presence of the solvent. As an alternative parameter, the concentration of the co-solvent at the point of 50% protein unfolding at a specific temperature T in shortc U 50 T is introduced. Analyzing a set of ene reductases,c U 50 T is shown to indicate the concentration of the co-solvent where also the activity of the enzyme drops fastest. Comparing possible rankings of enzymes according to melting temperature andc U 50 T reveals a clearly diverging outcome also depending on the specific solvent used. Additionally, plots ofc U 50 versus temperature enable a fast identification of possible reaction windows to deduce tolerated solvent concentrations and temperature.
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Affiliation(s)
- Frieda A Sorgenfrei
- Austrian Centre of Industrial Biotechnology c/o University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Jeremy J Sloan
- BASF SE, Carl-Bosch-Strasse 38, 67056, Ludwigshafen, Germany
| | - Florian Weissensteiner
- Austrian Centre of Industrial Biotechnology c/o University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- Department of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Marco Zechner
- Austrian Centre of Industrial Biotechnology c/o University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Niklas A Mehner
- BASF SE, Carl-Bosch-Strasse 38, 67056, Ludwigshafen, Germany
| | | | | | - Stefan Seemayer
- BASF SE, Carl-Bosch-Strasse 38, 67056, Ludwigshafen, Germany.
| | - Wolfgang Kroutil
- Austrian Centre of Industrial Biotechnology c/o University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
- Department of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010, Graz, Austria.
- BioTechMed Graz, 8010, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, 8010, Graz, Austria.
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2
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Valotta A, Stelzer D, Reiter T, Kroutil W, Gruber-Woelfler H. A multistep (semi)-continuous biocatalytic setup for the production of polycaprolactone. REACT CHEM ENG 2024; 9:713-727. [PMID: 38433980 PMCID: PMC10903532 DOI: 10.1039/d3re00536d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/12/2023] [Indexed: 03/05/2024]
Abstract
Biocatalysis has gained increasing importance as an eco-friendly alternative for the production of bulk and fine chemicals. Within this paradigm, Baeyer Villiger monoxygenases (BVMOs) serve as enzymatic catalysts that provide a safe and sustainable route to the conventional synthesis of lactones, such as caprolactone, which is employed for the production of polycaprolactone (PCL), a biocompatible polymer for medicinal applications. In this work, we present a three-step, semi-continuous production of PCL using an entirely biocatalytic process, highlighting the merits of continuous manufacturing for enhancing biocatalysis. First, caprolactone is produced in batch from cyclohexanol using a coenzymatic cascade involving an alcohol dehydrogenase (ADH) and BVMO. Different process parameters and aeration modes were explored to optimize the cascade's productivity. Secondly, the continuous extraction of caprolactone into an organic solvent, needed for the polymerization step, was optimized. 3D-printed mixers were applied to enhance the mass transfer between the organic and the aqueous phases. Lastly, we investigated the ring-opening polymerization of caprolactone to PCL catalyzed by Candida antarctica lipase B (CAL-B), with a focus on eco-friendly solvents like cyclopentyl-methyl-ether (CPME). Space-time-yields up to 58.5 g L-1 h-1 were achieved with our overall setup. By optimizing the individual process steps, we present an efficient and sustainable pathway for PCL production.
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Affiliation(s)
- Alessia Valotta
- Institute of Process and Particle Engineering, Graz University of Technology Inffeldgasse 13 8010 Graz Austria
| | - Daniela Stelzer
- Institute of Process and Particle Engineering, Graz University of Technology Inffeldgasse 13 8010 Graz Austria
| | - Tamara Reiter
- Department of Chemistry, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Wolfgang Kroutil
- Department of Chemistry, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Heidrun Gruber-Woelfler
- Institute of Process and Particle Engineering, Graz University of Technology Inffeldgasse 13 8010 Graz Austria
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3
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Guajardo N, Schrebler RA. Upstream and Downstream Bioprocessing in Enzyme Technology. Pharmaceutics 2023; 16:38. [PMID: 38258049 PMCID: PMC10818583 DOI: 10.3390/pharmaceutics16010038] [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: 11/16/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 01/24/2024] Open
Abstract
The development of biotransformation must integrate upstream and downstream processes. Upstream bioprocessing will influence downstream bioprocessing. It is essential to consider this because downstream processes can constitute the highest cost in bioprocessing. This review comprehensively overviews the most critical aspects of upstream and downstream bioprocessing in enzymatic biocatalysis. The main upstream processes discussed are enzyme production, enzyme immobilization methodologies, solvent selection, and statistical optimization methodologies. The main downstream processes reviewed in this work are biocatalyst recovery and product separation and purification. The correct selection and combination of upstream and downstream methodologies will allow the development of a sustainable and highly productive system.
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Affiliation(s)
- Nadia Guajardo
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile
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4
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Li G, Jia L, Wang K, Sun T, Huang J. Prediction of Thermostability of Enzymes Based on the Amino Acid Index (AAindex) Database and Machine Learning. Molecules 2023; 28:8097. [PMID: 38138586 PMCID: PMC10746113 DOI: 10.3390/molecules28248097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The combination of wet-lab experimental data on multi-site combinatorial mutations and machine learning is an innovative method in protein engineering. In this study, we used an innovative sequence-activity relationship (innov'SAR) methodology based on novel descriptors and digital signal processing (DSP) to construct a predictive model. In this paper, 21 experimental (R)-selective amine transaminases from Aspergillus terreus (AT-ATA) were used as an input to predict higher thermostability mutants than those predicted using the existing data. We successfully improved the coefficient of determination (R2) of the model from 0.66 to 0.92. In addition, root-mean-squared deviation (RMSD), root-mean-squared fluctuation (RMSF), solvent accessible surface area (SASA), hydrogen bonds, and the radius of gyration were estimated based on molecular dynamics simulations, and the differences between the predicted mutants and the wild-type (WT) were analyzed. The successful application of the innov'SAR algorithm in improving the thermostability of AT-ATA may help in directed evolutionary screening and open up new avenues for protein engineering.
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Affiliation(s)
- Gaolin Li
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China;
| | - Lili Jia
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China;
| | - Kang Wang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310023, China;
| | - Tingting Sun
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310023, China;
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China;
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5
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De Santis P, Wegstein D, Burek BO, Patzsch J, Alcalde M, Kroutil W, Bloh JZ, Kara S. Robust Light Driven Enzymatic Oxyfunctionalization via Immobilization of Unspecific Peroxygenase. CHEMSUSCHEM 2023; 16:e202300613. [PMID: 37357147 DOI: 10.1002/cssc.202300613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Unspecific peroxygenases have attracted interest in synthetic chemistry, especially for the oxidative activation of C-H bonds, as they only require hydrogen peroxide (H2 O2 ) instead of a cofactor. Due to their instability in even small amounts of H2 O2 , different strategies like enzyme immobilization or in situ H2 O2 production have been developed to improve the stability of these enzymes. While most strategies have been studied separately, a combination of photocatalysis with immobilized enzymes was only recently reported. To show the advantages and limiting factors of immobilized enzyme in a photobiocatalytic reaction, a comparison is made between free and immobilized enzymes. Adjustment of critical parameters such as (i) enzyme and substrate concentration, (ii) illumination wavelength and (iii) light intensity results in significantly increased enzyme stabilities of the immobilized variant. Moreover, under optimized conditions a turnover number of 334,500 was reached.
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Affiliation(s)
- Piera De Santis
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Deborah Wegstein
- DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt am, Main, Germany
| | - Bastien O Burek
- DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt am, Main, Germany
| | - Jacqueline Patzsch
- DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt am, Main, Germany
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis ICP CSIC, C/ Marie Curie 2, 28049, Madrid, Spain
| | - Wolfgang Kroutil
- Field of Excellence BioHealt, BioTechMed, Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Jonathan Z Bloh
- DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt am, Main, Germany
| | - Selin Kara
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstr. 5, 30167, Hannover, Germany
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6
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Hebbar A, Dey P, Vatti AK. Lysozyme stability in various deep eutectic solvents using molecular dynamics simulations. J Biomol Struct Dyn 2023:1-9. [PMID: 37909488 DOI: 10.1080/07391102.2023.2275178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
The ability of neat deep eutectic solvents (DESs) to influence protein structure and function has gained considerable interest due to the unstable nature of enzymes or therapeutic proteins, which are often exposed to thermal, chemical, or mechanical stresses when handled at an industrial scale. In this study, we simulated a model globular protein, lysozyme, in water and six choline chloride-based DES using molecular dynamics simulations, to investigate the structural changes in various solvent environments, giving insights into the overall stability of lysozyme. Root mean square deviation (RMSD) and root mean square fluctuations (RMSF) of the C-α backbone indicated that most DESs induced a less flexible and rigid lysozyme structure compared to water. The radius of gyration and end-to-end distance calculations pointed towards higher structural compactness in reline and levuline, while the structure of lysozyme considerably expanded in oxaline. Protein-solvent interactions were further analysed by hydrogen bonding interactions and radial distribution functions (RDF), which indicated a higher degree of lysozyme-hydrogen bond donor (HBD) interactions compared to lysozyme-choline hydrogen bonding. Surface area analysis revealed an overall % increase in total positive, negative, donor, and acceptor surface areas in malicine and oxaline compared to water and other DESs, indicating the exposure of a larger number of residues to interactions with the solvent. Reline, levuline, and polyol-based DESs comparatively stabilized lysozyme, even though changes in the secondary/tertiary structures were observed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akshatha Hebbar
- Department of Chemical Engineering, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Poulumi Dey
- Department of Materials Science and Engineering, Faculty of Mechanical, Maritime and Materials Engineering (3mE), Delft University of Technology, Delft, Netherlands
| | - Anoop Kishore Vatti
- Department of Chemical Engineering, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, India
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7
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Abellanas-Perez P, Carballares D, Fernandez-Lafuente R, Rocha-Martin J. Glutaraldehyde modification of lipases immobilized on octyl agarose beads: Roles of the support enzyme loading and chemical amination of the enzyme on the final enzyme features. Int J Biol Macromol 2023; 248:125853. [PMID: 37460068 DOI: 10.1016/j.ijbiomac.2023.125853] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
Lipase B from Candida antarctica (CALB) and lipase from Thermomyces lanuginosus (TLL) have been immobilized on octyl agarose at low loading and at a loading exceeding the maximum support capacity. Then, the enzymes have been treated with glutaraldehyde and inactivated at pH 7.0 in Tris-HCl, sodium phosphate and HEPES, giving different stabilities. Stabilization (depending on the buffer) of the highly loaded biocatalysts was found, very likely as a consequence of the detected intermolecular crosslinkings. This did not occur for the lowly loaded biocatalysts. Next, the enzymes were chemically aminated and then treated with glutaraldehyde. In the case of TLL, the intramolecular crosslinkings (visible by the apparent reduction of the protein size) increased enzyme stability of the lowly loaded biocatalysts, an effect that was further increased for the highly loaded biocatalysts due to intermolecular crosslinkings. Using CALB, the intramolecular crosslinkings were less intense, and the stabilization was lower, even though the intermolecular crosslinkings were quite intense for the highly loaded biocatalyst. The stabilization detected depended on the inactivation buffer. The interactions between enzyme loading and inactivating buffer on the effects of the chemical modifications suggest that the modification and inactivation studies must be performed under the target biocatalysts and conditions.
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Affiliation(s)
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
| | | | - Javier Rocha-Martin
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid Spain.
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8
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Hertel JS, Bitterwolf P, Kröll S, Winterhalter A, Weber AJ, Grösche M, Walkowsky LB, Heißler S, Schwotzer M, Wöll C, van de Kamp T, Zuber M, Baumbach T, Rabe KS, Niemeyer CM. Biocatalytic Foams from Microdroplet-Formulated Self-Assembling Enzymes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303952. [PMID: 37358068 DOI: 10.1002/adma.202303952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/16/2023] [Indexed: 06/27/2023]
Abstract
Industrial biocatalysis plays an important role in the development of a sustainable economy, as enzymes can be used to synthesize an enormous range of complex molecules under environmentally friendly conditions. To further develop the field, intensive research is being conducted on process technologies for continuous flow biocatalysis in order to immobilize large quantities of enzyme biocatalysts in microstructured flow reactors under conditions that are as gentle as possible in order to realize efficient material conversions. Here, monodisperse foams consisting almost entirely of enzymes covalently linked via SpyCatcher/SpyTag conjugation are reported. The biocatalytic foams are readily available from recombinant enzymes via microfluidic air-in-water droplet formation, can be directly integrated into microreactors, and can be used for biocatalytic conversions after drying. Reactors prepared by this method show surprisingly high stability and biocatalytic activity. The physicochemical characterization of the new materials is described and exemplary applications in biocatalysis are shown using two-enzyme cascades for the stereoselective synthesis of chiral alcohols and the rare sugar tagatose.
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Affiliation(s)
- Julian S Hertel
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Patrick Bitterwolf
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Sandra Kröll
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Astrid Winterhalter
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Annika J Weber
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Maximilian Grösche
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Laurenz B Walkowsky
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Heißler
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Matthias Schwotzer
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof Wöll
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), D-76344, Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), D-76131, Karlsruhe, Germany
| | - Marcus Zuber
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), D-76344, Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), D-76131, Karlsruhe, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), D-76344, Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), D-76131, Karlsruhe, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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9
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Rodríguez-Núñez K, López-Gallego F, Martínez R, Bernal C. Immobilized biocatalyst engineering: Biocatalytic tool to obtain attractive enzymes for industry. Int J Biol Macromol 2023; 242:125075. [PMID: 37230450 DOI: 10.1016/j.ijbiomac.2023.125075] [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: 03/21/2023] [Revised: 05/11/2023] [Accepted: 05/22/2023] [Indexed: 05/27/2023]
Abstract
Biocatalysis can improve current bioprocesses by identifying or improving enzymes that withstand harsh and unnatural operating conditions. Immobilized Biocatalyst Engineering (IBE) is a novel strategy integrating protein engineering and enzyme immobilization as a single workflow. Using IBE, it is possible to obtain immobilized biocatalysts whose soluble performance would not be selected. In this work, Bacillus subtilis lipase A (BSLA) variants obtained through IBE were characterized as soluble and immobilized biocatalysts, and how the interactions with the support affect their structure and catalytic performance were analyzed using intrinsic protein fluorescence. Variant P5G3 (Asn89Asp, Gln121Arg) showed a 2.6-fold increased residual activity after incubation at 76 °C compared to immobilized wild-type (wt) BSLA. On the other hand, variant P6C2 (Val149Ile) showed 4.4 times higher activity after incubation in 75 % isopropyl alcohol (36 °C) compared to Wt_BSLA. Furthermore, we studied the advancement of the IBE platform by performing synthesis and immobilizing the BSLA variants using a cell-free protein synthesis (CFPS) approach. The observed differences in immobilization performance, high temperature, and solvent resistance between the in vivo-produced variants and Wt_BSLA were confirmed for the in vitro synthesized enzymes. These results open the door for designing strategies integrating IBE and CFPS to generate and screen improved immobilized enzymes from genetic diversity libraries. Furthermore, it was confirmed that IBE is a platform that can be used to obtain improved biocatalysts, especially those with an unremarkable performance as soluble biocatalysts, which wouldn't be selected for immobilization and further development for specific applications.
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Affiliation(s)
- Karen Rodríguez-Núñez
- Laboratorio de Tecnología de Enzimas para Bioprocesos, Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, 1720010 La Serena, Chile.
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE) - Basque Research and Technology Alliance (BRTA) Paséo Miramón, 194, Donostia-San Sebastián 20014, Spain; KERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, Bilbao, 48013, Spain
| | - Ronny Martínez
- Laboratorio de Tecnología de Enzimas para Bioprocesos, Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, 1720010 La Serena, Chile
| | - Claudia Bernal
- Laboratorio de Tecnología de Enzimas para Bioprocesos, Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, 1720010 La Serena, Chile; Departamento de Química, Universidad de La Serena, Benavente 980, 1720010 La Serena, Chile
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10
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Wang Y, Yu L, Shao J, Zhu Z, Zhang L. Structure-driven protein engineering for production of valuable natural products. TRENDS IN PLANT SCIENCE 2023; 28:460-470. [PMID: 36473772 DOI: 10.1016/j.tplants.2022.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/25/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Proteins are the most frequently used biocatalysts, and their structures determine their functions. Modifying the functions of proteins on the basis of their structures lies at the heart of protein engineering, opening a new horizon for metabolic engineering by efficiently generating stable enzymes. Many attempts at classical metabolic engineering have focused on improving specific metabolic fluxes and producing more valuable natural products by increasing gene expression levels and enzyme concentrations. However, most naturally occurring enzymes show limitations, and such limitations have hindered practical applications. Here we review recent advances in protein engineering in synthetic biology, chemoenzymatic synthesis, and plant metabolic engineering and describe opportunities for designing and constructing novel enzymes or proteins with desirable properties to obtain more active natural products.
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Affiliation(s)
- Yun Wang
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China; Biomedical Innovation R&D Centre, School of Medicine, Shanghai University, Shanghai 200444, China
| | - Luyao Yu
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Jie Shao
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Zhanpin Zhu
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lei Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China; Biomedical Innovation R&D Centre, School of Medicine, Shanghai University, Shanghai 200444, China; Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China; Innovative Drug R&D Center, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
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11
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Becker M, Ziemińska-Stolarska A, Markowska D, Lütz S, Rosenthal K. Comparative Life Cycle Assessment of Chemical and Biocatalytic 2'3'-Cyclic GMP-AMP Synthesis. CHEMSUSCHEM 2023; 16:e202201629. [PMID: 36416867 DOI: 10.1002/cssc.202201629] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Life cycle assessments (LCAs) can provide insights into the environmental impact of production processes. In this study, a comparative LCA was performed for the synthesis of 2'3'-cyclic GMP-AMP (2'3'-cGAMP) in an early development stage. The cyclic dinucleotide (CDN) is of interest for pharmaceutical applications such as cancer immunotherapy. CDNs can be synthesized either by enzymes or chemical catalysis. It is not known which of the routes is more sustainable as both routes have their advantages and disadvantages, such as a poor yield for the chemical synthesis and low titers for the biocatalytic synthesis. The synthesis routes were compared for the production of 200 g 2'3'-cGAMP based on laboratory data to assess the environmental impacts. The biocatalytic synthesis turned out to be superior to the chemical synthesis in all considered categories by at least one magnitude, for example, a global warming potential of 3055.6 kg CO2 equiv. for the enzymatic route and 56454.0 kg CO2 equiv. for the chemical synthesis, which is 18 times higher. This study demonstrates the value of assessment at an early development stage, when the choice between different routes is still possible.
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Affiliation(s)
- Martin Becker
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany
| | | | - Dorota Markowska
- Faculty of Process and Environmental Engineering, Lodz University of Technology, Wolczanska 213, 90-924, Lodz, Poland
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany
| | - Katrin Rosenthal
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany
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12
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Fernández-Lucas J. Biocatalysis: An Eco-Friendly Scenario for the Manufacturing of APIs. Int J Mol Sci 2023; 24:ijms24054474. [PMID: 36901905 PMCID: PMC10003361 DOI: 10.3390/ijms24054474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Nowadays, the worldwide demand for Active Pharmaceutical Ingredients (APIs) requires novel, cost-effective, safe, and environmentally friendly synthetic processes [...].
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Affiliation(s)
- Jesús Fernández-Lucas
- Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Spain;
- Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55–66, Barranquilla 080002, Colombia
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13
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Bayesian Optimization for an ATP-Regenerating In Vitro Enzyme Cascade. Catalysts 2023. [DOI: 10.3390/catal13030468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Enzyme cascades are an emerging synthetic tool for the synthesis of various molecules, combining the advantages of biocatalysis and of one-pot multi-step reactions. However, the more complex the enzyme cascade is, the more difficult it is to achieve adequate productivities and product concentrations. Therefore, the whole process must be optimized to account for synergistic effects. One way to deal with this challenge involves data-driven models in combination with experimental validation. Here, Bayesian optimization was applied to an ATP-producing and -regenerating enzyme cascade consisting of polyphosphate kinases. The enzyme and co-substrate concentrations were adjusted for an ATP-dependent reaction, catalyzed by mevalonate kinase (MVK). With a total of 16 experiments, we were able to iteratively optimize the initial concentrations of the components used in the one-pot synthesis to improve the specific activity of MVK with 10.2 U mg−1. The specific activity even exceeded the results of the reference reaction with stoichiometrically added ATP amounts, with which a specific activity of 8.8 U mg−1 was reached. At the same time, the product concentrations were also improved so that complete yields were achieved.
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14
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Waluga T, Klein M, Skiborowski M. On the Use of the Adsorption Energy Distribution for the Analysis of Competing Substrate Kinetics. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c03878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Thomas Waluga
- Institute of Process Systems Engineering, Hamburg University of Technology, Am Schwarzenberg-Campus 4, Hamburg21073, Germany
| | - Maximilian Klein
- Institute of Process Systems Engineering, Hamburg University of Technology, Am Schwarzenberg-Campus 4, Hamburg21073, Germany
| | - Mirko Skiborowski
- Institute of Process Systems Engineering, Hamburg University of Technology, Am Schwarzenberg-Campus 4, Hamburg21073, Germany
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15
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Co-Enzymes with Dissimilar Stabilities: A Discussion of the Likely Biocatalyst Performance Problems and Some Potential Solutions. Catalysts 2022. [DOI: 10.3390/catal12121570] [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] Open
Abstract
Enzymes have several excellent catalytic features, and the last few years have seen a revolution in biocatalysis, which has grown from using one enzyme to using multiple enzymes in cascade reactions, where the product of one enzyme reaction is the substrate for the subsequent one. However, enzyme stability remains an issue despite the many benefits of using enzymes in a catalytic system. When enzymes are exposed to harsh process conditions, deactivation occurs, which changes the activity of the enzyme, leading to an increase in reaction time to achieve a given conversion. Immobilization is a well-known strategy to improve many enzyme properties, if the immobilization is properly designed and controlled. Enzyme co-immobilization is a further step in the complexity of preparing a biocatalyst, whereby two or more enzymes are immobilized on the same particle or support. One crucial problem when designing and using co-immobilized enzymes is the possibility of using enzymes with very different stabilities. This paper discusses different scenarios using two co-immobilized enzymes of the same or differing stability. The effect on operational performance is shown via simple simulations using Michaelis–Menten equations to describe kinetics integrated with a deactivation term. Finally, some strategies for overcoming some of these problems are discussed.
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16
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Büchler J, Hegarty E, Schroer K, Snajdrova R, Turner NJ, Loiseleur O, Buller R, Le Chapelain C. A Collaborative Journey towards the Late‐Stage Functionalization of Added‐Value Chemicals Using Engineered Halogenases. Helv Chim Acta 2022. [DOI: 10.1002/hlca.202200128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Johannes Büchler
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology, CH- 8820 Wädenswil Switzerland
- Department of Chemistry The University of Manchester Manchester Institute of Biotechnology, UK- Manchester M1 7DN United Kingdom
| | - Eimear Hegarty
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology, CH- 8820 Wädenswil Switzerland
| | - Kirsten Schroer
- Novartis Institutes for BioMedical Research Global Discovery Chemistry, CH- 4056 Basel Switzerland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry, CH- 4056 Basel Switzerland
| | - Nicholas J. Turner
- Department of Chemistry The University of Manchester Manchester Institute of Biotechnology, UK- Manchester M1 7DN United Kingdom
| | - Olivier Loiseleur
- Syngenta Crop Protection AG Schaffhauserstr. 101 CH-4332 Stein Switzerland
| | - Rebecca Buller
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology, CH- 8820 Wädenswil Switzerland
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17
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Valotta A, Malihan-Yap L, Hinteregger K, Kourist R, Gruber-Woelfler H. Design and Investigation of a Photocatalytic Setup for Efficient Biotransformations Within Recombinant Cyanobacteria in Continuous Flow. CHEMSUSCHEM 2022; 15:e202201468. [PMID: 36069133 PMCID: PMC9828554 DOI: 10.1002/cssc.202201468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Photo- and biocatalysis show many advantages as more sustainable solutions for the production of fine chemicals. In an effort to combine the benefits and the knowledge of both these areas, a continuous photobiocatalytic setup was designed and optimized to carry out whole-cell biotransformations within cells of the cyanobacterium Synechocystis sp. PCC 6803 expressing the gene of the ene-reductase YqjM from B. subtilis. The effect of the light intensity and flow rate on the specific activity in the stereoselective reduction of 2-methyl maleimide was investigated via a design-of-experiments approach. The cell density in the setup was further increased at the optimal operating conditions without loss in specific activity, demonstrating that the higher surface area/volume ratio in the coil reactor improved the illumination efficiency of the process. Furthermore, different reactor designs were compared, proving that the presented approach was the most cost- and time-effective solution for intensifying photobiotransformations within cyanobacterial cells.
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Affiliation(s)
- Alessia Valotta
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010, Graz, Austria
| | - Lenny Malihan-Yap
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Kerstin Hinteregger
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010, Graz, Austria
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- ACIB GmbH, Krenngasse 37, 8010, Graz, Austria
| | - Heidrun Gruber-Woelfler
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010, Graz, Austria
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18
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Croci F, Vilím J, Adamopoulou T, Tseliou V, Schoenmakers PJ, Knaus T, Mutti FG. Continuous Flow Biocatalytic Reductive Amination by Co-Entrapping Dehydrogenases with Agarose Gel in a 3D-Printed Mould Reactor. Chembiochem 2022; 23:e202200549. [PMID: 36173971 PMCID: PMC9828473 DOI: 10.1002/cbic.202200549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 09/28/2022] [Indexed: 02/03/2023]
Abstract
Herein, we show how the merge of biocatalysis with flow chemistry aided by 3D-printing technologies can facilitate organic synthesis. This concept was exemplified for the reductive amination of benzaldehyde catalysed by co-immobilised amine dehydrogenase and formate dehydrogenase in a continuous flow micro-reactor. For this purpose, we investigated enzyme co-immobilisation by covalent binding, or ion-affinity binding, or entrapment. Entrapment in an agarose hydrogel turned out to be the most promising solution for this biocatalytic reaction. Therefore, we developed a scalable and customisable approach whereby an agarose hydrogel containing the co-entrapped dehydrogenases was cast in a 3D-printed mould. The reactor was applied to the reductive amination of benzaldehyde in continuous flow over 120 h and afforded 47 % analytical yield and a space-time yield of 7.4 g L day-1 using 0.03 mol% biocatalysts loading. This work also exemplifies how rapid prototyping of enzymatic reactions in flow can be achieved through 3D-printing technology.
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Affiliation(s)
- Federico Croci
- van' t Hoff Institute for Molecular Sciences HIMS-Biocat & Analytical ChemistryUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Jan Vilím
- van' t Hoff Institute for Molecular Sciences HIMS-Biocat & Analytical ChemistryUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Theodora Adamopoulou
- van' t Hoff Institute for Molecular Sciences HIMS-Biocat & Analytical ChemistryUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Vasilis Tseliou
- van' t Hoff Institute for Molecular Sciences HIMS-Biocat & Analytical ChemistryUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Peter J. Schoenmakers
- van' t Hoff Institute for Molecular Sciences HIMS-Biocat & Analytical ChemistryUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Tanja Knaus
- van' t Hoff Institute for Molecular Sciences HIMS-Biocat & Analytical ChemistryUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Francesco G. Mutti
- van' t Hoff Institute for Molecular Sciences HIMS-Biocat & Analytical ChemistryUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
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19
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Carballares D, Fernandez-Lafuente R, Rocha-Martin J. Immobilization-stabilization of the dimeric D-amino acid oxidase from porcine kidney. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Abstract
Many enzymes possess high catalytic efficiency and selectivity that far surpass classical organic or organometallic catalysts. However, the initial starting enzyme for a given transformation does not always possess the right properties needed for broad utilization. Searching in genome/protein sequence libraries for homologs, aided with powerful bioinformatic tools developed in recent years, provides an avenue to identify superior biocatalysts. Herein, we highlight several case studies to illustrate the power of this concept. A brief discussion on its complementarity with contemporary approaches in protein engineering (such as directed evolution) and possible future developments is also provided.
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Affiliation(s)
- Yanlong Jiang
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX,77005, USA
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX,77005, USA
- Lead Contact
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21
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Rational Design of a Thermostable 2'-Deoxyribosyltransferase for Nelarabine Production by Prediction of Disulfide Bond Engineering Sites. Int J Mol Sci 2022; 23:ijms231911806. [PMID: 36233108 PMCID: PMC9570332 DOI: 10.3390/ijms231911806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
One of the major drawbacks of the industrial implementation of enzymatic processes is the low operational stability of the enzymes under tough industrial conditions. In this respect, the use of thermostable enzymes in the industry is gaining ground during the last decades. Herein, we report a structure-guided approach for the development of novel and thermostable 2′-deoxyribosyltransferases (NDTs) based on the computational design of disulfide bonds on hot spot positions. To this end, a small library of NDT variants from Lactobacillus delbrueckii (LdNDT) with introduced cysteine pairs was created. Among them, LdNDTS104C (100% retained activity) was chosen as the most thermostable variant, displaying a six- and two-fold enhanced long-term stability when stored at 55 °C (t1/255 °C ≈ 24 h) and 60 °C (t1/260 °C ≈ 4 h), respectively. Moreover, the biochemical characterization revealed that LdNDTS104C showed >60% relative activity across a broad range of temperature (30−90 °C) and pH (5−7). Finally, to study the potential application of LdNDTS104C as an industrial catalyst, the enzymatic synthesis of nelarabine was successfully carried out under different substrate conditions (1:1 and 3:1) at different reaction times. Under these experimental conditions, the production of nelarabine was increased up to 2.8-fold (72% conversion) compared with wild-type LdNDT.
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22
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Kumar S, Sindhu A, Venkatesu P. Unprecedented enhancement and preservation of the peroxidase activity of cytochrome- c packaged with ionic liquid-modified gold nanoparticles by offsetting temperature and time stresses. Phys Chem Chem Phys 2022; 24:23460-23471. [PMID: 36128951 DOI: 10.1039/d2cp03814e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inspired by the biocompatibility of ionic liquids and their dexterousness for the preservation of enzyme structure and activity, herein, the interactions of Cyt-c with naked AuNPs and four IL-mediated AuNPs, which were formed by the fabrication of ILs with common cation 1-ethyl-3-methyl-imidazolium (EMIM) and different anions, to obtain AuNP-IL1 [(BF4)-1 anion], AuNP-IL2 [(CH3OSO3)-1 anion], AuNP-IL3 [(CH3CH2OSO3)-1 anion], and (AuNP-IL4) [Cl-1 anion], were studied. Through this work, the peroxidase activity observed in the presence of a lower concentration IL-AuNPs is exceptionally increased (16 fold). IL-AuNPs preferentially counteract the temperature gradient change and long-term solvent preservation effects while persistently maintaining the Cyt-c peroxidase activity without much depreciation. The hydrodynamic diameter (dH) of the Cyt-c-AuNP system was obtained, which supported the TEM results. Furthermore, to evaluate the effect of Cyt-c interaction with the AuNPs, a Zeta potential analysis was performed. Taken together, the binding of IL-AuNPs with Cyt-c, diameter size analysis, zeta potential, structural integrity evaluation using the DichroWeb software and morphology results suggest the interaction order of the IL-AuNPs to be in a sequence of AuNP-IL2 > AuNP-IL3 > AuNP- IL4 > AuNP-IL1 > Naked AuNPs. Moreover, results indicate that the IL anions play a dominating role in the modulation of interactions between IL-mediated AuNPs and Cyt-c. The study strongly supports the promising character of sulfur-containing IL-mediated AuNPs for Cyt-c immobilization simultaneously opening new avenues for the application of greener and biocompatible nanoparticles with drug delivery and therapeutic applications.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, University of Delhi, Delhi 110 007, India.
| | - Anamika Sindhu
- Department of Chemistry, University of Delhi, Delhi 110 007, India.
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23
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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24
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Meyer L, Andersen MB, Kara S. A Deep Eutectic Solvent Thermomorphic Multiphasic System for Biocatalytic Applications. Angew Chem Int Ed Engl 2022; 61:e202203823. [PMID: 35587655 PMCID: PMC9400879 DOI: 10.1002/anie.202203823] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 01/13/2023]
Abstract
The applicability of a thermomorphic multiphasic system (TMS) composed of a hydrophobic deep eutectic solvent (DES) and an aqueous potassium phosphate buffer with a lower critical solution temperature (LCST) phase change for homogeneous biocatalysis was investigated. A lidocaine‐based DES with the fatty acid oleic acid as a hydrogen‐bond donor was studied. Phase diagrams were determined and presented within this study. We tested different additional components to the solvent system and observed a decrease in the cloud point of approximately 0.026 °C per concentration unit. Distribution studies revealed a clear distribution of the protein in the aqueous buffer phase (>95 %), whereas the hydrophobic substrate and educt accumulated (>95 %) in the DES‐enriched layer. Finally, a reduction catalyzed by horse liver alcohol dehydrogenase was performed in a larger‐scale experiment, and the biocatalyst could be recycled by simply removing the DES phase for three recycling runs.
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Affiliation(s)
- Lars‐Erik Meyer
- Department of Biological and Chemical Engineering Biocatalysis and Bioprocessing Group Aarhus University Gustav Wieds Vej 10 8000 Aarhus Denmark
| | - Mads Bruno Andersen
- Department of Biological and Chemical Engineering Biocatalysis and Bioprocessing Group Aarhus University Gustav Wieds Vej 10 8000 Aarhus Denmark
| | - Selin Kara
- Department of Biological and Chemical Engineering Biocatalysis and Bioprocessing Group Aarhus University Gustav Wieds Vej 10 8000 Aarhus Denmark
- Institute of Technical Chemistry Leibniz University Hannover Callinstr. 5 30167 Hannover Germany
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25
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Bolivar JM, Woodley JM, Fernandez-Lafuente R. Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization. Chem Soc Rev 2022; 51:6251-6290. [PMID: 35838107 DOI: 10.1039/d2cs00083k] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.
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Affiliation(s)
- Juan M Bolivar
- FQPIMA group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, 28040, Spain
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis. ICP-CSIC, C/Marie Curie 2, Campus UAM-CSIC Cantoblanco, Madrid 28049, Spain. .,Center of Excellence in Bionanoscience Research, External Scientific Advisory Academic, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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26
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Reetz M. Witnessing the Birth of Directed Evolution of Stereoselective Enzymes as Catalysts in Organic Chemistry. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Meyer L, Andersen MB, Kara S. Ein thermomorphes stark eutektisches Lösungsmittelmehrphasensystem für biokatalytische Anwendungen. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lars‐Erik Meyer
- Department of Biological and Chemical Engineering Biocatalysis and Bioprocessing Group Aarhus University Gustav Wieds Vej 10 8000 Aarhus Dänemark
| | - Mads Bruno Andersen
- Department of Biological and Chemical Engineering Biocatalysis and Bioprocessing Group Aarhus University Gustav Wieds Vej 10 8000 Aarhus Dänemark
| | - Selin Kara
- Department of Biological and Chemical Engineering Biocatalysis and Bioprocessing Group Aarhus University Gustav Wieds Vej 10 8000 Aarhus Dänemark
- Institut für Technische Chemie Leibniz Universität Hannover Callinstr. 5 30167 Hannover Deutschland
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28
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Morellon-Sterling R, Tavano O, Bolivar JM, Berenguer-Murcia Á, Vela-Gutiérrez G, Sabir JSM, Tacias-Pascacio VG, Fernandez-Lafuente R. A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values. Int J Biol Macromol 2022; 210:682-702. [PMID: 35508226 DOI: 10.1016/j.ijbiomac.2022.04.224] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/05/2022]
Abstract
Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.
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Affiliation(s)
- Roberto Morellon-Sterling
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Olga Tavano
- Faculty of Nutrition, Alfenas Federal Univ., 700 Gabriel Monteiro da Silva St, Alfenas, MG 37130-000, Brazil
| | - Juan M Bolivar
- Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., Madrid 28040, Spain
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, Alicante, Spain
| | - Gilber Vela-Gutiérrez
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Veymar G Tacias-Pascacio
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico; Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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29
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Reetz MT. Making Enzymes Suitable for Organic Chemistry by Rational Protein Design. Chembiochem 2022; 23:e202200049. [PMID: 35389556 PMCID: PMC9401064 DOI: 10.1002/cbic.202200049] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/07/2022] [Indexed: 11/25/2022]
Abstract
This review outlines recent developments in protein engineering of stereo‐ and regioselective enzymes, which are of prime interest in organic and pharmaceutical chemistry as well as biotechnology. The widespread application of enzymes was hampered for decades due to limited enantio‐, diastereo‐ and regioselectivity, which was the reason why most organic chemists were not interested in biocatalysis. This attitude began to change with the advent of semi‐rational directed evolution methods based on focused saturation mutagenesis at sites lining the binding pocket. Screening constitutes the labor‐intensive step (bottleneck), which is the reason why various research groups are continuing to develop techniques for the generation of small and smart mutant libraries. Rational enzyme design, traditionally an alternative to directed evolution, provides small collections of mutants which require minimal screening. This approach first focused on thermostabilization, and did not enter the field of stereoselectivity until later. Computational guides such as the Rosetta algorithms, HotSpot Wizard metric, and machine learning (ML) contribute significantly to decision making. The newest advancements show that semi‐rational directed evolution such as CAST/ISM and rational enzyme design no longer develop on separate tracks, instead, they have started to merge. Indeed, researchers utilizing the two approaches have learned from each other. Today, the toolbox of organic chemists includes enzymes, primarily because the possibility of controlling stereoselectivity by protein engineering has ensured reliability when facing synthetic challenges. This review was also written with the hope that undergraduate and graduate education will include enzymes more so than in the past.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut fur Kohlenforschung, Biocatalysis, Kaiser-Wilhelm-Platz 1, 45470, Muelheim an der Ruhr, GERMANY
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30
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Burke A, Birmingham WR, Zhuo Y, Thorpe TW, Zucoloto da Costa B, Crawshaw R, Rowles I, Finnigan JD, Young C, Holgate GM, Muldowney MP, Charnock SJ, Lovelock SL, Turner NJ, Green AP. An Engineered Cytidine Deaminase for Biocatalytic Production of a Key Intermediate of the Covid-19 Antiviral Molnupiravir. J Am Chem Soc 2022; 144:3761-3765. [PMID: 35224970 PMCID: PMC8915250 DOI: 10.1021/jacs.1c11048] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Indexed: 01/23/2023]
Abstract
The Covid-19 pandemic highlights the urgent need for cost-effective processes to rapidly manufacture antiviral drugs at scale. Here we report a concise biocatalytic process for Molnupiravir, a nucleoside analogue recently approved as an orally available treatment for SARS-CoV-2. Key to the success of this process was the development of an efficient biocatalyst for the production of N-hydroxy-cytidine through evolutionary adaption of the hydrolytic enzyme cytidine deaminase. This engineered biocatalyst performs >85 000 turnovers in less than 3 h, operates at 180 g/L substrate loading, and benefits from in situ crystallization of the N-hydroxy-cytidine product (85% yield), which can be converted to Molnupiravir by a selective 5'-acylation using Novozym 435.
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Affiliation(s)
- Ashleigh
J. Burke
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - William R. Birmingham
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Ying Zhuo
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Thomas W. Thorpe
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Bruna Zucoloto da Costa
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rebecca Crawshaw
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Ian Rowles
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - James D. Finnigan
- Prozomix
Ltd, Building 4, West
End Ind. Estate, Haltwhistle NE49 9HA, U.K.
| | - Carl Young
- Prozomix
Ltd, Building 4, West
End Ind. Estate, Haltwhistle NE49 9HA, U.K.
| | - Gregory M. Holgate
- Sterling
Pharma Solutions, Sterling Place, Dudley, Northumberland NE23 7QG, U.K.
| | - Mark P. Muldowney
- Sterling
Pharma Solutions, Sterling Place, Dudley, Northumberland NE23 7QG, U.K.
| | - Simon J. Charnock
- Prozomix
Ltd, Building 4, West
End Ind. Estate, Haltwhistle NE49 9HA, U.K.
| | - Sarah L. Lovelock
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nicholas J. Turner
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Anthony P. Green
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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31
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Barna B, Gáti T, Kotschy A, Tasnádi G. Chemo‐enzymatic One‐Pot Two‐Step Functionalization of 1,2,3,4‐Tetrahydroisoquinolines by Monoamine Oxidase‐Ugi‐Joullié‐reaction Sequence. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bence Barna
- Servier Research Institute of Medicinal Chemistry Servier Research Institute of Medicinal Chemistry Záhony utca 7 1031 HUNGARY
| | - Tamás Gáti
- Servier Research Institute of Medicinal Chemistry Servier Research Institute of Medicinal Chemistry Záhony utca 7 1031 HUNGARY
| | - András Kotschy
- Servier Research Institute of Medicinal Chemistry Servier Research Institute of Medicinal Chemistry Záhony utca 7 1031 HUNGARY
| | - Gábor Tasnádi
- Servier Research Institute of Medicinal Chemistry Servier Research Institute of Medicinal Chemistry Záhony utca 7 1031 Budapest HUNGARY
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32
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Kruschitz A, Nidetzky B. Biocatalytic Production of 2-α-d-Glucosyl-glycerol for Functional Ingredient Use: Integrated Process Design and Techno-Economic Assessment. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:1246-1255. [PMID: 35096492 PMCID: PMC8790807 DOI: 10.1021/acssuschemeng.1c07210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/24/2021] [Indexed: 05/06/2023]
Abstract
Advanced biomanufacturing builds on production processes that are both profitable and sustainable. Integrated design of process unit operations, geared to output efficiency and waste minimization and guided by a rigorous techno-economic assessment, is essential for development aligned to these central aims. Here, we demonstrate such a development for the biocatalytic production of the biological extremolyte 2-O-α-d-glucosyl-glycerol (2-GG) for functional ingredient application. The process was aligned in scale over all steps (∼180 g product; ∼2.5 L reaction mixture) and involved continuous enzymatic synthesis from sucrose and glycerol interlinked with reactive extraction and nanofiltration for product isolation (purity of ∼80 wt %) and side stream recovery. Glycerol used in ∼6-fold excess over sucrose was recycled, and hydrothermal conversion into 5-(hydroxymethyl)furfural was evaluated for the fructose by-product released from sucrose. Based on a process mass intensity (total mass input/mass product) of 146, ∼80% of the total mass input was utilized and an E-factor (mass waste/mass product) of 28 was obtained. EcoScale analysis revealed a penalty point score of 44, suggesting an acceptable process from a sustainability point of view. Process simulation for an annual production of 10 tons 2-GG was used for the techno-economic assessment with discounted cash flow analysis. The calculated operating costs involved 35 and 47% contributions from materials and labor, respectively. About 91% of the material costs were due to chemicals for the reactive extraction-acidic stripping step, emphasizing the importance of material reuse at this step. Glycerol recycling involved a trade-off between waste reduction and energy use for the removal of water. Collectively, the study identifies options and boundaries of a profitable 2-GG process. The minimum selling price for 2-GG was calculated as ∼240 € kg-1 or smaller. The framework of the methodology presented can be generally important in applied bio-catalysis: it facilitates closing of the gap between process design and implementation for accelerated development.
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Affiliation(s)
- Andreas Kruschitz
- Austrian
Centre of Industrial Biotechnology (acib), Krenngasse 37, 8010 Graz, Austria
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Bernd Nidetzky
- Austrian
Centre of Industrial Biotechnology (acib), Krenngasse 37, 8010 Graz, Austria
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
- . Phone: +433168738400. Fax: +433168738434
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33
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Cadet XF, Gelly JC, van Noord A, Cadet F, Acevedo-Rocha CG. Learning Strategies in Protein Directed Evolution. Methods Mol Biol 2022; 2461:225-275. [PMID: 35727454 DOI: 10.1007/978-1-0716-2152-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic biology is a fast-evolving research field that combines biology and engineering principles to develop new biological systems for medical, pharmacological, and industrial applications. Synthetic biologists use iterative "design, build, test, and learn" cycles to efficiently engineer genetic systems that are reliable, reproducible, and predictable. Protein engineering by directed evolution can benefit from such a systematic engineering approach for various reasons. Learning can be carried out before starting, throughout or after finalizing a directed evolution project. Computational tools, bioinformatics, and scanning mutagenesis methods can be excellent starting points, while molecular dynamics simulations and other strategies can guide engineering efforts. Similarly, studying protein intermediates along evolutionary pathways offers fascinating insights into the molecular mechanisms shaped by evolution. The learning step of the cycle is not only crucial for proteins or enzymes that are not suitable for high-throughput screening or selection systems, but it is also valuable for any platform that can generate a large amount of data that can be aided by machine learning algorithms. The main challenge in protein engineering is to predict the effect of a single mutation on one functional parameter-to say nothing of several mutations on multiple parameters. This is largely due to nonadditive mutational interactions, known as epistatic effects-beneficial mutations present in a genetic background may not be beneficial in another genetic background. In this work, we provide an overview of experimental and computational strategies that can guide the user to learn protein function at different stages in a directed evolution project. We also discuss how epistatic effects can influence the success of directed evolution projects. Since machine learning is gaining momentum in protein engineering and the field is becoming more interdisciplinary thanks to collaboration between mathematicians, computational scientists, engineers, molecular biologists, and chemists, we provide a general workflow that familiarizes nonexperts with the basic concepts, dataset requirements, learning approaches, model capabilities and performance metrics of this intriguing area. Finally, we also provide some practical recommendations on how machine learning can harness epistatic effects for engineering proteins in an "outside-the-box" way.
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Affiliation(s)
- Xavier F Cadet
- PEACCEL, Artificial Intelligence Department, Paris, France
| | - Jean Christophe Gelly
- Laboratoire d'Excellence GR-Ex, Paris, France
- BIGR, DSIMB, UMR_S1134, INSERM, University of Paris & University of Reunion, Paris, France
| | | | - Frédéric Cadet
- Laboratoire d'Excellence GR-Ex, Paris, France
- BIGR, DSIMB, UMR_S1134, INSERM, University of Paris & University of Reunion, Paris, France
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34
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Meyer J, Meyer L, Kara S. Enzyme immobilization in hydrogels: A perfect liaison for efficient and sustainable biocatalysis. Eng Life Sci 2021; 22:165-177. [PMID: 35382546 PMCID: PMC8961036 DOI: 10.1002/elsc.202100087] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Biocatalysis is an established chemical synthesis technology that has by no means been restricted to research laboratories. The use of enzymes for organic synthesis has evolved greatly from early development to proof‐of‐concept – from small batch production to industrial scale. Different enzyme immobilization strategies contributed to this success story. Recently, the use of hydrogel materials for the immobilization of enzymes has been attracting great interest. Within this review, we pay special attention to recent developments in this key emerging field of research. Firstly, we will briefly introduce the concepts of both biocatalysis and hydrogel worlds. Then, we list recent interesting publications that link both concepts. Finally, we provide an outlook and comment on future perspectives of further exploration of enzyme immobilization strategies in hydrogels.
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Affiliation(s)
- Johanna Meyer
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Lars‐Erik Meyer
- Biocatalysis and Bioprocessing Group Department of Biological and Chemical Engineering Aarhus University Aarhus Denmark
| | - Selin Kara
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
- Biocatalysis and Bioprocessing Group Department of Biological and Chemical Engineering Aarhus University Aarhus Denmark
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35
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3D printed ceramics as solid supports for enzyme immobilization: an automated DoE approach for applications in continuous flow. J Flow Chem 2021; 11:675-689. [PMID: 34745652 PMCID: PMC8563604 DOI: 10.1007/s41981-021-00163-4] [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: 03/10/2021] [Accepted: 04/12/2021] [Indexed: 11/03/2022]
Abstract
In recent years, 3D printing has emerged in the field of chemical engineering as a powerful manufacturing technique to rapidly design and produce tailor-made reaction equipment. In fact, reactors with complex internal geometries can be easily fabricated, optimized and interchanged in order to respond to precise process needs, such as improved mixing and increased surface area. These advantages make them interesting especially for catalytic applications, since customized structured bed reactors can be easily produced. 3D printing applications are not limited to reactor design, it is also possible to realize functional low cost alternatives to analytical equipment that can be used to increase the level of process understanding while keeping the investment costs low. In this work, in-house designed ceramic structured inserts printed via vat photopolymerization (VPP) are presented and characterized. The flow behavior inside these inserts was determined with residence time distribution (RTD) experiments enabled by in-house designed and 3D printed inline photometric flow cells. As a proof of concept, these structured inserts were fitted in an HPLC column to serve as solid inorganic supports for the immobilization of the enzyme Phenolic acid Decarboxylase (bsPAD), which catalyzes the decarboxylation of cinnamic acids. The conversion of coumaric acid to vinylphenol was chosen as a model system to prove the implementation of these engineered inserts in a continuous biocatalytic application with high product yield and process stability. The setup was further automated in order to quickly identify the optimum operating conditions via a Design of Experiments (DoE) approach. The use of a systematic optimization, together with the adaptability of 3D printed equipment to the process requirements, render the presented approach highly promising for a more feasible implementation of biocatalysts in continuous industrial processes. Graphical abstract. Supplementary Information The online version contains supplementary material available at 10.1007/s41981-021-00163-4.
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36
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Genetic fusion of P450 BM3 and formate dehydrogenase towards self-sufficient biocatalysts with enhanced activity. Sci Rep 2021; 11:21706. [PMID: 34737365 PMCID: PMC8568981 DOI: 10.1038/s41598-021-00957-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022] Open
Abstract
Fusion of multiple enzymes to multifunctional constructs has been recognized as a viable strategy to improve enzymatic properties at various levels such as stability, activity and handling. In this study, the genes coding for cytochrome P450 BM3 from B. megaterium and formate dehydrogenase from Pseudomonas sp. were fused to enable both substrate oxidation catalyzed by P450 BM3 and continuous cofactor regeneration by formate dehydrogenase within one construct. The order of the genes in the fusion as well as the linkers that bridge the enzymes were varied. The resulting constructs were compared to individual enzymes regarding substrate conversion, stability and kinetic parameters to examine whether fusion led to any substantial improvements of enzymatic properties. Most noticeably, an activity increase of up to threefold was observed for the fusion constructs with various substrates which were partly attributed to the increased diflavin reductase activity of the P450 BM3. We suggest that P450 BM3 undergoes conformational changes upon fusion which resulted in altered properties, however, no NADPH channeling was detected for the fusion constructs.
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37
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Hobisch M, Holtmann D, Gomez de Santos P, Alcalde M, Hollmann F, Kara S. Recent developments in the use of peroxygenases - Exploring their high potential in selective oxyfunctionalisations. Biotechnol Adv 2021; 51:107615. [PMID: 32827669 PMCID: PMC8444091 DOI: 10.1016/j.biotechadv.2020.107615] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022]
Abstract
Peroxygenases are an emerging new class of enzymes allowing selective oxyfunctionalisation reactions in a cofactor-independent way different from well-known P450 monooxygenases. Herein, we focused on recent developments from organic synthesis, molecular biotechnology and reaction engineering viewpoints that are devoted to bring these enzymes in industrial applications. This covers natural diversity from different sources, protein engineering strategies for expression, substrate scope, activity and selectivity, stabilisation of enzymes via immobilisation, and the use of peroxygenases in low water media. We believe that peroxygenases have much to offer for selective oxyfunctionalisations and we have much to study to explore the full potential of these versatile biocatalysts in organic synthesis.
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Affiliation(s)
- Markus Hobisch
- Department of Engineering, Biocatalysis and Bioprocessing Group, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark
| | - Dirk Holtmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstr. 14, Gießen 35390, Germany
| | | | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/Marie Curie 2, Madrid 28049, Spain; EvoEnzyme S.L, C/ Marie Curie 2, Madrid 28049, Spain
| | - Frank Hollmann
- Department of Biotechnology, Biocatalysis Group, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Selin Kara
- Department of Engineering, Biocatalysis and Bioprocessing Group, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark.
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38
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Kropp C, Bruckmann A, Babinger P. Controlling Enzymatic Activity by Modulating the Oligomerization State via Chemical Rescue and Optical Control. Chembiochem 2021; 23:e202100490. [PMID: 34633135 PMCID: PMC9298306 DOI: 10.1002/cbic.202100490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/08/2021] [Indexed: 12/22/2022]
Abstract
Selective switching of enzymatic activity has been a longstanding goal in synthetic biology. Drastic changes in activity upon mutational manipulation of the oligomerization state of enzymes have frequently been reported in the literature, but scarcely exploited for switching. Using geranylgeranylglyceryl phosphate synthase as a model, we demonstrate that catalytic activity can be efficiently controlled by exogenous modulation of the association state. We introduced a lysine‐to‐cysteine mutation, leading to the breakdown of the active hexamer into dimers with impaired catalytic efficiency. Addition of bromoethylamine chemically rescued the enzyme by restoring hexamerization and activity. As an alternative method, we incorporated the photosensitive unnatural amino acid o‐nitrobenzyl‐O‐tyrosine (ONBY) into the hexamerization interface. This again led to inactive dimers, but the hexameric state and activity could be recovered by UV‐light induced cleavage of ONBY. For both approaches, we obtained switching factors greater than 350‐fold, which compares favorably with previously reported activity changes that were caused by site‐directed mutagenesis.
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Affiliation(s)
- Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040, Regensburg, Germany
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39
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Boosting the kinetic efficiency of formate dehydrogenase by combining the effects of temperature, high pressure and co-solvent mixtures. Colloids Surf B Biointerfaces 2021; 208:112127. [PMID: 34626897 DOI: 10.1016/j.colsurfb.2021.112127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
The application of co-solvents and high pressure has been shown to be an efficient means to modify the kinetics of enzyme-catalyzed reactions without compromising enzyme stability, which is often limited by temperature modulation. In this work, the high-pressure stopped-flow methodology was applied in conjunction with fast UV/Vis detection to investigate kinetic parameters of formate dehydrogenase reaction (FDH), which is used in biotechnology for cofactor recycling systems. Complementary FTIR spectroscopic and differential scanning fluorimetric studies were performed to reveal pressure and temperature effects on the structure and stability of the FDH. In neat buffer solution, the kinetic efficiency increases by one order of magnitude by increasing the temperature from 25° to 45 °C and the pressure from ambient up to the kbar range. The addition of particular co-solvents further doubled the kinetic efficiency of the reaction, in particular the compatible osmolyte trimethylamine-N-oxide and its mixtures with the macromolecular crowding agent dextran. The thermodynamic model PC-SAFT was successfully applied within a simplified activity-based Michaelis-Menten framework to predict the effects of co-solvents on the kinetic efficiency by accounting for interactions involving substrate, co-solvent, water, and FDH. Especially mixtures of the co-solvents at high concentrations were beneficial for the kinetic efficiency and for the unfolding temperature.
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40
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Pleiss J. Standardized Data, Scalable Documentation, Sustainable Storage – EnzymeML As A Basis For FAIR Data Management In Biocatalysis. ChemCatChem 2021. [DOI: 10.1002/cctc.202100822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry University of Stuttgart Allmandring 31 70569 Stuttgart Germany
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41
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Heath RS, Ruscoe RE, Turner NJ. The beauty of biocatalysis: sustainable synthesis of ingredients in cosmetics. Nat Prod Rep 2021; 39:335-388. [PMID: 34879125 DOI: 10.1039/d1np00027f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2015 up to July 2021The market for cosmetics is consumer driven and the desire for green, sustainable and natural ingredients is increasing. The use of isolated enzymes and whole-cell organisms to synthesise these products is congruent with these values, especially when combined with the use of renewable, recyclable or waste feedstocks. The literature of biocatalysis for the synthesis of ingredients in cosmetics in the past five years is herein reviewed.
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Affiliation(s)
- Rachel S Heath
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Rebecca E Ruscoe
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nicholas J Turner
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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42
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Tavanti M, Hosford J, Lloyd RC, Brown MJB. Recent Developments and Challenges for the Industrial Implementation of Polyphosphate Kinases. ChemCatChem 2021. [DOI: 10.1002/cctc.202100688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Michele Tavanti
- Synthetic Biochemistry Medicinal Science and Technology Pharma R&D GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG12NY UK
- Early Chemical development Pharmaceutical Sciences, R&D AstraZeneca Astrazeneca PLC 1 Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB20AA UK
| | - Joseph Hosford
- Synthetic Biochemistry Medicinal Science and Technology Pharma R&D GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG12NY UK
| | - Richard C. Lloyd
- Chemical Development Medicinal Science and Technology Pharma R&D GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG12NY UK
| | - Murray J. B. Brown
- Synthetic Biochemistry Medicinal Science and Technology Pharma R&D GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG12NY UK
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43
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Ott F, Rabe KS, Niemeyer CM, Gygli G. Toward Reproducible Enzyme Modeling with Isothermal Titration Calorimetry. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Felix Ott
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Kersten S. Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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44
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Multicatalytic Hybrid Materials for Biocatalytic and Chemoenzymatic Cascades—Strategies for Multicatalyst (Enzyme) Co-Immobilization. Catalysts 2021. [DOI: 10.3390/catal11080936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
During recent decades, the use of enzymes or chemoenzymatic cascades for organic chemistry has gained much importance in fundamental and industrial research. Moreover, several enzymatic and chemoenzymatic reactions have also served in green and sustainable manufacturing processes especially in fine chemicals, pharmaceutical, and flavor/fragrance industries. Unfortunately, only a few processes have been applied at industrial scale because of the low stabilities of enzymes along with the problematic processes of their recovery and reuse. Immobilization and co-immobilization offer an ideal solution to these problems. This review gives an overview of all the pathways for enzyme immobilization and their use in integrated enzymatic and chemoenzymatic processes in cascade or in a one-pot concomitant execution. We place emphasis on the factors that must be considered to understand the process of immobilization. A better understanding of this fundamental process is an essential tool not only in the choice of the best route of immobilization but also in the understanding of their catalytic activity.
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Ribeaucourt D, Bissaro B, Lambert F, Lafond M, Berrin JG. Biocatalytic oxidation of fatty alcohols into aldehydes for the flavors and fragrances industry. Biotechnol Adv 2021; 56:107787. [PMID: 34147589 DOI: 10.1016/j.biotechadv.2021.107787] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 01/11/2023]
Abstract
From Egyptian mummies to the Chanel n°5 perfume, fatty aldehydes have long been used and keep impacting our senses in a wide range of foods, beverages and perfumes. Natural sources of fatty aldehydes are threatened by qualitative and quantitative variability while traditional chemical routes are insufficient to answer the society shift toward more sustainable and natural products. The production of fatty aldehydes using biotechnologies is therefore the most promising alternative for the flavors and fragrances industry. In this review, after drawing the portrait of the origin and characteristics of fragrant fatty aldehydes, we present the three main classes of enzymes that catalyze the reaction of fatty alcohols oxidation into aldehydes, namely alcohol dehydrogenases, flavin-dependent alcohol oxidases and copper radical alcohol oxidases. The constraints, challenges and opportunities to implement these oxidative enzymes in the flavors and fragrances industry are then discussed. By setting the scene on the biocatalytic production of fatty aldehydes, and providing a critical assessment of its potential, we expect this review to contribute to the development of biotechnology-based solutions in the flavors and fragrances industry.
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Affiliation(s)
- David Ribeaucourt
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France; V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France; Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | - Bastien Bissaro
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Fanny Lambert
- V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France
| | - Mickael Lafond
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France.
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Liu D, Rubin GM, Dhakal D, Chen M, Ding Y. Biocatalytic synthesis of peptidic natural products and related analogues. iScience 2021; 24:102512. [PMID: 34041453 PMCID: PMC8141463 DOI: 10.1016/j.isci.2021.102512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Peptidic natural products (PNPs) represent a rich source of lead compounds for the discovery and development of therapeutic agents for the treatment of a variety of diseases. However, the chemical synthesis of PNPs with diverse modifications for drug research is often faced with significant challenges, including the unavailability of constituent nonproteinogenic amino acids, inefficient cyclization protocols, and poor compatibility with other functional groups. Advances in the understanding of PNP biosynthesis and biocatalysis provide a promising, sustainable alternative for the synthesis of these compounds and their analogues. Here we discuss current progress in using native and engineered biosynthetic enzymes for the production of both ribosomally and nonribosomally synthesized peptides. In addition, we highlight new in vitro and in vivo approaches for the generation and screening of PNP libraries.
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Affiliation(s)
- Dake Liu
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Garret M. Rubin
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
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Immobilization of the Peroxygenase from Agrocybe aegerita. The Effect of the Immobilization pH on the Features of an Ionically Exchanged Dimeric Peroxygenase. Catalysts 2021. [DOI: 10.3390/catal11050560] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This paper outlines the immobilization of the recombinant dimeric unspecific peroxygenase from Agrocybe aegerita (rAaeUPO). The enzyme was quite stable (remaining unaltered its activity after 35 h at 47 °C and pH 7.0). Phosphate destabilized the enzyme, while glycerol stabilized it. The enzyme was not immobilized on glyoxyl-agarose supports, while it was immobilized albeit in inactive form on vinyl-sulfone-activated supports. rAaeUPO immobilization on glutaraldehyde pre-activated supports gave almost quantitative immobilization yield and retained some activity, but the biocatalyst was very unstable. Its immobilization via anion exchange on PEI supports also produced good immobilization yields, but the rAaeUPO stability dropped. However, using aminated agarose, the enzyme retained stability and activity. The stability of the immobilized enzyme strongly depended on the immobilization pH, being much less stable when rAaeUPO was adsorbed at pH 9.0 than when it was immobilized at pH 7.0 or pH 5.0 (residual activity was almost 0 for the former and 80% for the other preparations), presenting stability very similar to that of the free enzyme. This is a very clear example of how the immobilization pH greatly affects the final biocatalyst performance.
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Braham SA, Siar EH, Arana-Peña S, Bavandi H, Carballares D, Morellon-Sterling R, de Andrades D, Kornecki JF, Fernandez-Lafuente R. Positive effect of glycerol on the stability of immobilized enzymes: Is it a universal fact? Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Morellon-Sterling R, Siar EH, Braham SA, de Andrades D, Pedroche J, Millán MDC, Fernandez-Lafuente R. Effect of amine length in the interference of the multipoint covalent immobilization of enzymes on glyoxyl agarose beads. J Biotechnol 2021; 329:128-142. [PMID: 33600890 DOI: 10.1016/j.jbiotec.2021.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/25/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022]
Abstract
Trypsin, chymotrypsin, penicillin G acylase and ficin extract have been stabilized by immobilization on glyoxyl agarose, adding different aliphatic compounds bearing a primary amine group during the immobilization: ethyl amine, butyl amine, hexyl amine (at concentrations ranging from 0 to 20 mM) and octyl amine (from 0 to 10 mM) to analyze their effects on the immobilized enzyme stability. As expected, the presence of amines reduced the intensity of the enzyme-support multipoint covalent attachment, and therefore the enzyme stability. However, it is clear that this effect is higher using octyl amine for all enzymes (in some cases the enzyme immobilized in the presence of 10 mM octyl amine was almost inactivated while the reference kept over 50 % of the initial activity). This way, it seems that the most important effect of the presence of aminated compounds came from the generation of steric hindrances to the enzyme/support multi-reaction promoted by the ammines that are interacting with the aldehyde groups. In some instances, just 1 mM of aminated compounds is enough to greatly decrease enzyme stability. The results suggested that, if the composition of the enzyme extract is unknown, to eliminate small aminated compounds may be necessary to maximize the enzyme-support reaction.
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Affiliation(s)
| | - El-Hocine Siar
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, Campus UAM-CSIC Madrid, Spain; Transformation and Food Product Elaboration Laboratory, Nutrition and Food, Technology Institute (INATAA), University of Brothers Mentouri Constantine 1, Algeria
| | - Sabrina Ait Braham
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, Campus UAM-CSIC Madrid, Spain; Laboratoire de Biotechnologies Végétales et Ethnobotanique, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algeria
| | - Diandra de Andrades
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, Campus UAM-CSIC Madrid, Spain; Biotechnology, Bioprocess, and Biocatalysis Group, Food Science and Technology Institute, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Justo Pedroche
- Group of Plant Proteins, Department of Food and Health, Instituto de la Grasa-CSIC, Seville, Spain
| | - Mª Del Carmen Millán
- Group of Plant Proteins, Department of Food and Health, Instituto de la Grasa-CSIC, Seville, Spain
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, Campus UAM-CSIC Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
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Effect of Concentrated Salts Solutions on the Stability of Immobilized Enzymes: Influence of Inactivation Conditions and Immobilization Protocol. Molecules 2021; 26:molecules26040968. [PMID: 33673063 PMCID: PMC7918437 DOI: 10.3390/molecules26040968] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
This paper aims to investigate the effects of some salts (NaCl, (NH4)2SO4 and Na2SO4) at pH 5.0, 7.0 and 9.0 on the stability of 13 different immobilized enzymes: five lipases, three proteases, two glycosidases, and one laccase, penicillin G acylase and catalase. The enzymes were immobilized to prevent their aggregation. Lipases were immobilized via interfacial activation on octyl agarose or on glutaraldehyde-amino agarose beads, proteases on glyoxyl agarose or glutaraldehyde-amino agarose beads. The use of high concentrations of salts usually has some effects on enzyme stability, but the intensity and nature of these effects depends on the inactivation pH, nature and concentration of the salt, enzyme and immobilization protocol. The same salt can be a stabilizing or a destabilizing agent for a specific enzyme depending on its concentration, inactivation pH and immobilization protocol. Using lipases, (NH4)2SO4 generally permits the highest stabilities (although this is not a universal rule), but using the other enzymes this salt is in many instances a destabilizing agent. At pH 9.0, it is more likely to find a salt destabilizing effect than at pH 7.0. Results confirm the difficulty of foreseeing the effect of high concentrations of salts in a specific immobilized enzyme.
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