1
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Chen M, Jin T, Nian B, Cheng W. Solvent Tolerance Improvement of Lipases Enhanced Their Applications: State of the Art. Molecules 2024; 29:2444. [PMID: 38893320 PMCID: PMC11173743 DOI: 10.3390/molecules29112444] [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: 04/15/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Lipases, crucial catalysts in biochemical synthesis, find extensive applications across industries such as food, medicine, and cosmetics. The efficiency of lipase-catalyzed reactions is significantly influenced by the choice of solvents. Polar organic solvents often result in a decrease, or even loss, of lipase activity. Conversely, nonpolar organic solvents induce excessive rigidity in lipases, thereby affecting their activity. While the advent of new solvents like ionic liquids and deep eutectic solvents has somewhat improved the activity and stability of lipases, it fails to address the fundamental issue of lipases' poor solvent tolerance. Hence, the rational design of lipases for enhanced solvent tolerance can significantly boost their industrial performance. This review provides a comprehensive summary of the structural characteristics and properties of lipases in various solvent systems and emphasizes various strategies of protein engineering for non-aqueous media to improve lipases' solvent tolerance. This study provides a theoretical foundation for further enhancing the solvent tolerance and industrial properties of lipases.
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Affiliation(s)
| | | | | | - Wenjun Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China; (M.C.); (T.J.); (B.N.)
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2
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Cheng W, Nian B. Computer-Aided Lipase Engineering for Improving Their Stability and Activity in the Food Industry: State of the Art. Molecules 2023; 28:5848. [PMID: 37570817 PMCID: PMC10421223 DOI: 10.3390/molecules28155848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
As some of the most widely used biocatalysts, lipases have exhibited extreme advantages in many processes, such as esterification, amidation, and transesterification reactions, which causes them to be widely used in food industrial production. However, natural lipases have drawbacks in terms of organic solvent resistance, thermostability, selectivity, etc., which limits some of their applications in the field of foods. In this systematic review, the application of lipases in various food processes was summarized. Moreover, the general structure of lipases is discussed in-depth, and the engineering strategies that can be used in lipase engineering are also summarized. The protocols of some classical methods are compared and discussed, which can provide some information about how to choose methods of lipase engineering. Thermostability engineering and solvent tolerance engineering are highlighted in this review, and the basic principles for improving thermostability and solvent tolerance are summarized. In the future, comput er-aided technology should be more emphasized in the investigation of the mechanisms of reactions catalyzed by lipases and guide the engineering of lipases. The engineering of lipase tunnels to improve the diffusion of substrates is also a promising prospect for further enhanced lipase activity and selectivity.
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Affiliation(s)
| | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China;
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3
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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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4
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Peccati F, Alunno-Rufini S, Jiménez-Osés G. Accurate Prediction of Enzyme Thermostabilization with Rosetta Using AlphaFold Ensembles. J Chem Inf Model 2023; 63:898-909. [PMID: 36647575 PMCID: PMC9930118 DOI: 10.1021/acs.jcim.2c01083] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Thermostability enhancement is a fundamental aspect of protein engineering as a biocatalyst's half-life is key for its industrial and biotechnological application, particularly at high temperatures and under harsh conditions. Thermostability changes upon mutation originate from modifications of the free energy of unfolding (ΔGu), making thermostabilization extremely challenging to predict with computational methods. In this contribution, we combine global conformational sampling with energy prediction using AlphaFold and Rosetta to develop a new computational protocol for the quantitative prediction of thermostability changes upon laboratory evolution of acyltransferase LovD and lipase LipA. We highlight how using an ensemble of protein conformations rather than a single three-dimensional model is mandatory for accurate thermostability predictions. By comparing our approaches with existing ones, we show that ensembles based on AlphaFold models provide more accurate and robust calculated thermostability trends than ensembles based solely on crystallographic structures as the latter introduce a strong distortion (scaffold bias) in computed thermostabilities. Eliminating this bias is critical for computer-guided enzyme design and evaluating the effect of multiple mutations on protein stability.
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Affiliation(s)
- Francesca Peccati
- Basque
Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Building
800, 48160Derio, Spain,
| | - Sara Alunno-Rufini
- Basque
Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Building
800, 48160Derio, Spain
| | - Gonzalo Jiménez-Osés
- Basque
Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Technology Park, Building
800, 48160Derio, Spain,Ikerbasque, Basque
Foundation for Science, 48013Bilbao, Spain,
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5
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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6
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Thermostabilizing ketoreductase ChKRED20 by consensus mutagenesis at dimeric interfaces. Enzyme Microb Technol 2022; 158:110052. [DOI: 10.1016/j.enzmictec.2022.110052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/15/2022] [Accepted: 04/17/2022] [Indexed: 11/19/2022]
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7
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Pourhassan N. Z, Cui H, Khosa S, Davari MD, Jaeger K, Smits SHJ, Schwaneberg U, Schmitt L. Optimized Hemolysin Type 1 Secretion System in Escherichia coli by Directed Evolution of the Hly Enhancer Fragment and Including a Terminator Region. Chembiochem 2022; 23:e202100702. [PMID: 35062047 PMCID: PMC9306574 DOI: 10.1002/cbic.202100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Indexed: 11/26/2022]
Abstract
Type 1 secretion systems (T1SS) have a relatively simple architecture compared to other classes of secretion systems and therefore, are attractive to be optimized by protein engineering. Here, we report a KnowVolution campaign for the hemolysin (Hly) enhancer fragment, an untranslated region upstream of the hlyA gene, of the hemolysin T1SS of Escherichia coli to enhance its secretion efficiency. The best performing variant of the Hly enhancer fragment contained five nucleotide mutations at five positions (A30U, A36U, A54G, A81U, and A116U) resulted in a 2-fold increase in the secretion level of a model lipase fused to the secretion carrier HlyA1. Computational analysis suggested that altered affinity to the generated enhancer fragment towards the S1 ribosomal protein contributes to the enhanced secretion levels. Furthermore, we demonstrate that involving a native terminator region along with the generated Hly enhancer fragment increased the secretion levels of the Hly system up to 5-fold.
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Affiliation(s)
- Zohreh Pourhassan N.
- Institute of BiochemistryHeinrich Heine UniversityUniversitätsstrasse 140225DüsseldorfGermany
| | - Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstraße 5052056AachenGermany
- Present address: Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 West Gregory DriveUrbanaIl 61801USA
| | - Sakshi Khosa
- Institute of BiochemistryHeinrich Heine UniversityUniversitätsstrasse 140225DüsseldorfGermany
| | - Mehdi D. Davari
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120HalleGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine University and Institute of Bio- and Geosciences IBG-1Biotechnology, Forschungszentrum Jülich GmbH52426JülichGermany
| | - Sander H. J. Smits
- Institute of BiochemistryHeinrich Heine UniversityUniversitätsstrasse 140225DüsseldorfGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstraße 5052056AachenGermany
| | - Lutz Schmitt
- Institute of BiochemistryHeinrich Heine UniversityUniversitätsstrasse 140225DüsseldorfGermany
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8
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El Harrar T, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Critical assessment of structure-based approaches to improve protein resistance in aqueous ionic liquids by enzyme-wide saturation mutagenesis. Comput Struct Biotechnol J 2022; 20:399-409. [PMID: 35070165 PMCID: PMC8752993 DOI: 10.1016/j.csbj.2021.12.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 12/12/2022] Open
Abstract
Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for green industrial processes involving biocatalysts, but often reduce enzyme activity. Experimental and computational methods are applied to predict favorable substitution sites and, most often, subsequent site-directed surface charge modifications are introduced to enhance enzyme resistance towards aIL. However, almost no studies evaluate the prediction precision with random mutagenesis or the application of simple data-driven filtering processes. Here, we systematically and rigorously evaluated the performance of 22 previously described structure-based approaches to increase enzyme resistance to aIL based on an experimental complete site-saturation mutagenesis library of Bacillus subtilis Lipase A (BsLipA) screened against four aIL. We show that, surprisingly, most of the approaches yield low gain-in-precision (GiP) values, particularly for predicting relevant positions: 14 approaches perform worse than random mutagenesis. Encouragingly, exploiting experimental information on the thermostability of BsLipA or structural weak spots of BsLipA predicted by rigidity theory yields GiP = 3.03 and 2.39 for relevant variants and GiP = 1.61 and 1.41 for relevant positions. Combining five simple-to-compute physicochemical and evolutionary properties substantially increases the precision of predicting relevant variants and positions, yielding GiP = 3.35 and 1.29. Finally, combining these properties with predictions of structural weak spots identified by rigidity theory additionally improves GiP for relevant variants up to 4-fold to ∼10 and sustains or increases GiP for relevant positions, resulting in a prediction precision of ∼90% compared to ∼9% in random mutagenesis. This combination should be applicable to other enzyme systems for guiding protein engineering approaches towards improved aIL resistance.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany
| | - Holger Gohlke
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Corresponding author at: John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., 52428 Jülich, Germany.
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9
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Abstract
The CompassR rule enables to identify the beneficial substitutions, which can be recombined in directed evolution with gradually improving the enzymatic properties. However, the question of how to efficiently explore the protein sequence space when ten or more beneficial substitutions are identified has not yet been addressed. Two recombination strategies 2GenReP and InSiReP employing CompassR are systematically investigated to minimize experimental efforts and maximize possible improvements. Here we describe the details of the 2GenReP and InSiReP procedure with an example of recombining 15 substitutions and discuss some important practical issues that should be considered for the application of 2GenReP and InSiReP, such as placing the substitutions into subsets. The core part of the protocol (Step1 to Step5) is transferable to other enzymes and any recombination of potential substitutions.
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Affiliation(s)
- Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.
- DWI Leibniz-Institute for Interactive Materials, Aachen, Germany.
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10
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Imam HT, Krasňan V, Rebroš M, Marr AC. Applications of Ionic Liquids in Whole-Cell and Isolated Enzyme Biocatalysis. Molecules 2021; 26:4791. [PMID: 34443378 PMCID: PMC8399596 DOI: 10.3390/molecules26164791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Ionic liquids have unique chemical properties that have fascinated scientists in many fields. The effects of adding ionic liquids to biocatalysts are many and varied. The uses of ionic liquids in biocatalysis include improved separations and phase behaviour, reduction in toxicity, and stabilization of protein structures. As the ionic liquid state of the art has progressed, concepts of what can be achieved in biocatalysis using ionic liquids have evolved and more beneficial effects have been discovered. In this review ionic liquids for whole-cell and isolated enzyme biocatalysis will be discussed with an emphasis on the latest developments, and a look to the future.
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Affiliation(s)
- Hasan Tanvir Imam
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK;
| | - Vladimír Krasňan
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Martin Rebroš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Andrew Craig Marr
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK;
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11
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El Harrar T, Frieg B, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways. Comput Struct Biotechnol J 2021; 19:4248-4264. [PMID: 34429845 PMCID: PMC8355836 DOI: 10.1016/j.csbj.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/25/2023] Open
Abstract
Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for biocatalysis due to their unique properties. On the other hand, the incubation of enzymes in IL or aIL often reduces enzyme activity. Recent studies proposed various aIL-induced effects to explain the reduction, classified as direct effects, e.g., local dehydration or competitive inhibition, and indirect effects, e.g., structural perturbations or disturbed catalytic site integrity. However, the molecular origin of indirect effects has largely remained elusive. Here we show by multi-μs long molecular dynamics simulations, free energy computations, and rigidity analyses that aIL favorably interact with specific residues of Bacillus subtilis Lipase A (BsLipA) and modify the local structural stability of this model enzyme by inducing long-range perturbations of noncovalent interactions. The perturbations percolate over neighboring residues and eventually affect the catalytic site and the buried protein core. Validation against a complete experimental site saturation mutagenesis library of BsLipA (3620 variants) reveals that the residues of the perturbation pathways are distinguished sequence positions where substitutions highly likely yield significantly improved residual activity. Our results demonstrate that identifying these perturbation pathways and specific IL ion-residue interactions there effectively predicts focused variant libraries with improved aIL tolerance.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Benedikt Frieg
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany
| | - Holger Gohlke
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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12
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Cui H, Jaeger KE, Davari MD, Schwaneberg U. CompassR Yields Highly Organic-Solvent-Tolerant Enzymes through Recombination of Compatible Substitutions. Chemistry 2021; 27:2789-2797. [PMID: 33186477 DOI: 10.1002/chem.202004471] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/12/2020] [Indexed: 01/28/2023]
Abstract
The CompassR (computer-assisted recombination) rule enables, among beneficial substitutions, the identification of those that can be recombined in directed evolution. Herein, a recombination strategy is systematically investigated to minimize experimental efforts and maximize possible improvements. In total, 15 beneficial substitutions from Bacillus subtilis lipase A (BSLA), which improves resistance to the organic cosolvent 1,4-dioxane (DOX), were studied to compare two recombination strategies, the two-gene recombination process (2GenReP) and the in silico guided recombination process (InSiReP), employing CompassR. Remarkably, both strategies yielded a highly DOX-resistant variant, M4 (I12R/Y49R/E65H/N98R/K122E/L124K), with up to 14.6-fold improvement after screening of about 270 clones. M4 has a remarkably enhanced resistance in 60 % (v/v) acetone (6.0-fold), 30 % (v/v) ethanol (2.1-fold), and 60 % (v/v) methanol (2.4-fold) compared with wild-type BSLA. Molecular dynamics simulations revealed that attracting water molecules by charged surface substitutions is the main driver for increasing the DOX resistance of BSLA M4. Both strategies and obtained molecular knowledge can likely be used to improve the properties of other enzymes with a similar α/β-hydrolase fold.
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Affiliation(s)
- Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Wilhelm Johnen Strasse, 52426, Jülich, Germany.,Institute of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, 52426, Jülich, Germany
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.,DWI Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52074, Aachen, Germany
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13
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Rodríguez-Núñez K, Bernal C, Martínez R. Immobilized Biocatalyst Engineering: High throughput enzyme immobilization for the integration of biocatalyst improvement strategies. Int J Biol Macromol 2020; 170:61-70. [PMID: 33358947 DOI: 10.1016/j.ijbiomac.2020.12.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/05/2020] [Accepted: 12/12/2020] [Indexed: 10/22/2022]
Abstract
The increasing use of sustainable manufacturing technologies in the industry presents a constant challenge for the development of suitable biocatalysts. Traditionally, improved biocatalysts are developed either using protein engineering (PE) or enzyme immobilization (EI). However, these approaches are usually not simultaneously applied. In this work, we designed and validated an enzyme improvement platform, Immobilized Biocatalyst Engineering (IBE), which simultaneously integrates PE and EI, with a unique combination of improvement through amino acid substitutions and attachment to a support material, allowing to select variants that would not be found through single or subsequent PE and EI improvement strategies. Our results show that there is a significant difference on the best performing variants identified through IBE, when compared to those that could be identified as soluble enzymes and then immobilized, especially when evaluating variants with low enzyme as soluble enzymes and high activity when immobilized. IBE allows evaluating thousands of variants in a short time through an integrated screening, and selection can be made with more information, resulting in the detection of highly stable and active heterogeneous biocatalysts. This novel approach can translate into a higher probability of finding suitable biocatalysts for highly demanding processes.
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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
| | - 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; Instituto de Investigación Multidisciplinario en Ciencia y Tecnología, Universidad de La Serena, Benavente 980, 1720010 La Serena, Chile.
| | - 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.
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14
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Cui H, Stadtmüller THJ, Jiang Q, Jaeger K, Schwaneberg U, Davari MD. How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Tom H. J. Stadtmüller
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Qianjia Jiang
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf and Research Center Jülich Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstraße 50 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
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15
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Martínez R, Bernal C, Álvarez R, Concha C, Araya F, Cabrera R, Dhoke GV, Davari MD. Deletion and Randomization of Structurally Variable Regions in B. subtilis Lipase A (BSLA) Alter Its Stability and Hydrolytic Performance Against Long Chain Fatty Acid Esters. Int J Mol Sci 2020; 21:ijms21061990. [PMID: 32183336 PMCID: PMC7139672 DOI: 10.3390/ijms21061990] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
The continuous search for novel enzyme backbones and the engineering of already well studied enzymes for biotechnological applications has become an increasing challenge, especially by the increasing potential diversity space provided by directed enzyme evolution approaches and the demands of experimental data generated by rational design of enzymes. In this work, we propose a semi-rational mutational strategy focused on introducing diversity in structurally variable regions in enzymes. The identified sequences are subjected to a progressive deletion of two amino acids and the joining residues are subjected to saturation mutagenesis using NNK degenerate codons. This strategy offers a novel library diversity approach while simultaneously decreasing enzyme size in the variable regions. In this way, we intend to identify and reduce variable regions found in enzymes, probably resulting from neutral drift evolution, and simultaneously studying the functional effect of said regions. This strategy was applied to Bacillus. subtilis lipase A (BSLA), by selecting and deleting six variable enzyme regions (named regions 1 to 6) by the deletion of two amino acids and additionally randomizing the joining amino acid residues. After screening, no active variants were found in libraries 1% and 4%, 15% active variants were found in libraries 2% and 3%, and 25% for libraries 5 and 6 (n = 3000 per library, activity detected using tributyrin agar plates). Active variants were assessed for activity in microtiter plate assay (pNP-butyrate), thermal stability, substrate preference (pNP-butyrate, -palmitate), and compared to wildtype BSLA. From these analyses, variant P5F3 (F41L-ΔW42-ΔD43-K44P), from library 3 was identified, showing increased activity towards longer chain p-nitrophenyl fatty acid esters, when compared to BSLA. This study allowed to propose the targeted region 3 (positions 40-46) as a potential modulator for substrate specificity (fatty acid chain length) in BSLA, which can be further studied to increase its substrate spectrum and selectivity. Additionally, this variant showed a decreased thermal resistance but interestingly, higher isopropanol and Triton X-100 resistance. This deletion-randomization strategy could help to expand and explore sequence diversity, even in already well studied and characterized enzyme backbones such as BSLA. In addition, this strategy can contribute to investigate and identify important non-conserved regions in classic and novel enzymes, as well as generating novel biocatalysts with increased performance in specific processes, such as enzyme immobilization.
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Affiliation(s)
- Ronny Martínez
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
- Correspondence: ; Tel.: +56-51-2334661; Fax: +56-51-2204446
| | - Claudia Bernal
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
| | - Rodrigo Álvarez
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
- Escuela de Tecnología Médica, Facultad de Salud, Sede La Serena, Universidad Santo Tomás, La Serena 1710172, Chile
| | - Christopher Concha
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
| | - Fernando Araya
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile; (F.A.); (R.C.)
| | - Ricardo Cabrera
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile; (F.A.); (R.C.)
| | - Gaurao V. Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (G.V.D.); (M.D.D.)
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (G.V.D.); (M.D.D.)
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16
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Surface residues serine 69 and arginine 194 of metagenome-derived lipase influence catalytic activity. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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Nutschel C, Fulton A, Zimmermann O, Schwaneberg U, Jaeger KE, Gohlke H. Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. J Chem Inf Model 2020; 60:1568-1584. [PMID: 31905288 DOI: 10.1021/acs.jcim.9b00954] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Improving an enzyme's (thermo-)stability or tolerance against solvents and detergents is highly relevant in protein engineering and biotechnology. Recent developments have tended toward data-driven approaches, where available knowledge about the protein is used to identify substitution sites with high potential to yield protein variants with improved stability, and subsequently, substitutions are engineered by site-directed or site-saturation (SSM) mutagenesis. However, the development and validation of algorithms for data-driven approaches have been hampered by the lack of availability of large-scale data measured in a uniform way and being unbiased with respect to substitution types and locations. Here, we extend our knowledge on guidelines for protein engineering following a data-driven approach by scrutinizing the impact of substitution sites on thermostability or/and detergent tolerance for Bacillus subtilis lipase A (BsLipA) at very large scale. We systematically analyze a complete experimental SSM library of BsLipA containing all 3439 possible single variants, which was evaluated as to thermostability and tolerances against four detergents under respectively uniform conditions. Our results provide systematic and unbiased reference data at unprecedented scale for a biotechnologically important protein, identify consistently defined hot spot types for evaluating the performance of data-driven protein-engineering approaches, and show that the rigidity theory and ensemble-based approach Constraint Network Analysis yields hot spot predictions with an up to ninefold gain in precision over random classification.
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Affiliation(s)
- Christina Nutschel
- John von Neumann Institute for Computing (NIC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany
| | - Olav Zimmermann
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials, 52056 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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18
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Cui H, Cao H, Cai H, Jaeger K, Davari MD, Schwaneberg U. Computer-Assisted Recombination (CompassR) Teaches us How to Recombine Beneficial Substitutions from Directed Evolution Campaigns. Chemistry 2020; 26:643-649. [PMID: 31553080 PMCID: PMC7003928 DOI: 10.1002/chem.201903994] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Indexed: 01/09/2023]
Abstract
A main remaining challenge in protein engineering is how to recombine beneficial substitutions. Systematic recombination studies show that poorly performing variants are usually obtained after recombination of 3 to 4 beneficial substitutions. This limits researchers in exploiting nature's potential in generating better enzymes. The Computer-assisted Recombination (CompassR) strategy provides a selection guide for beneficial substitutions that can be recombined to gradually improve enzyme performance by analysis of the relative free energy of folding (ΔΔGfold ). The performance of CompassR was evaluated by analysis of 84 recombinants located on 13 positions of Bacillus subtilis lipase A. The finally obtained variant F17S/V54K/D64N/D91E had a 2.7-fold improved specific activity in 18.3 % (v/v) 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). In essence, the deducted CompassR rule allows recombination of beneficial substitutions in an iterative manner and empowers researchers to generate better enzymes in a time-efficient manner.
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Affiliation(s)
- Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Hao Cao
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Beijing Bioprocess Key Laboratory and College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Haiying Cai
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Karl‐Erich Jaeger
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Institute of Molecular Enzyme TechnologyHeinrich Heine University Düsseldorf and Research Center Jülich, Wilhelm Johnen Strasse52426JülichGermany
| | - Mehdi D. Davari
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
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19
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Siedhoff NE, Schwaneberg U, Davari MD. Machine learning-assisted enzyme engineering. Methods Enzymol 2020; 643:281-315. [DOI: 10.1016/bs.mie.2020.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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20
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Jimenez-Rosales A, Flores-Merino MV. Tailoring Proteins to Re-Evolve Nature: A Short Review. Mol Biotechnol 2018; 60:946-974. [DOI: 10.1007/s12033-018-0122-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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21
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Höck H, Engel S, Weingarten S, Keul H, Schwaneberg U, Möller M, Bocola M. Comparison of Candida antarctica Lipase B Variants for Conversion of ε-Caprolactone in Aqueous Medium-Part 2. Polymers (Basel) 2018; 10:E524. [PMID: 30966558 PMCID: PMC6415414 DOI: 10.3390/polym10050524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/26/2018] [Accepted: 05/10/2018] [Indexed: 12/22/2022] Open
Abstract
Enzyme-catalyzed ring-opening polymerization of lactones is a method of increasing interest for the synthesis of polyesters. In the present work, we investigated which changes in the structure of Candida antarctica lipase B (CaLB) shift the catalytic equilibrium between esterification and hydrolysis towards polymerization. Therefore, we present two concepts: (i) removing the glycosylation of CaLB to increase the surface hydrophobicity; and (ii) introducing a hydrophobic lid adapted from Pseudomonas cepacia lipase (PsCL) to enhance the interaction of a growing polymer chain to the elongated lid helix. The deglycosylated CaLB (CaLB-degl) was successfully generated by site-saturation mutagenesis of asparagine 74. Furthermore, computational modeling showed that the introduction of a lid helix at position Ala148 was structurally feasible and the geometry of the active site remained intact. Via overlap extension PCR the lid was successfully inserted, and the variant was produced in large scale in Pichia pastoris with glycosylation (CaLB-lid) and without (CaLB-degl-lid). While the lid variants show a minor positive effect on the polymerization activity, CaLB-degl showed a clearly reduced hydrolytic and enhanced polymerization activity. Immobilization in a hydrophobic polyglycidol-based microgel intensified this effect such that a higher polymerization activity was achieved, compared to the "gold standard" Novozym® 435.
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Affiliation(s)
- Heidi Höck
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Stefan Engel
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Simone Weingarten
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Helmut Keul
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Ulrich Schwaneberg
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Martin Möller
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Marco Bocola
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
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22
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Acevedo-Rocha CG, Gamble CG, Lonsdale R, Li A, Nett N, Hoebenreich S, Lingnau JB, Wirtz C, Fares C, Hinrichs H, Deege A, Mulholland AJ, Nov Y, Leys D, McLean KJ, Munro AW, Reetz MT. P450-Catalyzed Regio- and Diastereoselective Steroid Hydroxylation: Efficient Directed Evolution Enabled by Mutability Landscaping. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00389] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Charles G. Gamble
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Aitao Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University 368 Youyi Road, Wuchang Wuhan 430062, China
| | - Nathalie Nett
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Sabrina Hoebenreich
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Julia B. Lingnau
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Cornelia Wirtz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Christophe Fares
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Heike Hinrichs
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Alfred Deege
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Yuval Nov
- Department of Statistics, University of Haifa, Haifa 31905, Israel
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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23
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Frauenkron-Machedjou VJ, Fulton A, Zhao J, Weber L, Jaeger KE, Schwaneberg U, Zhu L. Exploring the full natural diversity of single amino acid exchange reveals that 40–60% of BSLA positions improve organic solvents resistance. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-017-0188-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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24
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Zhao J, Frauenkron-Machedjou VJ, Fulton A, Zhu L, Davari MD, Jaeger KE, Schwaneberg U, Bocola M. Unraveling the effects of amino acid substitutions enhancing lipase resistance to an ionic liquid: a molecular dynamics study. Phys Chem Chem Phys 2018; 20:9600-9609. [DOI: 10.1039/c7cp08470f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The key properties affecting lipase resistance towards an ionic liquid are uncovered through a molecular dynamics study.
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Affiliation(s)
- Jing Zhao
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- Tianjin Institute of Industrial Biotechnology
| | | | - Alexander Fulton
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52426 Jülich
- Germany
| | - Leilei Zhu
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- Tianjin Institute of Industrial Biotechnology
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52426 Jülich
- Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- DWI-Leibniz Institute for Interactive Materials
| | - Marco Bocola
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
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25
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Abstract
Directed evolution has emerged as one of the most effective protein engineering methods in basic research as well as in applications in synthetic organic chemistry and biotechnology. The successful engineering of protein activity, allostery, binding affinity, expression, folding, fluorescence, solubility, substrate scope, selectivity (enantio-, stereo-, and regioselectivity), and/or stability (temperature, organic solvents, pH) is just limited by the throughput of the genetic selection, display, or screening system that is available for a given protein. Sometimes it is possible to analyze millions of protein variants from combinatorial libraries per day. In other cases, however, only a few hundred variants can be screened in a single day, and thus the creation of smaller yet smarter libraries is needed. Different strategies have been developed to create these libraries. One approach is to perform mutational scanning or to construct "mutability landscapes" in order to understand sequence-function relationships that can guide the actual directed evolution process. Herein we provide a protocol for economically constructing scanning mutagenesis libraries using a cytochrome P450 enzyme in a high-throughput manner. The goal is to engineer activity, regioselectivity, and stereoselectivity in the oxidative hydroxylation of a steroid, a challenging reaction in synthetic organic chemistry. Libraries based on mutability landscapes can be used to engineer any fitness trait of interest. The protocol is also useful for constructing gene libraries for deep mutational scanning experiments.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany.
- Biosyntia ApS, 2100, Copenhagen, Denmark.
| | - Matteo Ferla
- Department of Biochemistry, Oxford University, Oxford, OX1 3QU, UK
| | - Manfred T Reetz
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany
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26
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Skoczinski P, Volkenborn K, Fulton A, Bhadauriya A, Nutschel C, Gohlke H, Knapp A, Jaeger KE. Contribution of single amino acid and codon substitutions to the production and secretion of a lipase by Bacillus subtilis. Microb Cell Fact 2017; 16:160. [PMID: 28946879 PMCID: PMC5613506 DOI: 10.1186/s12934-017-0772-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/13/2017] [Indexed: 01/07/2023] Open
Abstract
Background Bacillus subtilis produces and secretes proteins in amounts of up to 20 g/l under optimal conditions. However, protein production can be challenging if transcription and cotranslational secretion are negatively affected, or the target protein is degraded by extracellular proteases. This study aims at elucidating the influence of a target protein on its own production by a systematic mutational analysis of the homologous B. subtilis model protein lipase A (LipA). We have covered the full natural diversity of single amino acid substitutions at 155 positions of LipA by site saturation mutagenesis excluding only highly conserved residues and qualitatively and quantitatively screened about 30,000 clones for extracellular LipA production. Identified variants with beneficial effects on production were sequenced and analyzed regarding B. subtilis growth behavior, extracellular lipase activity and amount as well as changes in lipase transcript levels. Results In total, 26 LipA variants were identified showing an up to twofold increase in either amount or activity of extracellular lipase. These variants harbor single amino acid or codon substitutions that did not substantially affect B. subtilis growth. Subsequent exemplary combination of beneficial single amino acid substitutions revealed an additive effect solely at the level of extracellular lipase amount; however, lipase amount and activity could not be increased simultaneously. Conclusions Single amino acid and codon substitutions can affect LipA secretion and production by B. subtilis. Several codon-related effects were observed that either enhance lipA transcription or promote a more efficient folding of LipA. Single amino acid substitutions could improve LipA production by increasing its secretion or stability in the culture supernatant. Our findings indicate that optimization of the expression system is not sufficient for efficient protein production in B. subtilis. The sequence of the target protein should also be considered as an optimization target for successful protein production. Our results further suggest that variants with improved properties might be identified much faster and easier if mutagenesis is prioritized towards elements that contribute to enzymatic activity or structural integrity. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0772-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pia Skoczinski
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany.,Macromolecular Chemistry and New Polymeric Materials, Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Kristina Volkenborn
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Anuseema Bhadauriya
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Christina Nutschel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems - Structural Biochemistry (ICS6), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany. .,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Yang J, Ruff AJ, Arlt M, Schwaneberg U. Casting epPCR (cepPCR): A simple random mutagenesis method to generate high quality mutant libraries. Biotechnol Bioeng 2017; 114:1921-1927. [DOI: 10.1002/bit.26327] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/03/2017] [Accepted: 04/23/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Jianhua Yang
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 Aachen 52074 Germany
| | - Anna J. Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 Aachen 52074 Germany
| | - Marcus Arlt
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 Aachen 52074 Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 Aachen 52074 Germany
- DWI-Leibniz Institut für Interaktive Materialien; Aachen Germany
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28
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Are Directed Evolution Approaches Efficient in Exploring Nature’s Potential to Stabilize a Lipase in Organic Cosolvents? Catalysts 2017. [DOI: 10.3390/catal7050142] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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29
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Kaschner M, Schillinger O, Fettweiss T, Nutschel C, Krause F, Fulton A, Strodel B, Stadler A, Jaeger KE, Krauss U. A combination of mutational and computational scanning guides the design of an artificial ligand-binding controlled lipase. Sci Rep 2017; 7:42592. [PMID: 28218303 PMCID: PMC5316958 DOI: 10.1038/srep42592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/11/2017] [Indexed: 11/09/2022] Open
Abstract
Allostery, i.e. the control of enzyme activity by a small molecule at a location distant from the enzyme’s active site, represents a mechanism essential for sustaining life. The rational design of allostery is a non-trivial task but can be achieved by fusion of a sensory domain, which responds to environmental stimuli with a change in its structure. Hereby, the site of domain fusion is difficult to predict. We here explore the possibility to rationally engineer allostery into the naturally not allosterically regulated Bacillus subtilis lipase A, by fusion of the citrate-binding sensor-domain of the CitA sensory-kinase of Klebsiella pneumoniae. The site of domain fusion was rationally determined based on whole-protein site-saturation mutagenesis data, complemented by computational evolutionary-coupling analyses. Functional assays, combined with biochemical and biophysical studies suggest a mechanism for control, similar but distinct to the one of the parent CitA protein, with citrate acting as an indirect modulator of Triton-X100 inhibition of the fusion protein. Our study demonstrates that the introduction of ligand-dependent regulatory control by domain fusion is surprisingly facile, suggesting that the catalytic mechanism of some enzymes may be evolutionary optimized in a way that it can easily be perturbed by small conformational changes.
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Affiliation(s)
- Marco Kaschner
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Oliver Schillinger
- Institute of Complex Systems ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Timo Fettweiss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Christina Nutschel
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Frank Krause
- Nanolytics, Gesellschaft für Kolloidanalytik GmbH, Am Mühlenberg 11, 14476 Potsdam, Germany
| | - Alexander Fulton
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Andreas Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
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30
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Zhao J, Frauenkron-Machedjou VJ, Kardashliev T, Ruff AJ, Zhu L, Bocola M, Schwaneberg U. Amino acid substitutions in random mutagenesis libraries: lessons from analyzing 3000 mutations. Appl Microbiol Biotechnol 2017; 101:3177-3187. [DOI: 10.1007/s00253-016-8035-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/26/2016] [Accepted: 11/26/2016] [Indexed: 12/27/2022]
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31
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Umapathi R, Mkhize TY, Venkatesu P, Deenadayalu N. The influence of various alkylammonium-based ionic liquids on the hydration state of temperature-responsive polymer. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.11.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Wiedemann C, Ohlenschläger O, Mrestani-Klaus C, Bordusa F. NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state. Phys Chem Chem Phys 2017; 19:24115-24125. [DOI: 10.1039/c7cp03295a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The impact of ionic liquids on the chemical shifts and the cis/trans equilibrium state of a model peptide was systematically investigated by NMR spectroscopy.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
| | | | - Carmen Mrestani-Klaus
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
| | - Frank Bordusa
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
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33
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Körfer G, Pitzler C, Vojcic L, Martinez R, Schwaneberg U. In vitro flow cytometry-based screening platform for cellulase engineering. Sci Rep 2016; 6:26128. [PMID: 27184298 PMCID: PMC4869107 DOI: 10.1038/srep26128] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
Ultrahigh throughput screening (uHTS) plays an essential role in directed evolution for tailoring biocatalysts for industrial applications. Flow cytometry-based uHTS provides an efficient coverage of the generated protein sequence space by analysis of up to 107 events per hour. Cell-free enzyme production overcomes the challenge of diversity loss during the transformation of mutant libraries into expression hosts, enables directed evolution of toxic enzymes, and holds the promise to efficiently design enzymes of human or animal origin. The developed uHTS cell-free compartmentalization platform (InVitroFlow) is the first report in which a flow cytometry-based screened system has been combined with compartmentalized cell-free expression for directed cellulase enzyme evolution. InVitroFlow was validated by screening of a random cellulase mutant library employing a novel screening system (based on the substrate fluorescein-di-β-D-cellobioside), and yielded significantly improved cellulase variants (e.g. CelA2-H288F-M1 (N273D/H288F/N468S) with 13.3-fold increased specific activity (220.60 U/mg) compared to CelA2 wildtype: 16.57 U/mg).
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Affiliation(s)
| | | | - Ljubica Vojcic
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ronny Martinez
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ulrich Schwaneberg
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.,DWI an der RWTH Aachen e.V, Forckenbeckstraße 50, 52056 Aachen, Germany
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34
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Wolski PW, Dana CM, Clark DS, Blanch HW. Engineering ionic liquid-tolerant cellulases for biofuels production. Protein Eng Des Sel 2016; 29:117-22. [DOI: 10.1093/protein/gzv066] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 12/07/2015] [Indexed: 12/22/2022] Open
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35
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Nordwald EM, Plaks JG, Snell JR, Sousa MC, Kaar JL. Crystallographic Investigation of Imidazolium Ionic Liquid Effects on Enzyme Structure. Chembiochem 2015; 16:2456-9. [PMID: 26388426 DOI: 10.1002/cbic.201500398] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 01/11/2023]
Abstract
We present the first crystallographic insight into the interactions of an ionic liquid (IL) with an enzyme, which has widespread implications for stabilizing enzymes in IL media for biocatalysis. Structures of Bacillus subtilis lipase A (lipA) and an IL-stable variant (QM-lipA) were obtained in the presence of increasing concentrations of 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). These studies revealed that the [BMIM] cation interacts with surface residues through hydrophobic and cation-π interactions. Of specific interest was the disruption of internal stacking interactions of aromatic side chains by [BMIM], which provides structural evidence for the mechanism of enzyme denaturation by ILs. The interaction of [BMIM] and Cl ions with lipA was reduced by the stabilizing mutations Y49E and G158E in QM-lipA. Ultimately, these findings present the molecular basis for stabilizing enzymes from IL-induced inactivation, as well as the selection of ILs that are less denaturing.
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Affiliation(s)
- Erik M Nordwald
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Jared R Snell
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Marcelo C Sousa
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA.
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36
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Cheng F, Zhu L, Schwaneberg U. Directed evolution 2.0: improving and deciphering enzyme properties. Chem Commun (Camb) 2015; 51:9760-72. [DOI: 10.1039/c5cc01594d] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A KnowVolution: knowledge gaining directed evolution including four phases is proposed in this feature article, which generates improved enzyme variants and molecular understanding.
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Affiliation(s)
- Feng Cheng
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Leilei Zhu
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- DWI-Leibniz Institute for Interactive Materials
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