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Bollinger A, Molitor R, Thies S, Koch R, Coscolín C, Ferrer M, Jaeger KE. Organic-Solvent-Tolerant Carboxylic Ester Hydrolases for Organic Synthesis. Appl Environ Microbiol 2020; 86:e00106-20. [PMID: 32111588 PMCID: PMC7170478 DOI: 10.1128/aem.00106-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Biocatalysis has emerged as an important tool in synthetic organic chemistry enabling the chemical industry to execute reactions with high regio- or enantioselectivity and under usually mild reaction conditions while avoiding toxic waste. Target substrates and products of reactions catalyzed by carboxylic ester hydrolases are often poorly water soluble and require organic solvents, whereas enzymes are evolved by nature to be active in cells, i.e., in aqueous rather than organic solvents. Therefore, biocatalysts that withstand organic solvents are urgently needed. Current strategies to identify such enzymes rely on laborious tests carried out by incubation in different organic solvents and determination of residual activity. Here, we describe a simple assay useful for screening large libraries of carboxylic ester hydrolases for resistance and activity in water-miscible organic solvents. We have screened a set of 26 enzymes, most of them identified in this study, with four different water-miscible organic solvents. The triglyceride tributyrin was used as a substrate, and fatty acids released by enzymatic hydrolysis were detected by a pH shift indicated by the indicator dye nitrazine yellow. With this strategy, we succeeded in identifying a novel highly organic-solvent-tolerant esterase from Pseudomonas aestusnigri In addition, the newly identified enzymes were tested with sterically demanding substrates, which are common in pharmaceutical intermediates, and two enzymes from Alcanivorax borkumensis were identified which outcompeted the gold standard ester hydrolase CalB from Candida antarcticaIMPORTANCE Major challenges hampering biotechnological applications of esterases include the requirement to accept nonnatural and chemically demanding substrates and the tolerance of the enzymes toward organic solvents which are often required to solubilize such substrates. We describe here a high-throughput screening strategy to identify novel organic-solvent-tolerant carboxylic ester hydrolases (CEs). Among these enzymes, CEs active against water-insoluble bulky substrates were identified. Our results thus contribute to fostering the identification and biotechnological application of CEs.
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Affiliation(s)
- Alexander Bollinger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Rebecka Molitor
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | | | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
- Institute for Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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Kirkwood J, Hargreaves D, O’Keefe S, Wilson J. Analysis of crystallization data in the Protein Data Bank. Acta Crystallogr F Struct Biol Commun 2015; 71:1228-34. [PMID: 26457511 PMCID: PMC4601584 DOI: 10.1107/s2053230x15014892] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/08/2015] [Indexed: 11/10/2022] Open
Abstract
The Protein Data Bank (PDB) is the largest available repository of solved protein structures and contains a wealth of information on successful crystallization. Many centres have used their own experimental data to draw conclusions about proteins and the conditions in which they crystallize. Here, data from the PDB were used to reanalyse some of these results. The most successful crystallization reagents were identified, the link between solution pH and the isoelectric point of the protein was investigated and the possibility of predicting whether a protein will crystallize was explored.
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Affiliation(s)
- Jobie Kirkwood
- Department of Chemistry, University of York, York YO10 5DD, England
| | - David Hargreaves
- AstraZeneca, Darwin Building, Cambridge Science Park, Cambridge CB4 0WG, England
| | - Simon O’Keefe
- Department of Computer Science, University of York, York YO10 5DD, England
| | - Julie Wilson
- Department of Chemistry, University of York, York YO10 5DD, England
- Department of Mathematics, University of York, York YO10 5DD, England
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Kirkwood J, Hargreaves D, O'Keefe S, Wilson J. Using isoelectric point to determine the pH for initial protein crystallization trials. ACTA ACUST UNITED AC 2015; 31:1444-51. [PMID: 25573921 PMCID: PMC4410668 DOI: 10.1093/bioinformatics/btv011] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/05/2015] [Indexed: 11/12/2022]
Abstract
Motivation: The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, the pH is usually recorded as that of the buffer solution, which can be highly inaccurate. Results: Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes. Availability and implementation: Data used to generate models are available as Supplementary Material. Contact:julie.wilson@york.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jobie Kirkwood
- Department of Chemistry, University of York, YO10 5DD, UK, Discovery Sciences, Structure & Biophysics, AstraZeneca Darwin Building, Cambridge, Science Park, Milton Road, Cambridge, CB4 0WG, UK, Department of Computer Science, University of York, YO10 5GH, UK and Department of Mathematics, University of York, YO10 5DD, UK
| | - David Hargreaves
- Department of Chemistry, University of York, YO10 5DD, UK, Discovery Sciences, Structure & Biophysics, AstraZeneca Darwin Building, Cambridge, Science Park, Milton Road, Cambridge, CB4 0WG, UK, Department of Computer Science, University of York, YO10 5GH, UK and Department of Mathematics, University of York, YO10 5DD, UK
| | - Simon O'Keefe
- Department of Chemistry, University of York, YO10 5DD, UK, Discovery Sciences, Structure & Biophysics, AstraZeneca Darwin Building, Cambridge, Science Park, Milton Road, Cambridge, CB4 0WG, UK, Department of Computer Science, University of York, YO10 5GH, UK and Department of Mathematics, University of York, YO10 5DD, UK
| | - Julie Wilson
- Department of Chemistry, University of York, YO10 5DD, UK, Discovery Sciences, Structure & Biophysics, AstraZeneca Darwin Building, Cambridge, Science Park, Milton Road, Cambridge, CB4 0WG, UK, Department of Computer Science, University of York, YO10 5GH, UK and Department of Mathematics, University of York, YO10 5DD, UK Department of Chemistry, University of York, YO10 5DD, UK, Discovery Sciences, Structure & Biophysics, AstraZeneca Darwin Building, Cambridge, Science Park, Milton Road, Cambridge, CB4 0WG, UK, Department of Computer Science, University of York, YO10 5GH, UK and Department of Mathematics, University of York, YO10 5DD, UK
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