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Morris P, García-Arrazola R, Rios-Solis L, Dalby PA. Biophysical characterization of the inactivation of E. coli transketolase by aqueous co-solvents. Sci Rep 2021; 11:23584. [PMID: 34880340 PMCID: PMC8654844 DOI: 10.1038/s41598-021-03001-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Transketolase (TK) has been previously engineered, using semi-rational directed evolution and substrate walking, to accept increasingly aliphatic, cyclic, and then aromatic substrates. This has ultimately led to the poor water solubility of new substrates, as a potential bottleneck to further exploitation of this enzyme in biocatalysis. Here we used a range of biophysical studies to characterise the response of both E. coli apo- and holo-TK activity and structure to a range of polar organic co-solvents: acetonitrile (AcCN), n-butanol (nBuOH), ethyl acetate (EtOAc), isopropanol (iPrOH), and tetrahydrofuran (THF). The mechanism of enzyme deactivation was found to be predominantly via solvent-induced local unfolding. Holo-TK is thermodynamically more stable than apo-TK and yet for four of the five co-solvents it retained less activity than apo-TK after exposure to organic solvents, indicating that solvent tolerance was not simply correlated to global conformational stability. The co-solvent concentrations required for complete enzyme inactivation was inversely proportional to co-solvent log(P), while the unfolding rate was directly proportional, indicating that the solvents interact with and partially unfold the enzyme through hydrophobic contacts. Small amounts of aggregate formed in some cases, but this was not sufficient to explain the enzyme inactivation. TK was found to be tolerant to 15% (v/v) iPrOH, 10% (v/v) AcCN, or 6% (v/v) nBuOH over 3 h. This work indicates that future attempts to engineer the enzyme to better tolerate co-solvents should focus on increasing the stability of the protein to local unfolding, particularly in and around the cofactor-binding loops.
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Affiliation(s)
- Phattaraporn Morris
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
- Chemical Metrology and Biometry Department, National Institute of Metrology, 3/4-5 Moo 3, Klong 5, Klong Luang, 12120, Pathumthani, Thailand
| | - Ribia García-Arrazola
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, UK
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, King's Buildings, Edinburgh, EH9 3JL, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
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2
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Slagman S, Fessner WD. Biocatalytic routes to anti-viral agents and their synthetic intermediates. Chem Soc Rev 2021; 50:1968-2009. [DOI: 10.1039/d0cs00763c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An assessment of biocatalytic strategies for the synthesis of anti-viral agents, offering guidelines for the development of sustainable production methods for a future COVID-19 remedy.
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Affiliation(s)
- Sjoerd Slagman
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
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3
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Henríquez M, Braun‐Galleani S, Nesbeth DN. Whole cell biosynthetic activity ofKomagataella phaffii(Pichia pastoris) GS115 strains engineered with transgenes encodingChromobacterium violaceumω‐transaminase alone or combined with native transketolase. Biotechnol Prog 2019; 36:e2893. [DOI: 10.1002/btpr.2893] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 01/25/2023]
Affiliation(s)
| | | | - Darren N. Nesbeth
- Department of Biochemical EngineeringUniversity College London London UK
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4
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Optimisation of enzyme cascades for chiral amino alcohol synthesis in aid of host cell integration using a statistical experimental design approach. J Biotechnol 2018; 281:150-160. [PMID: 30009844 DOI: 10.1016/j.jbiotec.2018.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 01/20/2023]
Abstract
Chiral amino alcohols are compounds of pharmaceutical interest as they are building blocks of sphingolipids, antibiotics, and antiviral glycosidase inhibitors. Due to the challenges of chemical synthesis we recently developed two TK-TAm reaction cascades using natural and low cost feedstocks as substrates: a recycling cascade comprising of 2 enzymes and a sequential 3-step enzyme cascade yielding 30% and 1% conversion, respectively. In order to improve the conversion yield and aid the future host strain engineering for whole cell biocatalysis, we used a combination of microscale experiments and statistical experimental design. For this we implemented a full factorial design to optimise pH, temperature and buffer type, followed by the application of Response Surface Methodology for the optimisation of substrates and enzymes concentrations. Using purified enzymes we achieved 60% conversion for the recycling cascade and 3-fold improvement using the sequential pathway. Based on the results, limiting steps and individual requirements for host cell metabolic integration were identified expanding the understanding of the cascades without implementing extensive optimisation modelling. Therefore, the approach described here is well suited for optimising reaction conditions as well as defining the relative enzyme expression levels required for construction of microbial cell factories.
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5
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One-pot, two-step transaminase and transketolase synthesis of l-gluco-heptulose from l-arabinose. Enzyme Microb Technol 2018; 116:16-22. [PMID: 29887012 DOI: 10.1016/j.enzmictec.2018.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/21/2018] [Accepted: 05/10/2018] [Indexed: 11/23/2022]
Abstract
The use of biocatalysis for the synthesis of high value added chemical building blocks derived from biomass is becoming an increasingly important application for future sustainable technologies. The synthesis of a higher value chemical from l-arabinose, the predominant monosaccharide obtained from sugar beet pulp, is demonstrated here via a transketolase and transaminase coupled reaction. Thermostable transketolases derived from Deinococcus geothermalis and Deinococcus radiodurans catalysed the synthesis of l-gluco-heptulose from l-arabinose and β-hydroxypyruvate at elevated temperatures with high conversions. β-Hydroxypyruvate, a commercially expensive compound used in the transketolase reaction, was generated in situ from l-serine and α-ketoglutaric acid via a thermostable transaminase, also from Deinococcus geothermalis. The two steps were investigated and implemented in a one-pot system for the sustainable and efficient production of l-gluco-heptulose.
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6
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Gruber P, Carvalho F, Marques MPC, O'Sullivan B, Subrizi F, Dobrijevic D, Ward J, Hailes HC, Fernandes P, Wohlgemuth R, Baganz F, Szita N. Enzymatic synthesis of chiral amino-alcohols by coupling transketolase and transaminase-catalyzed reactions in a cascading continuous-flow microreactor system. Biotechnol Bioeng 2017; 115:586-596. [PMID: 28986983 PMCID: PMC5813273 DOI: 10.1002/bit.26470] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 11/12/2022]
Abstract
Rapid biocatalytic process development and intensification continues to be challenging with currently available methods. Chiral amino‐alcohols are of particular interest as they represent key industrial synthons for the production of complex molecules and optically pure pharmaceuticals. (2S,3R)‐2‐amino‐1,3,4‐butanetriol (ABT), a building block for the synthesis of protease inhibitors and detoxifying agents, can be synthesized from simple, non‐chiral starting materials, by coupling a transketolase‐ and a transaminase‐catalyzed reaction. However, until today, full conversion has not been shown and, typically, long reaction times are reported, making process modifications and improvement challenging. In this contribution, we present a novel microreactor‐based approach based on free enzymes, and we report for the first time full conversion of ABT in a coupled enzyme cascade for both batch and continuous‐flow systems. Using the compartmentalization of the reactions afforded by the microreactor cascade, we overcame inhibitory effects, increased the activity per unit volume, and optimized individual reaction conditions. The transketolase‐catalyzed reaction was completed in under 10 min with a volumetric activity of 3.25 U ml−1. Following optimization of the transaminase‐catalyzed reaction, a volumetric activity of 10.8 U ml−1 was attained which led to full conversion of the coupled reaction in 2 hr. The presented approach illustrates how continuous‐flow microreactors can be applied for the design and optimization of biocatalytic processes.
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Affiliation(s)
- Pia Gruber
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Filipe Carvalho
- Department of Bioengineering and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Marco P C Marques
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Brian O'Sullivan
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Fabiana Subrizi
- Department of Chemistry, University College London, London, United Kingdom
| | - Dragana Dobrijevic
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - John Ward
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Helen C Hailes
- Department of Chemistry, University College London, London, United Kingdom
| | - Pedro Fernandes
- Department of Bioengineering and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Faculty of Engineering, Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal
| | | | - Frank Baganz
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Nicolas Szita
- Department of Biochemical Engineering, University College London, London, United Kingdom
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7
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Schrittwieser JH, Velikogne S, Hall M, Kroutil W. Artificial Biocatalytic Linear Cascades for Preparation of Organic Molecules. Chem Rev 2017; 118:270-348. [DOI: 10.1021/acs.chemrev.7b00033] [Citation(s) in RCA: 371] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joerg H. Schrittwieser
- Institute
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Stefan Velikogne
- ACIB
GmbH, Department of Chemistry, University of Graz, Heinrichstrasse
28, 8010 Graz, Austria
| | - Mélanie Hall
- Institute
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010 Graz, Austria
- ACIB
GmbH, Department of Chemistry, University of Graz, Heinrichstrasse
28, 8010 Graz, Austria
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8
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Cárdenas-Fernández M, Bawn M, Hamley-Bennett C, Bharat PKV, Subrizi F, Suhaili N, Ward DP, Bourdin S, Dalby PA, Hailes HC, Hewitson P, Ignatova S, Kontoravdi C, Leak DJ, Shah N, Sheppard TD, Ward JM, Lye GJ. An integrated biorefinery concept for conversion of sugar beet pulp into value-added chemicals and pharmaceutical intermediates. Faraday Discuss 2017; 202:415-431. [DOI: 10.1039/c7fd00094d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over 8 million tonnes of sugar beet are grown annually in the UK. Sugar beet pulp (SBP) is the main by-product of sugar beet processing which is currently dried and sold as a low value animal feed. SBP is a rich source of carbohydrates, mainly in the form of cellulose and pectin, including d-glucose (Glu), l-arabinose (Ara) and d-galacturonic acid (GalAc). This work describes the technical feasibility of an integrated biorefinery concept for the fractionation of SBP and conversion of these monosaccharides into value-added products. SBP fractionation is initially carried out by steam explosion under mild conditions to yield soluble pectin and insoluble cellulose fractions. The cellulose is readily hydrolysed by cellulases to release Glu that can then be fermented by a commercial yeast strain to produce bioethanol at a high yield. The pectin fraction can be either fully hydrolysed, using physico-chemical methods, or selectively hydrolysed, using cloned arabinases and galacturonases, to yield Ara-rich and GalAc-rich streams. These monomers can be separated using either Centrifugal Partition Chromatography (CPC) or ultrafiltration into streams suitable for subsequent enzymatic upgrading. Building on our previous experience with transketolase (TK) and transaminase (TAm) enzymes, the conversion of Ara and GalAc into higher value products was explored. In particular the conversion of Ara into l-gluco-heptulose (GluHep), that has potential therapeutic applications in hypoglycaemia and cancer, using a mutant TK is described. Preliminary studies with TAm also suggest GluHep can be selectively aminated to the corresponding chiral aminopolyol. The current work is addressing the upgrading of the remaining SBP monomer, GalAc, and the modelling of the biorefinery concept to enable economic and Life Cycle Analysis (LCA).
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9
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Morris P, Rios-Solis L, García-Arrazola R, Lye G, Dalby P. Impact of cofactor-binding loop mutations on thermotolerance and activity of E. coli transketolase. Enzyme Microb Technol 2016; 89:85-91. [DOI: 10.1016/j.enzmictec.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/08/2016] [Accepted: 04/03/2016] [Indexed: 10/22/2022]
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10
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Villegas-Torres MF, Martinez-Torres RJ, Cázares-Körner A, Hailes H, Baganz F, Ward J. Multi-step biocatalytic strategies for chiral amino alcohol synthesis. Enzyme Microb Technol 2015; 81:23-30. [PMID: 26453469 DOI: 10.1016/j.enzmictec.2015.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 07/02/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
Abstract
Chiral amino alcohols are structural motifs present in sphingolipids, antibiotics, and antiviral glycosidase inhibitors. Their chemical synthesis presents several challenges in establishing at least two chiral centres. Here a de novo metabolic pathway using a transketolase enzyme coupled with a transaminase enzyme has been assembled. To synthesise this motif one of the strategies to obtain high conversions from the transaminase/transketolase cascade is the use of hydroxypyruvate (HPA) as a two-carbon donor for the transketolase reaction; although commercially available it is relatively expensive limiting application of the pathway on an industrial scale. Alternately, HPA can be synthesised but this introduces a further synthetic step. In this study two different biocatalytic strategies were developed for the synthesis of (2S,3R)-2-amino-1,3,4-butanetriol (ABT) without adding HPA into the reaction. Firstly, a sequential cascade of three enzymatic steps (two transaminases and one transketolase) for the synthesis of ABT from serine, pyruvate and glycolaldehyde as substrates. Secondly, a two-step recycling cascade where serine is used as donor to aminate erythrulose (catalysed by a transketolase) for the simultaneous synthesis of ABT and HPA. In order to test the novel pathways, three new transaminases are described, two ω-transaminases able to accept a broad range of amine acceptors with serine as amine donor; and an α-transaminase, which showed high affinity towards serine (KM: 18mM) using pyruvate as amine acceptor. After implementation of the above enzymes in the biocatalytic pathways proposed in this paper, the two-step recycling pathway was found to be the most promising for its integration with E. coli metabolism. It was more efficient (10-fold higher conversion), more sustainable and cost-effective (use of low cost natural substrates and only two enzymes), and the reaction could be performed in a one-pot system.
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Affiliation(s)
- Maria F Villegas-Torres
- The Advanced Centre for Biochemical Engineering, University College London, Department of Biochemical Engineering, Gordon Street, London WC1H 0AH, United Kingdom.
| | - R Julio Martinez-Torres
- Research Department of Structural and Molecular Biology, ISMB, The Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Armando Cázares-Körner
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Helen Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom.
| | - Frank Baganz
- The Advanced Centre for Biochemical Engineering, University College London, Department of Biochemical Engineering, Gordon Street, London WC1H 0AH, United Kingdom
| | - John Ward
- The Advanced Centre for Biochemical Engineering, University College London, Department of Biochemical Engineering, Gordon Street, London WC1H 0AH, United Kingdom.
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11
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Deszcz D, Affaticati P, Ladkau N, Gegel A, Ward JM, Hailes HC, Dalby PA. Single active-site mutants are sufficient to enhance serine:pyruvate α-transaminase activity in an ω-transaminase. FEBS J 2015; 282:2512-26. [PMID: 25846556 DOI: 10.1111/febs.13293] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/19/2015] [Accepted: 04/01/2015] [Indexed: 11/28/2022]
Abstract
We have analyzed the natural evolution of transaminase structure and sequence between an α-transaminase serine-pyruvate aminotransferase and an ω-transaminase from Chromobacterium violaceum with < 20% sequence identity, and identified the active-site regions that are least conserved structurally. We also show that these structural changes correlate strongly with transaminase substrate specificity during evolution and therefore might normally be presumed to be essential determinants of substrate specificity. However, key residues are often conserved spatially during evolution and yet originate from within a different region of the sequence via structural reorganizations. In the present study, we also show that α-transaminase-type serine-pyruvate aminotransferase activity can be engineered into the CV2025 ω-transaminase scaffold with any one of many possible single-point mutations at three key positions, without the requirement for significant backbone remodeling, or repositioning of the residue from a different region of sequence. This finding has significant implications for enzyme redesign in which solutions to substrate specificity changes may be found more efficiently than is achieved by engineering in all sequence and structure determinants identified by correlation to substrate specificity.
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Affiliation(s)
- Dawid Deszcz
- Department of Biochemical Engineering, University College London, UK
| | - Pierre Affaticati
- Department of Biochemical Engineering, University College London, UK
| | - Nadine Ladkau
- Department of Chemistry, University College London, UK
| | - Alex Gegel
- Department of Biochemical Engineering, University College London, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, UK
| | | | - Paul A Dalby
- Department of Biochemical Engineering, University College London, UK
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12
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Payongsri P, Steadman D, Hailes HC, Dalby PA. Second generation engineering of transketolase for polar aromatic aldehyde substrates. Enzyme Microb Technol 2015; 71:45-52. [DOI: 10.1016/j.enzmictec.2015.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 10/24/2022]
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13
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Modelling and optimisation of the one-pot, multi-enzymatic synthesis of chiral amino-alcohols based on microscale kinetic parameter determination. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.09.046] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Characterization and multi-step transketolase-ω-transaminase bioconversions in an immobilized enzyme microreactor (IEMR) with packed tube. J Biotechnol 2013; 168:567-75. [DOI: 10.1016/j.jbiotec.2013.09.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/29/2013] [Accepted: 09/09/2013] [Indexed: 11/21/2022]
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15
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Microscale methods to rapidly evaluate bioprocess options for increasing bioconversion yields: application to the ω-transaminase synthesis of chiral amines. Bioprocess Biosyst Eng 2013; 37:931-41. [DOI: 10.1007/s00449-013-1065-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 09/12/2013] [Indexed: 10/26/2022]
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16
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Rios-Solis L, Bayir N, Halim M, Du C, Ward J, Baganz F, Lye G. Non-linear kinetic modelling of reversible bioconversions: Application to the transaminase catalyzed synthesis of chiral amino-alcohols. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Payongsri P, Steadman D, Strafford J, MacMurray A, Hailes HC, Dalby PA. Rational substrate and enzyme engineering of transketolase for aromatics. Org Biomol Chem 2012; 10:9021-9. [DOI: 10.1039/c2ob25751c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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