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Rizzo A, Aranda C, Galman J, Alcasabas A, Pandya A, Bornadel A, Costa B, Hailes HC, Ward JM, Jeffries JWE, Dominguez B. Broadening The Substrate Scope of Aldolases Through Metagenomic Enzyme Discovery. Chembiochem 2024:e202400278. [PMID: 38953596 DOI: 10.1002/cbic.202400278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
Bio-processes based on enzymatic catalysis play a major role in the development of green, sustainable processes, and the discovery of new enzymes is key to this approach. In this work, we analysed ten metagenomes and retrieved 48 genes coding for deoxyribose-5-phosphate aldolases (DERAs, EC 4.1.2.4) using a sequence-based approach. These sequences were recombinantly expressed in Escherichia coli and screened for activity towards a range of aldol additions. Among these, one enzyme, DERA-61, proved to be particularly interesting and catalysed the aldol addition of furfural or benzaldehyde with acetone, butanone and cyclobutanone with unprecedented activity. The product of these reactions, aldols, can find applications as building blocks in the synthesis of biologically active compounds. Screening was carried out to identify optimized reaction conditions targeting temperature, pH, and salt concentrations. Lastly, the kinetics and the stereochemistry of the products were investigated, revealing that DERA-61 and other metagenomic DERAs have superior activity and stereoselectivity when they are provided with non-natural substrates, compared to well-known DERAs.
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Affiliation(s)
- Andrea Rizzo
- Johnson Matthey, Unit 260, Cambridge Science Park, Cambridge, CB4 0PZ
| | - Carmen Aranda
- Johnson Matthey, Unit 260, Cambridge Science Park, Cambridge, CB4 0PZ
| | - James Galman
- Johnson Matthey, Unit 260, Cambridge Science Park, Cambridge, CB4 0PZ
| | - Annette Alcasabas
- Johnson Matthey, Unit 260, Cambridge Science Park, Cambridge, CB4 0PZ
| | - Akash Pandya
- Johnson Matthey, Unit 260, Cambridge Science Park, Cambridge, CB4 0PZ
| | - Amin Bornadel
- Johnson Matthey, Unit 260, Cambridge Science Park, Cambridge, CB4 0PZ
| | - Bruna Costa
- Johnson Matthey, Unit 260, Cambridge Science Park, Cambridge, CB4 0PZ
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AK, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, Gower Street, Bernard Katz Building, London, WC1E 6BT, UK
| | - Jack W E Jeffries
- Department of Biochemical Engineering, University College London, Gower Street, Bernard Katz Building, London, WC1E 6BT, UK
| | - Beatriz Dominguez
- Johnson Matthey, Unit 260, Cambridge Science Park, Cambridge, CB4 0PZ
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2
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Wang G. Thermal Ring-Based Heat Switches in Hyperthermophilic Class II Bacterial Fructose Aldolase. ACS OMEGA 2023; 8:24624-24634. [PMID: 37457467 PMCID: PMC10339327 DOI: 10.1021/acsomega.3c03001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/24/2023] [Indexed: 07/18/2023]
Abstract
Both thermophilic and hyperthermophilic enzymes in bacterial and archaeal species are activated above a specific temperature threshold but inactivated at another higher temperature. However, the underlying structural basis for these two heat switches is still unresolved. Here, graph theory was used to test if the temperature-dependent noncovalent interactions and metal bridges as identified in a series of crystal structures of the class II bacterial fructose 1,6-bisphosphate aldolase homodimer or homotetramer with or without natural substrates and products bound could form systematic fluidic grid-like mesh networks with topological grids as thermal rings to regulate their structural thermostability and functional thermoactivity. The results indicated that the second biggest grid in the Thermus aquaticus fructose 1,6-diphosphate aldolase dimer may control the specific temperature threshold to release the swapping flexible active sites at the dimeric interface for heat-evoked activation. Meanwhile, the third biggest grid may serve as a necessary structural motif against heat inactivation. Finally, the smallest grid may act as a stiff thermostable anchor. Its dissociation at the maximal melting temperature threshold may stop the catalytic activity. Taken as a whole, this computational study may render the structural motifs for the optimal growth temperature and the extreme heat stability of hyperthermophiles.
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3
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Wang G. Network Basis for the Heat-Adapted Structural Thermostability of Bacterial Class II Fructose Bisphosphate Aldolase. ACS OMEGA 2023; 8:17731-17739. [PMID: 37251155 PMCID: PMC10210171 DOI: 10.1021/acsomega.3c00473] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
The sufficient structural thermostability of a biological macromolecule is an overriding need for green nanoreactors and nanofactories to secure high activity. However, little is still known about what specific structural motif is responsible for it. Here, graph theory was employed to examine if the temperature-dependent noncovalent interactions and metal bridges, as identified in the structures of Escherichia coli class II fructose 1,6-bisphosphate aldolase, could shape a systematic fluidic grid-like mesh network with topological grids to regulate the structural thermostability of the wild-type construct and its evolved variants in each generation upon decyclization. The results indicated that the biggest grids may govern the temperature thresholds for their tertiary structural perturbations but without affecting the catalytic activities. Moreover, lower grid-based systematic thermal instability may facilitate structural thermostability, but a highly independent thermostable grid may still be required to serve as a critical anchor to secure the stereospecific thermoactivity. Its end melting temperature thresholds, together with the start ones of the biggest grids in the evolved variants, may confer high temperature sensitivity against thermal inactivation. Collectively, this computational study may have widespread significance in advancing our complete understanding and biotechnology of the thermoadaptive mechanism of the structural thermostability of a biological macromolecule.
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4
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Marasco R, Fusi M, Coscolín C, Barozzi A, Almendral D, Bargiela R, Nutschel CGN, Pfleger C, Dittrich J, Gohlke H, Matesanz R, Sanchez-Carrillo S, Mapelli F, Chernikova TN, Golyshin PN, Ferrer M, Daffonchio D. Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes. Nat Commun 2023; 14:1045. [PMID: 36828822 PMCID: PMC9958047 DOI: 10.1038/s41467-023-36610-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, Edinburgh Napier University Sighthill Campus, Edinburgh, UK
| | | | - Alan Barozzi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Almendral
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | | | - Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jonas Dittrich
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC) and Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ruth Matesanz
- Spectroscopy Laboratory, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
| | - Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Tatyana N Chernikova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain.
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Wäscher M, Classen T, Pietruszka J. Simple Enzyme Immobilization for Flow Chemistry? An Assessment of Available Strategies for an Acetaldehyde-Dependent Aldolase. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196483. [PMID: 36235018 PMCID: PMC9570893 DOI: 10.3390/molecules27196483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Enzyme immobilization is a technology that enables (bio-)catalysts to be applied in continuous-flow systems. However, there is a plethora of immobilization methods available with individual advantages and disadvantages. Here, we assessed the influence of simple and readily available methods with respect to the performance of 2-deoxy-d-ribose-5-phosphate aldolase (DERA) in continuous-flow conditions. The investigated immobilization strategies cover the unspecific attachment to carriers via epoxides, affinity-based attachment via metal ion affinity, StrepTag™-StrepTactin™ interaction as well as the covalent affinity attachment of an enzyme to a matrix tethered by the HaloTag®. The metal-ion-affinity-based approach outperformed the other methods in terms of immobilized activity and stability under applied conditions. As most enzymes examined today already have a HisTag for purification purposes, effective immobilization may be applied, as simple as a standard purification, if needed.
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Affiliation(s)
- Martin Wäscher
- Institute for Bioorganic Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas Classen
- Institute for Bio- and Geosciences 1: Bioorganic Chemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jörg Pietruszka
- Institute for Bioorganic Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Institute for Bio- and Geosciences 1: Bioorganic Chemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
- Correspondence: ; Tel.: +49-(0)2461-61-4158
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6
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Biosynthesis of 4-hydroxybenzylideneacetone by Whole-Cell Escherichia coli. Catalysts 2022. [DOI: 10.3390/catal12090997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
4-Hydroxy benzylideneacetone (4-HBA) is an organic synthesis intermediate and can be used as a precursor for the synthesis of raspberry ketone. Herein, 2-deoxy-D-ribose 5-phosphate aldolase (DERA) was overexpressed in E. coli BL21 (DE3) as an attractive catalyst for enzymatic aldol reactions. The aldol reaction between 4-hydroxybenzaldehyde (4-HBD) and acetone to biosynthesize 4-HBA was catalyzed by whole-cell E. coli BL21 (DE3) (pRSF-Deoc). The yield and 4-HBA concentration were 92.8% and 111.35 mM, respectively, when using 120 mM 4-HBD and acetone as substrates. When the concentration of 4-HBD was increased to 480 mM, 376.4 mM 4-HBA was obtained by a fed-batch strategy with a yield of 78.4%, which was about a 28% improvement compared to the one-time addition strategy. E. coli BL21 (DE3) (pRSF-Deoc) cells were further immobilized with K-carrageenan, and the immobilized cells still maintained a residual activity of above 90% after 10 repeated uses. Our study provides a promising method of biosynthesizing 4-HBA.
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7
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Hindges J, Döbber J, Hayes MR, Classen T, Pohl M, Pietruszka J. Covalently Immobilized 2‐Deoxyribose‐5‐phosphate Aldolase (DERA) for Biocatalysis in Flow: Utilization of the 3‐Hydroxyaldehyde Intermediate in Reaction Cascades. ChemCatChem 2022. [DOI: 10.1002/cctc.202200390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Julia Hindges
- Heinrich-Heine-Universitat Dusseldorf Institute for bioorganic chemistry GERMANY
| | - Johannes Döbber
- Forschungszentrum Julich Institut fur Bio und Geowissenschaften Biotechnologie GERMANY
| | - Marc Richard Hayes
- Heinrich-Heine-Universitat Dusseldorf Institute for bioorganic chemistry GERMANY
| | - Thomas Classen
- Forschungszentrum Julich Institut fur Bio und Geowissenschaften Biotechnologie GERMANY
| | - Martina Pohl
- Forschungszentrum Julich Institut fur Bio und Geowissenschaften Biotechnologie GERMANY
| | - Joerg Pietruszka
- Heinrich-Heine-Universitat Dusseldorf Institut für Bioorganische Chemie Im Forschungszentrum JülichGeb. 15.8 52426 Jülich GERMANY
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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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Carré L, Girard É, Franzetti B. Experimental study of proteome halophilicity using nanoDSF: a proof of concept. Extremophiles 2021; 26:1. [PMID: 34878593 DOI: 10.1007/s00792-021-01250-z] [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: 06/25/2021] [Accepted: 09/30/2021] [Indexed: 10/19/2022]
Abstract
Adaption to environmental conditions is reflected by protein adaptation. In particular, proteins of extremophiles display distinctive traits ensuring functional, structural and dynamical properties under permanently extreme physical and chemical conditions. While it has mostly been studied with approaches focusing on specific proteins, biophysical approaches have also confirmed this link between environmental and protein adaptation at the more complex and diverse scale of the proteome. However, studies of this type remain challenging and often require large amounts of biological material. We report here the use of nanoDSF as a tool to study proteome stability and solubility in cell lysates of the model halophilic archaeon Haloarcula marismortui. Notably, our results show that, as with single halophilic protein studies, proteome stability was correlated to the concentration of NaCl or KCl under which the cells were lysed and hence the proteome exposed. This work highlights that adaptation to environmental conditions can be experimentally observed at the scale of the proteome. Still, we show that the biochemical properties of single halophilic proteins can only be partially extrapolated to the whole proteome.
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Affiliation(s)
- Lorenzo Carré
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Éric Girard
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
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10
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Current state of and need for enzyme engineering of 2-deoxy-D-ribose 5-phosphate aldolases and its impact. Appl Microbiol Biotechnol 2021; 105:6215-6228. [PMID: 34410440 PMCID: PMC8403123 DOI: 10.1007/s00253-021-11462-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 01/28/2023]
Abstract
Abstract Deoxyribose-5-phosphate aldolases (DERAs, EC 4.1.2.4) are acetaldehyde-dependent, Class I aldolases catalyzing in nature a reversible aldol reaction between an acetaldehyde donor (C2 compound) and glyceraldehyde-3-phosphate acceptor (C3 compound, C3P) to generate deoxyribose-5-phosphate (C5 compound, DR5P). DERA enzymes have been found to accept also other types of aldehydes as their donor, and in particular as acceptor molecules. Consequently, DERA enzymes can be applied in C–C bond formation reactions to produce novel compounds, thus offering a versatile biocatalytic alternative for synthesis. DERA enzymes, found in all kingdoms of life, share a common TIM barrel fold despite the low overall sequence identity. The catalytic mechanism is well-studied and involves formation of a covalent enzyme-substrate intermediate. A number of protein engineering studies to optimize substrate specificity, enzyme efficiency, and stability of DERA aldolases have been published. These have employed various engineering strategies including structure-based design, directed evolution, and recently also machine learning–guided protein engineering. For application purposes, enzyme immobilization and usage of whole cell catalysis are preferred methods as they improve the overall performance of the biocatalytic processes, including often also the stability of the enzyme. Besides single-step enzymatic reactions, DERA aldolases have also been applied in multi-enzyme cascade reactions both in vitro and in vivo. The DERA-based applications range from synthesis of commodity chemicals and flavours to more complicated and high-value pharmaceutical compounds. Key points • DERA aldolases are versatile biocatalysts able to make new C–C bonds. • Synthetic utility of DERAs has been improved by protein engineering approaches. • Computational methods are expected to speed up the future DERA engineering efforts. Graphical abstract ![]()
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11
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Cao L, Zhang R, Zhou J, Huang Z. Biotechnological Aspects of Salt-Tolerant Xylanases: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8610-8624. [PMID: 34324332 DOI: 10.1021/acs.jafc.1c03192] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
β-1,4-Xylan is the main component of hemicelluloses in land plant cell walls, whereas β-1,3-xylan is widely found in seaweed cell walls. Complete hydrolysis of xylan requires a series of synergistically acting xylanases. High-saline environments, such as saline-alkali lands and oceans, frequently occur in nature and are also involved in a broad range of various industrial processes. Thus, salt-tolerant xylanases may contribute to high-salt and marine food processing, aquatic feed production, industrial wastewater treatment, saline-alkali soil improvement, and global carbon cycle, with great commercial and environmental benefits. This review mainly introduces the definition, sources, classification, biochemical and molecular characteristics, adaptation mechanisms, and biotechnological applications of salt-tolerant xylanases. The scope of development for salt-tolerant xylanases is also discussed. It is anticipated that this review would serve as a reference for further development and utilization of salt-tolerant xylanases and other salt-tolerant enzymes.
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Affiliation(s)
- Lijuan Cao
- College of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
| | - Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, Yunnan 650500, People's Republic of China
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12
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Becker D, Bharatam PV, Gohlke H. F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism. J Chem Inf Model 2021; 61:4023-4030. [PMID: 34370479 DOI: 10.1021/acs.jcim.1c00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Of 57 human cytochrome P450 (CYP) enzymes, 12 metabolize 90% of xenobiotics. To our knowledge, no study has addressed the relation between enzyme dynamics and substrate promiscuity for more than three CYPs. Here, we show by constraint dilution simulations with the Constraint Network Analysis for the 12 isoforms that structural rigidity of the F/G region is significantly inversely correlated to the enzymes' substrate promiscuity. This highlights the functional importance of structural dynamics of the substrate tunnel.
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Affiliation(s)
- Daniel Becker
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, Sahibzada Ajit Singh Nagar, Mohali 160062, Punjab, India
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, 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, 52425 Jülich, Germany
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13
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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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14
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Nutschel C, Coscolín C, David B, Mulnaes D, Ferrer M, Jaeger KE, Gohlke H. Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones. J Chem Inf Model 2021; 61:2383-2395. [PMID: 33949194 DOI: 10.1021/acs.jcim.1c00152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Understanding mechanisms of promiscuity is increasingly important from a fundamental and application point of view. As to enzyme structural dynamics, more promiscuous enzymes generally have been recognized to also be more flexible. However, examples for the opposite received much less attention. Here, we exploit comprehensive experimental information on the substrate promiscuity of 147 esterases tested against 96 esters together with computationally efficient rigidity analyses to understand the molecular origin of the observed promiscuity range. Unexpectedly, our data reveal that promiscuous esterases are significantly less flexible than specific ones, are significantly more thermostable, and have a significantly increased specific activity. These results may be reconciled with a model according to which structural flexibility in the case of specific esterases serves for conformational proofreading. Our results signify that an esterase sequence space can be screened by rigidity analyses for promiscuous esterases as starting points for further exploration in biotechnology and synthetic chemistry.
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Affiliation(s)
- Christina Nutschel
- 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, 52425 Jülich, Germany
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Benoit David
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Daniel Mulnaes
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - 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), 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, 52425 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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15
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Huysmans GHM, Ciftci D, Wang X, Blanchard SC, Boudker O. The high-energy transition state of the glutamate transporter homologue GltPh. EMBO J 2021; 40:e105415. [PMID: 33185289 PMCID: PMC7780239 DOI: 10.15252/embj.2020105415] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 01/03/2023] Open
Abstract
Membrane transporters mediate cellular uptake of nutrients, signaling molecules, and drugs. Their overall mechanisms are often well understood, but the structural features setting their rates are mostly unknown. Earlier single-molecule fluorescence imaging of the archaeal model glutamate transporter homologue GltPh from Pyrococcus horikoshii suggested that the slow conformational transition from the outward- to the inward-facing state, when the bound substrate is translocated from the extracellular to the cytoplasmic side of the membrane, is rate limiting to transport. Here, we provide insight into the structure of the high-energy transition state of GltPh that limits the rate of the substrate translocation process. Using bioinformatics, we identified GltPh gain-of-function mutations in the flexible helical hairpin domain HP2 and applied linear free energy relationship analysis to infer that the transition state structurally resembles the inward-facing conformation. Based on these analyses, we propose an approach to search for allosteric modulators for transporters.
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Affiliation(s)
- Gerard H M Huysmans
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
- Mass Spectrometry for Biology Unit, USR 2000CNRSInstitut PasteurParisFrance
| | - Didar Ciftci
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
- Tri‐Institutional Training Program in Chemical BiologyNew YorkNYUSA
| | - Xiaoyu Wang
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
| | - Scott C Blanchard
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
- Tri‐Institutional Training Program in Chemical BiologyNew YorkNYUSA
- St. Jude Children’s Research HospitalMemphisTNUSA
| | - Olga Boudker
- Department of Physiology and BiophysicsWeill Cornell MedicineNew YorkNYUSA
- Tri‐Institutional Training Program in Chemical BiologyNew YorkNYUSA
- Howard Hughes Medical InstituteChevy ChaseMDUSA
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16
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Contreras F, Nutschel C, Beust L, Davari MD, Gohlke H, Schwaneberg U. Can constraint network analysis guide the identification phase of KnowVolution? A case study on improved thermostability of an endo-β-glucanase. Comput Struct Biotechnol J 2020; 19:743-751. [PMID: 33552446 PMCID: PMC7822948 DOI: 10.1016/j.csbj.2020.12.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 01/02/2023] Open
Abstract
Cellulases are industrially important enzymes, e.g., in the production of bioethanol, in pulp and paper industry, feedstock, and textile. Thermostability is often a prerequisite for high process stability and improving thermostability without affecting specific activities at lower temperatures is challenging and often time-consuming. Protein engineering strategies that combine experimental and computational are emerging in order to reduce experimental screening efforts and speed up enzyme engineering campaigns. Constraint Network Analysis (CNA) is a promising computational method that identifies beneficial positions in enzymes to improve thermostability. In this study, we compare CNA and directed evolution in the identification of beneficial positions in order to evaluate the potential of CNA in protein engineering campaigns (e.g., in the identification phase of KnowVolution). We engineered the industrially relevant endoglucanase EGLII from Penicillium verruculosum towards increased thermostability. From the CNA approach, six variants were obtained with an up to 2-fold improvement in thermostability. The overall experimental burden was reduced to 40% utilizing the CNA method in comparison to directed evolution. On a variant level, the success rate was similar for both strategies, with 0.27% and 0.18% improved variants in the epPCR and CNA-guided library, respectively. In essence, CNA is an effective method for identification of positions that improve thermostability.
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Affiliation(s)
- Francisca Contreras
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Christina Nutschel
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Laura Beust
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
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17
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Xia YL, Li YP, Fu YX, Liu SQ. The Energetic Origin of Different Catalytic Activities in Temperature-Adapted Trypsins. ACS OMEGA 2020; 5:25077-25086. [PMID: 33043186 PMCID: PMC7542600 DOI: 10.1021/acsomega.0c02401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/09/2020] [Indexed: 05/08/2023]
Abstract
Psychrophilic enzymes were always observed to have higher catalytic activity (k cat) than their mesophilic homologs at room temperature, while the origin of this phenomenon remains obscure. Here, we used two different temperature-adapted trypsins, the psychrophilic Atlantic cod trypsin (ACT) and the mesophilic bovine trypsin (BT), as a model system to explore the energetic origin of their different catalytic activities using computational methods. The results reproduce the characteristic changing trends in the activation free energy, activation enthalpy, and activation entropy between the psychrophilic and mesophilic enzymes, where, in particular, the slightly decreased activation free energy of ACT is determined by its considerably reduced activation enthalpy rather than by its more negative activation entropy compared to BT. The calculated electrostatic contributions to the solvation free energies in the reactant state/ground sate (RS/GS) and transition state (TS) show that, going from BT to ACT, the TS stabilization has a predominant effect over the RS stabilization on lowering the activation enthalpy of ACT. Comparison between the solvation energy components reveals a more optimized electrostatic preorganization to the TS in ACT, which provides a larger stabilization to the TS through reducing the reorganization energy, thus resulting in the lower activation enthalpy and hence lower activation free energy of ACT. Thus, it can be concluded that it is the difference in the protein electrostatic environment, and hence its different stabilizing effects on the TS, that brings about the different catalytic activities of different temperature-adapted trypsins.
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Affiliation(s)
- Yuan-Ling Xia
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
- Editorial
Office of Journal of Yunnan University (Natural Sciences Edition), Yunnan University, Kunming 650091, Yunnan, China
| | - Yong-Ping Li
- School
of Agriculture, Yunnan University, Kunming 650091, Yunnan, China
| | - Yun-Xin Fu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
- Human
Genetics Center and Division of Biostatistics, School of Public Health, The University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Shu-Qun Liu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
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18
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DERA in Flow: Synthesis of a Statin Side Chain Precursor in Continuous Flow Employing Deoxyribose-5-Phosphate Aldolase Immobilized in Alginate-Luffa Matrix. Catalysts 2020. [DOI: 10.3390/catal10010137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Statins, cholesterol-lowering drugs used for the treatment of coronary artery disease (CAD), are among the top 10 prescribed drugs worldwide. However, the synthesis of their characteristic side chain containing two chiral hydroxyl groups can be challenging. The application of deoxyribose-5-phosphate aldolase (DERA) is currently one of the most promising routes for the synthesis of this side chain. Herein, we describe the development of a continuous flow process for the biosynthesis of a side chain precursor. Design of experiments (DoE) was used to optimize the reaction conditions (pH value and temperature) in batch. A pH of 7.5 and a temperature of 32.5 °C were identified to be the optimal process settings within the reaction space considered. Additionally, an immobilization method was developed using the alginate-luffa matrix (ALM), which is a fast, simple, and inexpensive method for enzyme immobilization. Furthermore, it is non-toxic, biodegradable, and from renewable resources. The final continuous process was operated stable for 4 h and can produce up to 4.5 g of product per day.
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19
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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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20
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Hait S, Mallik S, Basu S, Kundu S. Finding the generalized molecular principles of protein thermal stability. Proteins 2019; 88:788-808. [PMID: 31872464 DOI: 10.1002/prot.25866] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/05/2019] [Accepted: 12/14/2019] [Indexed: 11/09/2022]
Abstract
Are there any generalized molecular principles of thermal adaptation? Here, integrating the concepts of structural bioinformatics, sequence analysis, and classical knot theory, we develop a robust computational framework that seeks for mechanisms of thermal adaptation by comparing orthologous mesophilic-thermophilic and mesophilic-hyperthermophilic proteins of remarkable structural and topological similarities, and still leads us to context-independent results. A comprehensive analysis of 4741 high-resolution, non-redundant X-ray crystallographic structures collected from 11 hyperthermophilic, 32 thermophilic and 53 mesophilic prokaryotes unravels at least five "nearly universal" signatures of thermal adaptation, irrespective of the enormous sequence, structure, and functional diversity of the proteins compared. A careful investigation further extracts a set of amino acid changes that can potentially enhance protein thermal stability, and remarkably, these mutations are overrepresented in protein crystallization experiments, in disorder-to-order transitions and in engineered thermostable variants of existing mesophilic proteins. These results could be helpful to find a precise, global picture of thermal adaptation.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Saurav Mallik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
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21
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Kim T, Stogios PJ, Khusnutdinova AN, Nemr K, Skarina T, Flick R, Joo JC, Mahadevan R, Savchenko A, Yakunin AF. Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of ( R)-1,3-butanediol. J Biol Chem 2019; 295:597-609. [PMID: 31806708 DOI: 10.1074/jbc.ra119.011363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Carbon-carbon bond formation is one of the most important reactions in biocatalysis and organic chemistry. In nature, aldolases catalyze the reversible stereoselective aldol addition between two carbonyl compounds, making them attractive catalysts for the synthesis of various chemicals. In this work, we identified several 2-deoxyribose-5-phosphate aldolases (DERAs) having acetaldehyde condensation activity, which can be used for the biosynthesis of (R)-1,3-butanediol (1,3BDO) in combination with aldo-keto reductases (AKRs). Enzymatic screening of 20 purified DERAs revealed the presence of significant acetaldehyde condensation activity in 12 of the enzymes, with the highest activities in BH1352 from Bacillus halodurans, TM1559 from Thermotoga maritima, and DeoC from Escherichia coli The crystal structures of BH1352 and TM1559 at 1.40-2.50 Å resolution are the first full-length DERA structures revealing the presence of the C-terminal Tyr (Tyr224 in BH1352). The results from structure-based site-directed mutagenesis of BH1352 indicated a key role for the catalytic Lys155 and other active-site residues in the 2-deoxyribose-5-phosphate cleavage and acetaldehyde condensation reactions. These experiments also revealed a 2.5-fold increase in acetaldehyde transformation to 1,3BDO (in combination with AKR) in the BH1352 F160Y and F160Y/M173I variants. The replacement of the WT BH1352 by the F160Y or F160Y/M173I variants in E. coli cells expressing the DERA + AKR pathway increased the production of 1,3BDO from glucose five and six times, respectively. Thus, our work provides detailed insights into the molecular mechanisms of substrate selectivity and activity of DERAs and identifies two DERA variants with enhanced activity for in vitro and in vivo 1,3BDO biosynthesis.
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Affiliation(s)
- Taeho Kim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Future Technology Center, LG Chem, Gangseo-gu, Seoul 150-721, Korea
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jeong Chan Joo
- Center for Bio-Based Chemistry, Division of Convergence Chemistry, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon 34114, Korea
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, United Kingdom.
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22
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Huffman MA, Fryszkowska A, Alvizo O, Borra-Garske M, Campos KR, Canada KA, Devine PN, Duan D, Forstater JH, Grosser ST, Halsey HM, Hughes GJ, Jo J, Joyce LA, Kolev JN, Liang J, Maloney KM, Mann BF, Marshall NM, McLaughlin M, Moore JC, Murphy GS, Nawrat CC, Nazor J, Novick S, Patel NR, Rodriguez-Granillo A, Robaire SA, Sherer EC, Truppo MD, Whittaker AM, Verma D, Xiao L, Xu Y, Yang H. Design of an in vitro biocatalytic cascade for the manufacture of islatravir. Science 2019; 366:1255-1259. [DOI: 10.1126/science.aay8484] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/24/2019] [Indexed: 12/14/2022]
Abstract
Enzyme-catalyzed reactions have begun to transform pharmaceutical manufacturing, offering levels of selectivity and tunability that can dramatically improve chemical synthesis. Combining enzymatic reactions into multistep biocatalytic cascades brings additional benefits. Cascades avoid the waste generated by purification of intermediates. They also allow reactions to be linked together to overcome an unfavorable equilibrium or avoid the accumulation of unstable or inhibitory intermediates. We report an in vitro biocatalytic cascade synthesis of the investigational HIV treatment islatravir. Five enzymes were engineered through directed evolution to act on non-natural substrates. These were combined with four auxiliary enzymes to construct islatravir from simple building blocks in a three-step biocatalytic cascade. The overall synthesis requires fewer than half the number of steps of the previously reported routes.
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Affiliation(s)
- Mark A. Huffman
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Anna Fryszkowska
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Oscar Alvizo
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | | | - Kevin R. Campos
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Keith A. Canada
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Paul N. Devine
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Da Duan
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Jacob H. Forstater
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Shane T. Grosser
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Holst M. Halsey
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Gregory J. Hughes
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Junyong Jo
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Leo A. Joyce
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Joshua N. Kolev
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jack Liang
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Kevin M. Maloney
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Benjamin F. Mann
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Mark McLaughlin
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jeffrey C. Moore
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Grant S. Murphy
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Jovana Nazor
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Scott Novick
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Niki R. Patel
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Sandra A. Robaire
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C. Sherer
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Matthew D. Truppo
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Aaron M. Whittaker
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Deeptak Verma
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Li Xiao
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Yingju Xu
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Hao Yang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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23
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Reinicke S, Fischer T, Bramski J, Pietruszka J, Böker A. Biocatalytically active microgels by precipitation polymerization of N-isopropyl acrylamide in the presence of an enzyme. RSC Adv 2019; 9:28377-28386. [PMID: 35529607 PMCID: PMC9071056 DOI: 10.1039/c9ra04000e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/02/2019] [Indexed: 11/21/2022] Open
Abstract
We present a novel protocol for the synthesis of enzymatically active microgels. The protocol is based on the precipitation polymerization of N-isopropylacrylamide (NIPAm) in the presence of an enzyme and a protein binding comonomer. A basic investigation on the influence of different reaction parameters such as monomer concentration and reaction temperature on the microgel size and size distribution is performed and immobilization yields are determined. Microgels exhibiting hydrodynamic diameters between 100 nm and 1 μm and narrow size distribution could be synthesized while about 31-44% of the enzyme present in the initial reaction mixture can be immobilized. Successful immobilization including a verification of enzymatic activity of the microgels is achieved for glucose oxidase (GOx) and 2-deoxy-d-ribose-5-phosphate aldolase (DERA). The thermoresponsive properties of the microgels are assessed and discussed in the light of activity evolution with temperature. The positive correlation of enzymatic activity with temperature for the GOx containing microgel originates from a direct interaction of the enzyme with the PNIPAm based polymer matrix whose magnitude is highly influenced by temperature.
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Affiliation(s)
- Stefan Reinicke
- Fraunhofer Institute for Applied Polymer Research (IAP) Geiselbergstraße 69 Potsdam-Golm 14476 Germany
- Chair of Polymer Materials and Polymer Technologies, University of Potsdam Potsdam-Golm 14476 Germany
| | - Thilo Fischer
- Fraunhofer Institute for Applied Polymer Research (IAP) Geiselbergstraße 69 Potsdam-Golm 14476 Germany
- Chair of Polymer Materials and Polymer Technologies, University of Potsdam Potsdam-Golm 14476 Germany
| | - Julia Bramski
- Institut of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich Stetternicher Forst D-52426 Jülich Germany
| | - Jörg Pietruszka
- Institut of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich Stetternicher Forst D-52426 Jülich Germany
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH 52425 Jülich Germany
| | - Alexander Böker
- Fraunhofer Institute for Applied Polymer Research (IAP) Geiselbergstraße 69 Potsdam-Golm 14476 Germany
- Chair of Polymer Materials and Polymer Technologies, University of Potsdam Potsdam-Golm 14476 Germany
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24
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Huijbers MME, Wu JW, Westphal AH, Berkel WJH. Dimerization of Proline Dehydrogenase from
Thermus thermophilus
Is Crucial for Its Thermostability. Biotechnol J 2019; 14:e1800540. [DOI: 10.1002/biot.201800540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/22/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Mieke M. E. Huijbers
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4, 6708 WE Wageningen The Netherlands
| | - Jenny W. Wu
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4, 6708 WE Wageningen The Netherlands
| | - Adrie H. Westphal
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4, 6708 WE Wageningen The Netherlands
| | - Willem J. H. Berkel
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4, 6708 WE Wageningen The Netherlands
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25
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Magnusson AO, Szekrenyi A, Joosten HJ, Finnigan J, Charnock S, Fessner WD. nanoDSF as screening tool for enzyme libraries and biotechnology development. FEBS J 2018; 286:184-204. [PMID: 30414312 PMCID: PMC7379660 DOI: 10.1111/febs.14696] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/24/2018] [Accepted: 11/07/2018] [Indexed: 12/24/2022]
Abstract
Enzymes are attractive tools for synthetic applications. To be viable for industrial use, enzymes need sufficient stability towards the desired reaction conditions such as high substrate and cosolvent concentration, non-neutral pH and elevated temperatures. Thermal stability is an attractive feature not only because it allows for protein purification by thermal treatment and higher process temperatures but also due to the associated higher stability against other destabilising factors. Therefore, high-throughput screening (HTS) methods are desirable for the identification of thermostable biocatalysts by discovery from nature or by protein engineering but current methods have low throughput and require time-demanding purification of protein samples. We found that nanoscale differential scanning fluorimetry (nanoDSF) is a valuable tool to rapidly and reliably determine melting points of native proteins. To avoid intrinsic problems posed by crude protein extracts, hypotonic extraction of overexpressed protein from bacterial host cells resulted in higher sample quality and accurate manual determination of several hundred melting temperatures per day. We have probed the use of nanoDSF for HTS of a phylogenetically diverse aldolase library to identify novel thermostable enzymes from metagenomic sources and for the rapid measurements of variants from saturation mutagenesis. The feasibility of nanoDSF for the screening of synthetic reaction conditions was proved by studies of cosolvent tolerance, which showed protein melting temperature to decrease linearly with increasing cosolvent concentration for all combinations of six enzymes and eight water-miscible cosolvents investigated, and of substrate affinity, which showed stabilisation of hexokinase by sugars in the absence of ATP cofactor. ENZYMES: Alcohol dehydrogenase (NADP+ ) (EC 1.1.1.2), transketolase (EC 2.2.1.1), hexokinase (EC 2.7.1.1), 2-deoxyribose-5-phosphate aldolase (EC 4.1.2.4), fructose-6-phosphate aldolase (EC 4.1.2.n).
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Affiliation(s)
- Anders O Magnusson
- Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Germany
| | - Anna Szekrenyi
- 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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26
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Haridas M, Abdelraheem EMM, Hanefeld U. 2-Deoxy-D-ribose-5-phosphate aldolase (DERA): applications and modifications. Appl Microbiol Biotechnol 2018; 102:9959-9971. [PMID: 30284013 PMCID: PMC6244999 DOI: 10.1007/s00253-018-9392-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022]
Abstract
2-Deoxy-D-ribose-5-phosphate aldolase (DERA) is a class I aldolase that offers access to several building blocks for organic synthesis. It catalyzes the stereoselective C-C bond formation between acetaldehyde and numerous other aldehydes. However, the practical application of DERA as a biocatalyst is limited by its poor tolerance towards industrially relevant concentrations of aldehydes, in particular acetaldehyde. Therefore, the development of proper experimental conditions, including protein engineering and/or immobilization on appropriate supports, is required. The present review is aimed to provide a brief overview of DERA, its history, and progress made in understanding the functioning of the enzyme. Furthermore, the current understanding regarding aldehyde resistance of DERA and the various optimizations carried out to modify this property are discussed.
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Affiliation(s)
- Meera Haridas
- Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Eman M M Abdelraheem
- Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Ulf Hanefeld
- Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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27
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Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [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: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
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28
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Pazhang M, Younesi FS, Mehrnejad F, Najavand S, Tarinejad A, Haghi M, Rashno F, Khajeh K. Ig-like Domain in Endoglucanase Cel9A from Alicyclobacillus acidocaldarius Makes Dependent the Enzyme Stability on Calcium. Mol Biotechnol 2018; 60:698-711. [PMID: 30062637 DOI: 10.1007/s12033-018-0105-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) has an Ig-like domain and the enzyme stability is dependent to calcium. In this study the effect of calcium on the structure and stability of the wild-type enzyme and the truncated form (the wild-type enzyme without Ig-like domain, AaCel9AΔN) was investigated. Fluorescence quenching results indicated that calcium increased and decreased the rigidity of the wild-type and truncated enzymes, respectively. RMSF results indicated that AaCel9A has two flexible regions (regions A and B) and deleting the Ig-like domain increased the truncated enzyme stability by decreasing the flexibility of region B probably through increasing the hydrogen bonds. Calcium contact map analysis showed that deleting the Ig-like domain decreased the calcium contacting residues and their calcium binding affinities, especially, in region B which has a role in calcium binding site in AaCel9A. Metal depletion and activity recovering as well as stability results showed that the structure and stability of the wild-type and truncated enzymes are completely dependent on and independent of calcium, respectively. Finally, one can conclude that the deletion of Ig-like domain makes AaCel9AΔN independent of calcium via decreasing the flexibility of region B through increasing the hydrogen bonds. This suggests a new role for the Ig-like domain which makes AaCel9A structure dependent on calcium.
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Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Fereshteh S Younesi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Saeed Najavand
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Tarinejad
- Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mehrnaz Haghi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Fatemeh Rashno
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
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29
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Cai ZW, Ge HH, Yi ZW, Zeng RY, Zhang GY. Characterization of a novel psychrophilic and halophilic β-1, 3-xylanase from deep-sea bacterium, Flammeovirga pacifica strain WPAGA1. Int J Biol Macromol 2018; 118:2176-2184. [PMID: 30021136 DOI: 10.1016/j.ijbiomac.2018.07.090] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/01/2018] [Accepted: 07/13/2018] [Indexed: 11/30/2022]
Abstract
β-1, 3-Xylanase is one of the most important hydrolytic enzymes to prepare oligosaccharides as functional foods in seaweed industry. However, less than five β-1, 3-xylanases have been experimentally expressed and characterized; moreover, none of them is psychrophilic and salt tolerant. Here, we mined a novel β-1, 3-xylanase (Xyl512) from the genome of the deep-sea bacterium Flammeovirga pacifica strain WPAGA1 and biochemically characterized it in detail. The Xyl512 did not contain any carbohydrate-binding module; the catalytic domain of it belonged to the glycoside hydrolase family 26. The optimum temperature and pH of the purified β-1, 3-xylanase was 20 °C and pH 7.0 in the condition of no NaCl. However, they shifted to 30 °C and 7.5 with 1.5 mol/L NaCl, respectively. In this condition (1.5 mol/L NaCl), the overall activity was 2-fold as high as that without NaCl. Based on the residue interactions and the electrostatic surfaces, we addressed the possible mechanism of its adaption to low temperature and relative high NaCl concentration. The Xyl512 showed significantly reduced numbers of hydrogen bonds leading to a more flexible structure, which is likely to be responsible for its cold adaptation. While the negatively charged surface may contribute to its salt tolerance. The β-1, 3-xylanase we identified here was the first reported psychrophilic and halophilic one with functionally characterized. It could make new contributions to exploring and studying the β-1, 3-xylanase for further associated investigations.
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Affiliation(s)
- Zheng-Wen Cai
- Department of Biotechnology and Bioengineering, Huaqiao University, Xiamen 361021, Fujian, PR China
| | - Hui-Hua Ge
- Department of Biotechnology and Bioengineering, Huaqiao University, Xiamen 361021, Fujian, PR China
| | - Zhi-Wei Yi
- Department of Biotechnology and Bioengineering, Huaqiao University, Xiamen 361021, Fujian, PR China; State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Xiamen, Fujian 361005, PR China
| | - Run-Ying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Xiamen, Fujian 361005, PR China
| | - Guang-Ya Zhang
- Department of Biotechnology and Bioengineering, Huaqiao University, Xiamen 361021, Fujian, PR China.
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30
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Schulte M, Petrović D, Neudecker P, Hartmann R, Pietruszka J, Willbold S, Willbold D, Panwalkar V. Conformational Sampling of the Intrinsically Disordered C-Terminal Tail of DERA Is Important for Enzyme Catalysis. ACS Catal 2018; 8:3971-3984. [PMID: 30101036 PMCID: PMC6080863 DOI: 10.1021/acscatal.7b04408] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/24/2018] [Indexed: 12/13/2022]
Abstract
2-Deoxyribose-5-phosphate aldolase (DERA) catalyzes the reversible conversion of acetaldehyde and glyceraldehyde-3-phosphate into deoxyribose-5-phosphate. DERA is used as a biocatalyst for the synthesis of drugs such as statins and is a promising pharmaceutical target due to its involvement in nucleotide catabolism. Despite previous biochemical studies suggesting the catalytic importance of the C-terminal tyrosine residue found in several bacterial DERAs, the structural and functional basis of its participation in catalysis remains elusive because the electron density for the last eight to nine residues (i.e., the C-terminal tail) is absent in all available crystal structures. Using a combination of NMR spectroscopy and molecular dynamics simulations, we conclusively show that the rarely studied C-terminal tail of E. coli DERA (ecDERA) is intrinsically disordered and exists in equilibrium between open and catalytically relevant closed states, where the C-terminal tyrosine (Y259) enters the active site. Nuclear Overhauser effect distance restraints, obtained due to the presence of a substantial closed state population, were used to derive the solution-state structure of the ecDERA closed state. Real-time NMR hydrogen/deuterium exchange experiments reveal that Y259 is required for efficiency of the proton abstraction step of the catalytic reaction. Phosphate titration experiments show that, in addition to the phosphate-binding residues located near the active site, as observed in the available crystal structures, ecDERA contains previously unknown auxiliary phosphate-binding residues on the C-terminal tail which could facilitate in orienting Y259 in an optimal position for catalysis. Thus, we present significant insights into the structural and mechanistic importance of the ecDERA C-terminal tail and illustrate the role of conformational sampling in enzyme catalysis.
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Affiliation(s)
- Marianne Schulte
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems 6 (ICS-6): Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dušan Petrović
- Institute of Complex Systems 6 (ICS-6): Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Philipp Neudecker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems 6 (ICS-6): Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rudolf Hartmann
- Institute of Complex Systems 6 (ICS-6): Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine-Universität im Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Bio- and Geosciences 1 (IBG-1): Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Sabine Willbold
- Central Institute of Engineering, Electronics and Analytics (ZEA-3), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems 6 (ICS-6): Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Vineet Panwalkar
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems 6 (ICS-6): Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
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31
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Zhang S, Bisterfeld C, Bramski J, Vanparijs N, De Geest BG, Pietruszka J, Böker A, Reinicke S. Biocatalytically Active Thin Films via Self-Assembly of 2-Deoxy-d-ribose-5-phosphate Aldolase-Poly(N-isopropylacrylamide) Conjugates. Bioconjug Chem 2017; 29:104-116. [PMID: 29182313 DOI: 10.1021/acs.bioconjchem.7b00645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
2-Deoxy-d-ribose-5-phosphate aldolase (DERA) is a biocatalyst that is capable of converting acetaldehyde and a second aldehyde as acceptor into enantiomerically pure mono- and diyhydroxyaldehydes, which are important structural motifs in a number of pharmaceutically active compounds. However, substrate as well as product inhibition requires a more-sophisticated process design for the synthesis of these motifs. One way to do so is to the couple aldehyde conversion with transport processes, which, in turn, would require an immobilization of the enzyme within a thin film that can be deposited on a membrane support. Consequently, we developed a fabrication process for such films that is based on the formation of DERA-poly(N-isopropylacrylamide) conjugates that are subsequently allowed to self-assemble at an air-water interface to yield the respective film. In this contribution, we discuss the conjugation conditions, investigate the interfacial properties of the conjugates, and, finally, demonstrate a successful film formation under the preservation of enzymatic activity.
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Affiliation(s)
- Shuhao Zhang
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute for Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476 Potsdam-Golm, Germany.,Polymer Materials and Polymer Technologies, University of Potsdam , 14476, Potsdam-Golm, Germany
| | - Carolin Bisterfeld
- Institute of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, 52426 Jülich, Germany
| | - Julia Bramski
- Institute of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, 52426 Jülich, Germany
| | - Nane Vanparijs
- Department of Pharmaceutics, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Bruno G De Geest
- Department of Pharmaceutics, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, 52426 Jülich, Germany.,IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
| | - Alexander Böker
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute for Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476 Potsdam-Golm, Germany.,Polymer Materials and Polymer Technologies, University of Potsdam , 14476, Potsdam-Golm, Germany
| | - Stefan Reinicke
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute for Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476 Potsdam-Golm, Germany
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32
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Ernst FGM, Erber L, Sammler J, Jühling F, Betat H, Mörl M. Cold adaptation of tRNA nucleotidyltransferases: A tradeoff in activity, stability and fidelity. RNA Biol 2017; 15:144-155. [PMID: 29099323 DOI: 10.1080/15476286.2017.1391445] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Cold adaptation is an evolutionary process that has dramatic impact on enzymatic activity. Increased flexibility of the protein structure represents the main evolutionary strategy for efficient catalysis and reaction rates in the cold, but is achieved at the expense of structural stability. This results in a significant activity-stability tradeoff, as it was observed for several metabolic enzymes. In polymerases, however, not only reaction rates, but also fidelity plays an important role, as these enzymes have to synthesize copies of DNA and RNA as exact as possible. Here, we investigate the effects of cold adaptation on the highly accurate CCA-adding enzyme, an RNA polymerase that uses an internal amino acid motif within the flexible catalytic core as a template to synthesize the CCA triplet at tRNA 3'-ends. As the relative orientation of these residues determines nucleotide selection, we characterized how cold adaptation impacts template reading and fidelity. In a comparative analysis of closely related psychro-, meso-, and thermophilic enzymes, the cold-adapted polymerase shows a remarkable error rate during CCA synthesis in vitro as well as in vivo. Accordingly, CCA-adding activity at low temperatures is not only achieved at the expense of structural stability, but also results in a reduced polymerization fidelity.
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Affiliation(s)
- Felix G M Ernst
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
| | - Lieselotte Erber
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
| | - Joana Sammler
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
| | - Frank Jühling
- b INSERM Unit 1110 , Institute of Viral and Liver Diseases, University of Strasbourg , Strasbourg , France
| | - Heike Betat
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
| | - Mario Mörl
- a Institute for Biochemistry, University of Leipzig , Leipzig , Germany
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33
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Schulte M, Stoldt M, Neudecker P, Pietruszka J, Willbold D, Panwalkar V. 1H, 13C, and 15N backbone and sidechain resonance assignments of a monomeric variant of E. coli deoxyribose-5-phosphate aldolase. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:197-201. [PMID: 28560616 DOI: 10.1007/s12104-017-9747-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Deoxyribose-5-phosphate aldolase (DERA) catalyses the reversible conversion of 2-deoxyribose-5-phosphate (dR5P) into glyceraldehyde-3-phosphate (G3P) and acetaldehyde. For industrial applications, this enzyme is used in organic synthesis for aldol reactions between acetaldehyde as a donor and a wide range of aldehydes as acceptors. Here, we present a near complete set of sequence-specific 1H, 13C and 15N resonance assignments of a 28 kDa monomeric variant of the Escherichia coli DERA. These assignments provide the basis for ongoing structural and dynamic analysis of DERA substrate specificity.
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Affiliation(s)
- Marianne Schulte
- ICS-6 (Strukturbiochemie), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Matthias Stoldt
- ICS-6 (Strukturbiochemie), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Philipp Neudecker
- ICS-6 (Strukturbiochemie), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Jӧrg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine-Universität im Forschungszentrum Jülich, 40225, Düsseldorf, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Dieter Willbold
- ICS-6 (Strukturbiochemie), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany
| | - Vineet Panwalkar
- ICS-6 (Strukturbiochemie), Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany.
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Bramski J, Dick M, Pietruszka J, Classen T. Probing the acetaldehyde-sensitivity of 2-deoxy-ribose-5-phosphate aldolase (DERA) leads to resistant variants. J Biotechnol 2017; 258:56-58. [DOI: 10.1016/j.jbiotec.2017.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/19/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
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35
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Attri P, Kim M, Sarinont T, Ha Choi E, Seo H, Cho AE, Koga K, Shiratani M. The protective action of osmolytes on the deleterious effects of gamma rays and atmospheric pressure plasma on protein conformational changes. Sci Rep 2017; 7:8698. [PMID: 28821765 PMCID: PMC5562882 DOI: 10.1038/s41598-017-08643-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/28/2017] [Indexed: 01/07/2023] Open
Abstract
Both gamma rays and atmospheric pressure plasma are known to have anticancer properties. While their mechanism actions are still not clear, in some contexts they work in similar manner, while in other contexts they work differently. So to understand these relationships, we have studied Myoglobin protein after the treatment of gamma rays and dielectric barrier discharge (DBD) plasma, and analyzed the changes in thermodynamic properties and changes in the secondary structure of protein after both treatments. The thermodynamic properties were analyzed using chemical and thermal denaturation after both treatments. We have also studied the action of gamma rays and DBD plasma on myoglobin in the presence of osmolytes, such as sorbitol and trehalose. For deep understanding of the action of gamma rays and DBD plasma, we have analyzed the reactive species generated by them in buffer at all treatment conditions. Finally, we have used molecular dynamic simulation to understand the hydrogen peroxide action on myoglobin with or without osmolytes, to gain deeper insight into how the osmolytes can protect the protein structure from the reactive species generated by gamma rays and DBD plasma.
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Affiliation(s)
- Pankaj Attri
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, Korea.,Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan
| | - Minsup Kim
- Department of Bioinformatics, Korea University, Sejong, 02841, Korea
| | - Thapanut Sarinont
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan
| | - Eun Ha Choi
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, Korea
| | - Hyunwoong Seo
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan
| | - Art E Cho
- Department of Bioinformatics, Korea University, Sejong, 02841, Korea.
| | - Kazunori Koga
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan.
| | - Masaharu Shiratani
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan.
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36
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Hermans SM, Pfleger C, Nutschel C, Hanke CA, Gohlke H. Rigidity theory for biomolecules: concepts, software, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Susanne M.A. Hermans
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christina Nutschel
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christian A. Hanke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
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37
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Gohlke H, Ben-Shalom IY, Kopitz H, Pfeiffer-Marek S, Baringhaus KH. Rigidity Theory-Based Approximation of Vibrational Entropy Changes upon Binding to Biomolecules. J Chem Theory Comput 2017; 13:1495-1502. [DOI: 10.1021/acs.jctc.7b00014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ido Y. Ben-Shalom
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Hannes Kopitz
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Stefania Pfeiffer-Marek
- R&D/Pre-Development Sciences, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Karl-Heinz Baringhaus
- R&D Resources/Site Direction, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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38
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Reinicke S, Rees HC, Espeel P, Vanparijs N, Bisterfeld C, Dick M, Rosencrantz RR, Brezesinski G, de Geest BG, Du Prez FE, Pietruszka J, Böker A. Immobilization of 2-Deoxy-d-ribose-5-phosphate Aldolase in Polymeric Thin Films via the Langmuir-Schaefer Technique. ACS APPLIED MATERIALS & INTERFACES 2017; 9:8317-8326. [PMID: 28186396 DOI: 10.1021/acsami.6b13632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A synthetic protocol for the fabrication of ultrathin polymeric films containing the enzyme 2-deoxy-d-ribose-5-phosphate aldolase from Escherichia coli (DERAEC) is presented. Ultrathin enzymatically active films are useful for applications in which only small quantities of active material are needed and at the same time quick response and contact times without diffusion limitation are wanted. We show how DERA as an exemplary enzyme can be immobilized in a thin polymer layer at the air-water interface and transferred to a suitable support by the Langmuir-Schaefer technique under full conservation of enzymatic activity. The polymer in use is a poly(N-isopropylacrylamide-co-N-2-thiolactone acrylamide) (P(NIPAAm-co-TlaAm)) statistical copolymer in which the thiolactone units serve a multitude of purposes including hydrophobization of the polymer, covalent binding of the enzyme and the support and finally cross-linking of the polymer matrix. The application of this type of polymer keeps the whole approach simple as additional cocomponents such as cross-linkers are avoided.
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Affiliation(s)
- Stefan Reinicke
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute of Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476, Potsdam-Golm, Germany
| | - Huw C Rees
- Department of Chemistry, University of Chicago , Chicago, Illinois 60637, United States
| | - Pieter Espeel
- Department of Organic and Macromolecular Chemistry, Polymer Chemistry Research Group, Ghent University , Krijgslaan 281 S4-bis, 9000 Ghent, Belgium
| | - Nane Vanparijs
- Department of Pharmaceutics, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Carolin Bisterfeld
- Institut of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, D-52426 Jülich, Germany
| | - Markus Dick
- Institut of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, D-52426 Jülich, Germany
| | - Ruben R Rosencrantz
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute of Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476, Potsdam-Golm, Germany
- Polymer Materials and Polymer Technologies, University of Potsdam , 14476, Potsdam-Golm, Germany
| | - Gerald Brezesinski
- Max Planck Institute of Colloids and Interfaces , Science Park Potsdam-Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Bruno G de Geest
- Department of Pharmaceutics, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Filip E Du Prez
- Department of Organic and Macromolecular Chemistry, Polymer Chemistry Research Group, Ghent University , Krijgslaan 281 S4-bis, 9000 Ghent, Belgium
| | - Jörg Pietruszka
- Institut of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, D-52426 Jülich, Germany
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
| | - Alexander Böker
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute of Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476, Potsdam-Golm, Germany
- Polymer Materials and Polymer Technologies, University of Potsdam , 14476, Potsdam-Golm, Germany
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39
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Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 2016; 42:117-128. [PMID: 28040640 DOI: 10.1016/j.sbi.2016.12.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/15/2016] [Accepted: 12/11/2016] [Indexed: 11/20/2022]
Abstract
The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design.
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40
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Zhang XF, Yang GY, Zhang Y, Xie Y, Withers SG, Feng Y. A general and efficient strategy for generating the stable enzymes. Sci Rep 2016; 6:33797. [PMID: 27667190 PMCID: PMC5036031 DOI: 10.1038/srep33797] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/31/2016] [Indexed: 11/09/2022] Open
Abstract
The local flexibility of an enzyme's active center plays pivotal roles in catalysis, however, little is known about how the flexibility of these flexible residues affects stability. In this study, we proposed an active center stabilization (ACS) strategy to improve the kinetic thermostability of Candida rugosa lipase1. Based on the B-factor ranking at the region ~10 Å within the catalytic Ser209, 18 residues were selected for site-saturation mutagenesis. Based on three-tier high-throughput screening and ordered recombination mutagenesis, the mutant VarB3 (F344I/F434Y/F133Y/F121Y) was shown to be the most stable, with a 40-fold longer in half-life at 60 °C and a 12.7 °C higher Tm value than that of the wild type, without a decrease in catalytic activity. Further analysis of enzymes with different structural complexities revealed that focusing mutations on the flexible residues within around 10 Å of the catalytic residue might increase the success rate for enzyme stabilization. In summary, this study identifies a panel of flexible residues within the active center that affect enzyme stability. This finding not only provides clues regarding the molecular evolution of enzyme stability but also indicates that ACS is a general and efficient strategy for exploring the functional robustness of enzymes for industrial applications.
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Affiliation(s)
- Xiao-Fei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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41
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Dick M, Hartmann R, Weiergräber OH, Bisterfeld C, Classen T, Schwarten M, Neudecker P, Willbold D, Pietruszka J. Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies. Chem Sci 2016; 7:4492-4502. [PMID: 30155096 PMCID: PMC6016325 DOI: 10.1039/c5sc04574f] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/29/2016] [Indexed: 11/21/2022] Open
Abstract
2-Deoxy-d-ribose-5-phosphate aldolase (DERA) is used in organic synthesis for the enantioselective reaction between acetaldehyde and a broad range of other aldehydes as acceptor molecules. Nevertheless, its application is hampered by a poor tolerance towards high concentrations of acetaldehyde, its natural substrate. While numerous studies have been performed searching for new, more acetaldehyde-resistant DERAs, the mechanism underlying this deactivation process has remained elusive. By using NMR spectroscopy on both the protein and the small-molecule scale, we could show that a reaction product binds to the inner part of the enzyme, and that this effect can be partly reversed via heating. The crystal structure of DERA before and after acetaldehyde incubation was determined at high resolution, revealing a covalently bound reaction product bridging the catalytically active lysine (K167) to a nearby cysteine (C47) in the deactivated enzyme. A reaction mechanism is proposed where crotonaldehyde as the aldol product of two acetaldehyde molecules after water elimination forms a Schiff base with the lysine side chain, followed by Michael addition of the cysteine thiol group to the Cβ atom of the inhibitor. In support of this mechanism, direct incubation of DERA with crotonaldehyde results in a more than 100-fold stronger inhibition, compared to acetaldehyde, whereas mutation of C47 gives rise to a fully acetaldehyde-resistant DERA. Thus this variant appears perfectly suited for synthetic applications. A similar diagnostic and preventive strategy should be applicable to other biocatalysts suffering from mechanism-based inhibition by a reactive substrate, a condition that may be more common than currently appreciated in biotechnology.
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Affiliation(s)
- Markus Dick
- Institute of Bioorganic Chemistry , Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich , 52426 Jülich , Germany .
| | - Rudolf Hartmann
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Oliver H Weiergräber
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Carolin Bisterfeld
- Institute of Bioorganic Chemistry , Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich , 52426 Jülich , Germany .
| | - Thomas Classen
- Institute of Bio- and Geosciences , IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Melanie Schwarten
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Philipp Neudecker
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Institut für Physikalische Biologie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany
| | - Dieter Willbold
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Institut für Physikalische Biologie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry , Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich , 52426 Jülich , Germany .
- Institute of Bio- and Geosciences , IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
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42
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Bisterfeld C, Classen T, Küberl I, Henßen B, Metz A, Gohlke H, Pietruszka J. Redesigning Aldolase Stereoselectivity by Homologous Grafting. PLoS One 2016; 11:e0156525. [PMID: 27327271 PMCID: PMC4915726 DOI: 10.1371/journal.pone.0156525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/16/2016] [Indexed: 11/18/2022] Open
Abstract
The 2-deoxy-d-ribose-5-phosphate aldolase (DERA) offers access to highly desirable building blocks for organic synthesis by catalyzing a stereoselective C-C bond formation between acetaldehyde and certain electrophilic aldehydes. DERA´s potential is particularly highlighted by the ability to catalyze sequential, highly enantioselective aldol reactions. However, its synthetic use is limited by the absence of an enantiocomplementary enzyme. Here, we introduce the concept of homologous grafting to identify stereoselectivity-determining amino acid positions in DERA. We identified such positions by structural analysis of the homologous aldolases 2-keto-3-deoxy-6-phosphogluconate aldolase (KDPG) and the enantiocomplementary enzyme 2-keto-3-deoxy-6-phosphogalactonate aldolase (KDPGal). Mutation of these positions led to a slightly inversed enantiopreference of both aldolases to the same extent. By transferring these sequence motifs onto DERA we achieved the intended change in enantioselectivity.
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Affiliation(s)
- Carolin Bisterfeld
- Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Thomas Classen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Irene Küberl
- Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Birgit Henßen
- Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Alexander Metz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jörg Pietruszka
- Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- * E-mail:
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43
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Rathi PC, Fulton A, Jaeger KE, Gohlke H. Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis. PLoS Comput Biol 2016; 12:e1004754. [PMID: 27003415 PMCID: PMC4803202 DOI: 10.1371/journal.pcbi.1004754] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/14/2016] [Indexed: 11/29/2022] Open
Abstract
Protein thermostability is a crucial factor for biotechnological enzyme applications. Protein engineering studies aimed at improving thermostability have successfully applied both directed evolution and rational design. However, for rational approaches, the major challenge remains the prediction of mutation sites and optimal amino acid substitutions. Recently, we showed that such mutation sites can be identified as structural weak spots by rigidity theory-based thermal unfolding simulations of proteins. Here, we describe and validate a unique, ensemble-based, yet highly efficient strategy to predict optimal amino acid substitutions at structural weak spots for improving a protein’s thermostability. For this, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state has been found as the cause for thermostability. When applied prospectively to lipase A from Bacillus subtilis, we achieved both a high success rate (25% over all experimentally tested mutations, which raises to 60% if small-to-large residue mutations and mutations in the active site are excluded) in predicting significantly thermostabilized lipase variants and a remarkably large increase in those variants’ thermostability (up to 6.6°C) based on single amino acid mutations. When considering negative controls in addition and evaluating the performance of our approach as a binary classifier, the accuracy is 63% and increases to 83% if small-to-large residue mutations and mutations in the active site are excluded. The gain in precision (predictive value for increased thermostability) over random classification is 1.6-fold (2.4-fold). Furthermore, an increase in thermostability predicted by our approach significantly points to increased experimental thermostability (p < 0.05). These results suggest that our strategy is a valuable complement to existing methods for rational protein design aimed at improving thermostability. Protein thermostability is a crucial factor for biotechnological enzyme applications. However, performance studies of computational approaches for predicting effects of mutations on protein (thermo)stability have suggested that there is still room for improvement. We describe and validate a novel and unique strategy to predict optimal amino acid substitutions at structural weak spots. At variance with other rational approaches, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state is the underlying cause for thermostability. When applied prospectively on lipase LipA from Bacillus subtilis, a high success rate in predicting thermostabilized lipase variants and a remarkably large increase in their thermostability is achieved. This demonstrates the value of the novel strategy, which extends the existing portfolio of methods for rational protein design.
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Affiliation(s)
- Prakash Chandra Rathi
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Düsseldorf, Germany
| | - Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University, Düsseldorf, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail: (KEJ); (HG)
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail: (KEJ); (HG)
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