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Zhu B, Wang D, Wei N. Enzyme Discovery and Engineering for Sustainable Plastic Recycling. Trends Biotechnol 2021; 40:22-37. [PMID: 33676748 DOI: 10.1016/j.tibtech.2021.02.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
The drastically increasing amount of plastic waste is causing an environmental crisis that requires innovative technologies for recycling post-consumer plastics to achieve waste valorization while meeting environmental quality goals. Biocatalytic depolymerization mediated by enzymes has emerged as an efficient and sustainable alternative for plastic treatment and recycling. A variety of plastic-degrading enzymes have been discovered from microbial sources. Meanwhile, protein engineering has been exploited to modify and optimize plastic-degrading enzymes. This review highlights the recent trends and up-to-date advances in mining novel plastic-degrading enzymes through state-of-the-art omics-based techniques and improving the enzyme catalytic efficiency and stability via various protein engineering strategies. Future research prospects and challenges are also discussed.
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Affiliation(s)
- Baotong Zhu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA
| | - Dong Wang
- Department of Computer Science and Engineering, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA
| | - Na Wei
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA.
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2
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Abstract
In the past years, several serine hydrolases such as cutinases, esterases and lipases have shown the ability to degrade not only natural polymers but also synthetic polyesters, even aromatic representatives like polyethylene terephthalate (PET). Hence, cutinases and related ester hydrolases have become very important to be applied in the biocatalytic plastic recycling as green alternative to chemical recycling as well as to the functionalization of polyester surfaces in order to change superficial properties like hydrophobicity or hydrophilicity. Sorption characteristics of the enzymes to the polymers have turned out to be a crucial process for efficient polymer hydrolysis. Hence, special attention was paid on tuning the sorption of the enzymes to the hydrophobic polymers. Engineering of the enzyme surface, fusion of hydrophobic substrate-binding domains or truncation of domains hindering the access of the polymer to the enzyme has led to significant improvement of sorption processes and consequently increased activity on the bulky substrate. Finally, the combination of engineering approaches has proved that they can bring additional advantages in improving the enzyme activity when used in a synergistic manner.
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Affiliation(s)
- Doris Ribitsch
- Institute for Environmental Biotechnology, IFA Tulln, University of Natural Resources and Life Sciences, Vienna, Austria; ACIB-Austrian Centre of Industrial Biotechnology, Graz, Austria.
| | - Georg M Guebitz
- Institute for Environmental Biotechnology, IFA Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
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3
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Buruaga-Ramiro C, Valenzuela SV, Pastor FIJ, Martínez J, Diaz P. Unexplored lipolytic activity of Escherichia coli: Implications for lipase cloning. Enzyme Microb Technol 2020; 139:109590. [PMID: 32732039 DOI: 10.1016/j.enzmictec.2020.109590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022]
Abstract
Recent investigations on cloned bacterial lipases performed in our laboratory revealed the presence of lipolytic activity that was not due to the cloned lipase-coding gene but was probably the result of an intrinsic activity of Escherichia coli itself. To confirm such a hypothesis, we assayed the activity of frequently used E. coli strains by fast paper tests, zymograms and spectrofluorometry. A band of Ca. 18-20 kDa showing activity on MUF-butyrate was detected in zymogram analysis of crude cell extracts in all E. coli strains assayed. Moreover, the spectrofluorometric results obtained confirmed the presence of low but significant lipolytic activity in E. coli, with strain BL21 showing the highest activity. Detailed characterization of such a lipolytic activity was performed using E. coli BL21 cell extracts, where preference for C7 substrates was found, although shorter substrates were also hydrolysed to a minor extent. Interestingly, E. coli lipolytic activity displays traits of a thermophilic enzyme, showing maximum activity at 50 °C and pH 8, an unexpected feature never described before. Kinetic and inhibition analysis were also performed showing that activity can be inhibited by several metal ions or by Triton X-100® and SDS, used in zymogram analysis. Such properties ‒ low activity, preference for medium chain-length substrates, and high operational temperature ‒ might justify why this activity had gone unexplored until now, even when many lipases and esterases have been cloned and expressed in E. coli strains in the past. From now on, lipase researchers should take into consideration the presence of such a basal lipolytic activity before starting their lipase cloning or expression experiments in E.coli.
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Affiliation(s)
- Carolina Buruaga-Ramiro
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain
| | - Susana V Valenzuela
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain
| | - F I J Pastor
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain
| | - Josefina Martínez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain
| | - Pilar Diaz
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain.
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Biundo A, Braunschmid V, Pretzler M, Kampatsikas I, Darnhofer B, Birner-Gruenberger R, Rompel A, Ribitsch D, Guebitz GM. Polyphenol oxidases exhibit promiscuous proteolytic activity. Commun Chem 2020; 3:62. [PMID: 36703476 PMCID: PMC9814219 DOI: 10.1038/s42004-020-0305-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/16/2020] [Indexed: 01/29/2023] Open
Abstract
Tyrosinases catalyse both the cresolase and catecholase reactions for the formation of reactive compounds which are very important for industrial applications. In this study, we describe a proteolytic activity of tyrosinases. Two different tyrosinases originating from mushroom and apple are able to cleave the carboxylesterase EstA. The cleavage reaction correlates with the integrity of the active site of tyrosinase and is independent of other possible influencing factors, which could be present in the reaction. Therefore, the cleavage of EstA represents a novel functionality of tyrosinases. EstA was previously reported to degrade synthetic polyesters, albeit slowly. However, the EstA truncated by tyrosinase shows higher degradation activity on the non-biodegradable polyester polyethylene terephthalate (PET), which is a well-established environmental threat.
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Affiliation(s)
- A Biundo
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Straße 22, 3430, Tulln, Austria
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Edoardo Orabona, 70125, Bari, Italy
| | - V Braunschmid
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Straße 22, 3430, Tulln, Austria
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Straße 22, 3430 Tulln, Austria and Petersgasse 14, 8010, Graz, Austria
| | - M Pretzler
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090, Wien, Austria
| | - I Kampatsikas
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090, Wien, Austria
| | - B Darnhofer
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Straße 22, 3430 Tulln, Austria and Petersgasse 14, 8010, Graz, Austria
- Medical University of Graz, Diagnostic and Research Institute of Pathology, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - R Birner-Gruenberger
- Medical University of Graz, Diagnostic and Research Institute of Pathology, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
- Vienna University of Technology, Institute for Chemical Technologies and Analytics, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - A Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090, Wien, Austria
| | - D Ribitsch
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Straße 22, 3430, Tulln, Austria.
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Straße 22, 3430 Tulln, Austria and Petersgasse 14, 8010, Graz, Austria.
| | - G M Guebitz
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Straße 22, 3430, Tulln, Austria
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Straße 22, 3430 Tulln, Austria and Petersgasse 14, 8010, Graz, Austria
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Sharma A, Sharma D, Verma SK. Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190369. [PMID: 31598288 PMCID: PMC6774946 DOI: 10.1098/rsos.190369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/21/2019] [Indexed: 05/15/2023]
Abstract
Xanthomonas translucens pv. undulosa (Xtu) is a proteobacteria which causes bacterial leaf streak (BLS) or bacterial chaff disease in wheat and barley. The constant competition for zinc (Zn) metal nutrients contributes significantly in plant-pathogen interactions. In this study, we have employed a systematic in silico approach to study the Zn-binding proteins of Xtu. From the whole proteome of Xtu, we have identified approximately 7.9% of proteins having Zn-binding sequence and structural motifs. Further, 115 proteins were found homologous to plant-pathogen interaction database. Among these 115 proteins, 11 were predicted as putative secretory proteins. The functional diversity in Zn-binding proteins was revealed by functional domain, gene ontology and subcellular localization analysis. The roles of Zn-binding proteins were found to be varied in the range from metabolism, proteolysis, protein biosynthesis, transport, cell signalling, protein folding, transcription regulation, DNA repair, response to oxidative stress, RNA processing, antimicrobial resistance, DNA replication and DNA integration. This study provides preliminary information on putative Zn-binding proteins of Xtu which may further help in designing new metal-based antimicrobial agents for controlling BLS and bacterial chaff infections on staple crops.
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Veno J, Rahman RNZRA, Masomian M, Ali MSM, Kamarudin NHA. Insight into Improved Thermostability of Cold-Adapted Staphylococcal Lipase by Glycine to Cysteine Mutation. Molecules 2019; 24:molecules24173169. [PMID: 31480403 PMCID: PMC6749283 DOI: 10.3390/molecules24173169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/17/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022] Open
Abstract
Thermostability remains one of the most desirable traits in many lipases. Numerous studies have revealed promising strategies to improve thermostability and random mutagenesis often leads to unexpected yet interesting findings in engineering stability. Previously, the thermostability of C-terminal truncated cold-adapted lipase from Staphylococcus epidermidis AT2 (rT-M386) was markedly enhanced by directed evolution. The newly evolved mutant, G210C, demonstrated an optimal temperature shift from 25 to 45 °C and stability up to 50 °C. Interestingly, a cysteine residue was randomly introduced on the loop connecting the two lids and accounted for the only cysteine found in the lipase. We further investigated the structural and mechanistic insights that could possibly cause the significant temperature shift. Both rT-M386 and G210C were modeled and simulated at 25 °C and 50 °C. The results clearly portrayed the effect of cysteine substitution primarily on the lid stability. Comparative molecular dynamics simulation analysis revealed that G210C exhibited greater stability than the wild-type at high temperature simulation. The compactness of the G210C lipase structure increased at 50 °C and resulted in enhanced rigidity hence stability. This observation is supported by the improved and stronger non-covalent interactions formed in the protein structure. Our findings suggest that the introduction of a single cysteine residue at the lid region of cold-adapted lipase may result in unexpected increased in thermostability, thus this approach could serve as one of the thermostabilization strategies in engineering lipase stability.
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Affiliation(s)
- Jiivittha Veno
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Malihe Masomian
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Centre of Vaccine Research, School of Science and Technology, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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Shift in Bacillus sp. JR3 esterase LipJ activity profile after addition of essential residues from family I.5 thermophilic lipases. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Curia S, Biundo A, Fischer I, Braunschmid V, Gübitz GM, Stanzione JF. Towards Sustainable High-Performance Thermoplastics: Synthesis, Characterization, and Enzymatic Hydrolysis of Bisguaiacol-Based Polyesters. CHEMSUSCHEM 2018; 11:2529-2539. [PMID: 29924915 DOI: 10.1002/cssc.201801059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Indexed: 06/08/2023]
Abstract
The utilization of wood-derived building blocks (xylochemicals) to replace fossil-based precursors is an attractive research subject of modern polymer science. Here, we demonstrate that bisguaiacol (BG), a lignin-derived bisphenol analogue, can be used to prepare biobased polyesters with remarkable thermal properties. BG was treated with different activated diacids to investigate the effect of co-monomer structures on the physical properties of the products. Namely, derivatives of adipic acid, succinic acid, and 2,5-furandicarboxylic acid were used. Moreover, a terephthalic acid derivative was used for comparison purposes. The products were characterized by 1 H NMR spectroscopy, attenuated total reflectance FTIR spectroscopy, gel-permeation chromatography, thermogravimetric analysis, and differential scanning calorimetry to assess their structural and thermal properties in detail. The polymers showed glass-transition temperatures ranging up to 160 °C and thermal stabilities in excess of 300 °C. Furthermore, the susceptibility of the polyester to enzymatic hydrolysis was investigated to assess the potential for further surface functionalization and/or recycling and biodegradation. Indeed, hydrolysis with two different enzymes from the bacteria Thermobifida cellulosilytica led to the release of monomers, as quantified by HPLC. The results of this study indicate that our new polyesters represent promising renewable and biodegradable alternatives to petroleum-based polyesters currently employed in the plastics industry, specifically for applications in which high-temperature stability is essential to ensure overall system integrity.
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Affiliation(s)
- Silvio Curia
- Department of Chemical Engineering, Rowan University, 201 Mullica Hill Road, Glassboro, NJ, 08028, USA
| | - Antonino Biundo
- Austrian Centre of Industrial Biotechnology (ACIB), Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Isabel Fischer
- Austrian Centre of Industrial Biotechnology (ACIB), Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Verena Braunschmid
- Austrian Centre of Industrial Biotechnology (ACIB), Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Georg M Gübitz
- Austrian Centre of Industrial Biotechnology (ACIB), Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
- University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Joseph F Stanzione
- Department of Chemical Engineering, Rowan University, 201 Mullica Hill Road, Glassboro, NJ, 08028, USA
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Biundo A, Ribitsch D, Guebitz GM. Surface engineering of polyester-degrading enzymes to improve efficiency and tune specificity. Appl Microbiol Biotechnol 2018; 102:3551-3559. [PMID: 29511846 DOI: 10.1007/s00253-018-8850-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/08/2018] [Accepted: 02/10/2018] [Indexed: 01/06/2023]
Abstract
Certain members of the carboxylesterase superfamily can act at the interface between water and water-insoluble substrates. However, nonnatural bulky polyesters usually are not efficiently hydrolyzed. In the recent years, the potential of enzyme engineering to improve hydrolysis of synthetic polyesters has been demonstrated. Regions on the enzyme surface have been modified by using site-directed mutagenesis in order to tune sorption processes through increased hydrophobicity of the enzyme surface. Such modifications can involve specific amino acid substitutions, addition of binding modules, or truncation of entire domains improving sorption properties and/or dynamics of the enzyme. In this review, we provide a comprehensive overview on different strategies developed in the recent years for enzyme surface engineering to improve the activity of polyester-hydrolyzing enzymes.
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Affiliation(s)
- Antonino Biundo
- Austrian Centre of Industrial Biotechnology (ACIB), Tulln an der Donau, Austria
| | - Doris Ribitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Tulln an der Donau, Austria. .,Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Tulln an der Donau, Austria.
| | - Georg M Guebitz
- Austrian Centre of Industrial Biotechnology (ACIB), Tulln an der Donau, Austria.,Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Tulln an der Donau, Austria
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Biundo A, Reich J, Ribitsch D, Guebitz GM. Synergistic effect of mutagenesis and truncation to improve a polyesterase from Clostridium botulinum for polyester hydrolysis. Sci Rep 2018; 8:3745. [PMID: 29487314 PMCID: PMC5829244 DOI: 10.1038/s41598-018-21825-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
The activity of the esterase (Cbotu_EstA) from Clostridium botulinum on the polyester poly(ethylene terephthalate) (PET) was improved by concomitant engineering of two different domains. On the one hand, the zinc-binding domain present in Cbotu_EstA was subjected to site-directed mutagenesis. On the other hand, a specific domain consisting of 71 amino acids at the N-terminus of the enzyme was deleted. Interestingly, a combination of substitution of residues present in the zinc-binding domain (e.g. S199A) synergistically increased the activity of the enzyme on PET seven fold when combined to the truncation of 71 amino acids at the N-terminus of the enzyme only. Overall, when compared to the native enzyme, the combination of truncation and substitutions in the zinc-binding domain lead to a 50-fold activity improvement. Moreover, analysis of the kinetic parameters of the Cbotu_EstA variants indicated a clear shift of activity from water soluble (i.e. para-nitrophenyl butyrate) to insoluble polymeric substrates. These results evidently show that the interaction with non-natural polymeric substrates provides targets for enzyme engineering.
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Affiliation(s)
- Antonino Biundo
- Austrian Centre for Industrial Biotechnology (ACIB), 3430, Tulln an der Donau, Austria
| | - Johanna Reich
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), 3430, Tulln an der Donau, Austria
| | - Doris Ribitsch
- Austrian Centre for Industrial Biotechnology (ACIB), 3430, Tulln an der Donau, Austria. .,Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), 3430, Tulln an der Donau, Austria.
| | - Georg M Guebitz
- Austrian Centre for Industrial Biotechnology (ACIB), 3430, Tulln an der Donau, Austria.,Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), 3430, Tulln an der Donau, Austria
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