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Savino S, Desmet T, Franceus J. Insertions and deletions in protein evolution and engineering. Biotechnol Adv 2022; 60:108010. [PMID: 35738511 DOI: 10.1016/j.biotechadv.2022.108010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
Protein evolution or engineering studies are traditionally focused on amino acid substitutions and the way these contribute to fitness. Meanwhile, the insertion and deletion of amino acids is often overlooked, despite being one of the most common sources of genetic variation. Recent methodological advances and successful engineering stories have demonstrated that the time is ripe for greater emphasis on these mutations and their understudied effects. This review highlights the evolutionary importance and biotechnological relevance of insertions and deletions (indels). We provide a comprehensive overview of approaches that can be employed to include indels in random, (semi)-rational or computational protein engineering pipelines. Furthermore, we discuss the tolerance to indels at the structural level, address how domain indels can link the function of unrelated proteins, and feature studies that illustrate the surprising and intriguing potential of frameshift mutations.
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Affiliation(s)
- Simone Savino
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium..
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2
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Alejaldre L, Pelletier JN, Quaglia D. Methods for enzyme library creation: Which one will you choose?: A guide for novices and experts to introduce genetic diversity. Bioessays 2021; 43:e2100052. [PMID: 34263468 DOI: 10.1002/bies.202100052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022]
Abstract
Enzyme engineering allows to explore sequence diversity in search for new properties. The scientific literature is populated with methods to create enzyme libraries for engineering purposes, however, choosing a suitable method for the creation of mutant libraries can be daunting, in particular for the novices. Here, we address both novices and experts: how can one enter the arena of enzyme library design and what guidelines can advanced users apply to select strategies best suited to their purpose? Section I is dedicated to the novices and presents an overview of established and standard methods for library creation, as well as available commercial solutions. The expert will discover an up-to-date tool to freshen up their repertoire (Section I) and learn of the newest methods that are likely to become a mainstay (Section II). We focus primarily on in vitro methods, presenting the advantages of each method. Our ultimate aim is to offer a selection of methods/strategies that we believe to be most useful to the enzyme engineer, whether a first-timer or a seasoned user.
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Affiliation(s)
- Lorea Alejaldre
- Département de biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, Quebec, Canada.,PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, Quebec, Canada
| | - Joelle N Pelletier
- Département de biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, Quebec, Canada.,PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, Quebec, Canada.,Département de chimie, Université de Montréal, Montréal, Quebec, Canada
| | - Daniela Quaglia
- Département de chimie, Université de Montréal, Montréal, Quebec, Canada.,School of Chemistry, University of Nottingham, Nottingham, UK
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Emond S, Petek M, Kay EJ, Heames B, Devenish SRA, Tokuriki N, Hollfelder F. Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis. Nat Commun 2020; 11:3469. [PMID: 32651386 PMCID: PMC7351745 DOI: 10.1038/s41467-020-17061-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/01/2020] [Indexed: 11/22/2022] Open
Abstract
Insertions and deletions (InDels) are frequently observed in natural protein evolution, yet their potential remains untapped in laboratory evolution. Here we introduce a transposon-based mutagenesis approach (TRIAD) to generate libraries of random variants with short in-frame InDels, and screen TRIAD libraries to evolve a promiscuous arylesterase activity in a phosphotriesterase. The evolution exhibits features that differ from previous point mutagenesis campaigns: while the average activity of TRIAD variants is more compromised, a larger proportion has successfully adapted for the activity. Different functional profiles emerge: (i) both strong and weak trade-off between activities are observed; (ii) trade-off is more severe (20- to 35-fold increased kcat/KM in arylesterase with 60-400-fold decreases in phosphotriesterase activity) and (iii) improvements are present in kcat rather than just in KM, suggesting adaptive solutions. These distinct features make TRIAD an alternative to widely used point mutagenesis, accessing functional innovations and traversing unexplored fitness landscape regions.
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Affiliation(s)
- Stephane Emond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
- Evonetix Ltd, Coldhams Business Park, Norman Way, Cambridge, CB1 3LH, UK.
| | - Maya Petek
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Emily J Kay
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Brennen Heames
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149, Münster, Germany
| | - Sean R A Devenish
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Fluidic Analytics, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening. Methods Mol Biol 2010; 634:239-56. [PMID: 20676989 DOI: 10.1007/978-1-60761-652-8_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Marker genes, such as gusA, lacZ, and gfp, have been applied comprehensively in biological studies. Directed in vitro evolution provides a powerful tool for modifying genes and for studying gene structure, expression, and function. Here, we describe a strategy for directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening. The protocol involves two processes of DNA shuffling and screening. The first DNA shuffling and screening process involves eight steps: (1) amplifying the target gene by PCR, (2) cutting the product into random fragments with DNase I, (3) purification of 50-100 bp fragments, (4) reassembly of the fragments in a primerless PCR, (5) amplification of the reassembled product by primer PCR, (6) cloning into expression vector, (7) transformation of E. coli by electroporation, and (8) screening the target mutants using a nitrocellulose filter. The second DNA shuffling and screening process also involves the same eight steps, except that degenerate oligonucleotide primers are based on the sequence of the selected mutant.
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Abstract
Motif-programming is a method for creating artificial proteins by combining functional peptide motifs in a combinatorial manner. Motifs are often short amino acid sequences within natural proteins that are associated with particular biological functions. Motifs also can be created de novo using molecular engineering. In particular, peptide aptamers, which have been isolated as specific binders against various targets, are believed to be promising motif blocks for creating novel biomaterials through motif-programming. It is now known, however, that simple arithmetic addition does not always work with motif-programming-e.g., simple conjugation of motifs-A and -B does not always result in a bifunctional peptide-AB. To solve this nonlinearity in motif-programming, we have been employing a combinatorial approach, which we called MolCraft. In MolCraft, we prepare a library of artificial proteins that contain multiple motifs in various numbers and orders, from which clones having the desired functions are selected. In MolCraft, a microgene is first rationally designed so that the encoded peptides contain motifs, and then tandemly polymerized with insertion or deletion mutations at the junctions between microgene units. Because of junctional perturbations, proteins translated from a single microgene polymer are molecularly diverse, originating from the combinatorics of three reading frames, and are thus combinatorial polymers of three peptides. By embedding functional motifs into different reading frames of a single microgene, combinatorial polymers of functional motifs are easily prepared. Notably, repetitiousness retained in the overall structure of proteins contributes to the formation of ordered structures, and enhances the chances of reconstituting biological activity. This method is particularly well suited for developing liaison molecules that interface between cells and inorganic materials. Examples of multifunctional artificial proteins created from this method will be introduced.
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Affiliation(s)
- Kiyotaka Shiba
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan.
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Kashiwagi K, Tsuji T, Shiba K. Directional BMP-2 for functionalization of titanium surfaces. Biomaterials 2008; 30:1166-75. [PMID: 19022501 DOI: 10.1016/j.biomaterials.2008.10.040] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 10/17/2008] [Indexed: 11/16/2022]
Abstract
Efficient immobilization of biomacromolecules on material surfaces is a key to development in areas of regenerative medicine and tissue engineering. However, strong and irreversible immobilization of cytokines on surfaces often diminishes their biological functionality. A destructive hydrophobic interaction between the material surface and the biomolecule may underlie this inactivation. Alternatively, dissociation of the cytokine from the material may be necessary for signal transduction. Here we propose a new method for immobilizing cytokines on material surfaces: a material-binding artificial peptide is used to mediate reversible interaction between the cytokine and the material surface. We created artificial proteins that contained three copies of a Ti-binding motif, and fused them to the N-terminal of BMP-2. The engineered BMP-2 showed reversible binding to Ti surfaces and induced BMP signaling activity. When a hydrophobic protein devoid of the Ti-binding motif was fused to BMP-2, the protein tightly bound to Ti surfaces but showed little BMP activity, confirming the importance of the mode of immobilization.
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Affiliation(s)
- Kenji Kashiwagi
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, 3-10-6 Ariake, Koto-ku, Tokyo 135-8550, Japan
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Pressure-adaptive differences in lactate dehydrogenases of three hagfishes: Eptatretus burgeri, Paramyxine atami and Eptatretus okinoseanus. Extremophiles 2008; 12:477-80. [DOI: 10.1007/s00792-008-0140-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 12/26/2007] [Indexed: 10/22/2022]
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Xiong AS, Peng RH, Zhuang J, Liu JG, Gao F, Xu F, Cai B, Yao QH. A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences. Biol Chem 2008; 388:1291-300. [PMID: 18020945 DOI: 10.1515/bc.2007.153] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Directed evolution in vitro is a powerful molecular tool for the creation of new biological phenotypes. It is unclear whether it is more efficient to mutate an enzyme randomly or to mutate just the active sites or key sites. In this study, the strategy of a semi-rational design of directed evolution combined with whole sequence and sites was developed. The 1553 bp gene encoding the thermostable beta-galactosidase of Pyrococcus woesei was chemically synthesized and optimized for G+C content and mRNA secondary structures. The synthesized gene product was used as a template or as a wild-type control. On the basis of the first round of DNA shuffling, library construction and screening, one mutant of YH6754 was isolated with higher activity. Eight potential key sites were deduced from the sequence of the shuffled gene, and 16 degenerate oligonucleotides were designed according to those eight amino acids. Two variants of YG6765 and YG8252 were screened in the second part of DNA shuffling, library construction and screening. For comparison, one mutant of YH8757 was screened through the same routine rounds of directed evolution with YH6754 as template. The purified beta-galactosidase from YH8757 exhibited a lower specific activity at 25 degrees C than those purified from mutated YG6755 and YG8252.
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Affiliation(s)
- Ai-Sheng Xiong
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
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10
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Saito H, Kashida S, Inoue T, Shiba K. The role of peptide motifs in the evolution of a protein network. Nucleic Acids Res 2007; 35:6357-66. [PMID: 17881369 PMCID: PMC2095796 DOI: 10.1093/nar/gkm692] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Naturally occurring proteins in cellular networks often share peptide motifs. These motifs have been known to play a pivotal role in protein interactions among the components of a network. However, it remains unknown how these motifs have contributed to the evolution of the protein network. Here we addressed this issue by a synthetic biology approach. Through the motif programming method, we have constructed an artificial protein library by mixing four peptide motifs shared among the Bcl-2 family proteins that positively or negatively regulate the apoptosis networks. We found one strong pro-apoptotic protein, d29, and two proteins having moderate, but unambiguous anti-apoptotic functions, a10 and d16, from the 28 tested clones. Thus both the pro- and anti-apoptotic modulators were present in the library, demonstrating that functional proteins with opposing effects can emerge from a single pool prepared from common motifs. Motif programming studies have exhibited that the annotated function of the motifs were significantly influenced by the context that the motifs embedded. The results further revealed that reshuffling of a set of motifs realized the promiscuous state of protein, from which disparate functions could emerge. Our finding suggests that motifs contributed to the plastic evolvability of the protein network.
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Affiliation(s)
- Hirohide Saito
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, CREST, Japan Science and Technology Corporation (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 and ICORP, JST, Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
- *To whom correspondence should be addressed. +81 3 3570 0489+81 3 3570 0461 Correspondence may also be addressed to Hirohide Saito. +81 75 753 3997+81 75 753 3996
| | - Shunnichi Kashida
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, CREST, Japan Science and Technology Corporation (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 and ICORP, JST, Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Tan Inoue
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, CREST, Japan Science and Technology Corporation (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 and ICORP, JST, Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kiyotaka Shiba
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, CREST, Japan Science and Technology Corporation (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 and ICORP, JST, Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
- *To whom correspondence should be addressed. +81 3 3570 0489+81 3 3570 0461 Correspondence may also be addressed to Hirohide Saito. +81 75 753 3997+81 75 753 3996
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Rothe A, Surjadi RN, Power BE. Novel proteins in emulsions using in vitro compartmentalization. Trends Biotechnol 2006; 24:587-92. [PMID: 17055094 DOI: 10.1016/j.tibtech.2006.10.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 09/05/2006] [Accepted: 10/12/2006] [Indexed: 01/26/2023]
Abstract
IVC (in vitro compartmentalization) provides a complete cell-free approach for the production of novel targeted proteins. IVC uses aqueous droplets, which contain DNA and components for protein production, within water-in-oil emulsions. Recent advances in the composition and formation, as well as the detection, sorting and recovery, of the droplets enable the evolution of the encoded protein. Furthermore, IVC technology permits the step-wise addition of reagents into the droplets, making them suitable for high-throughput applications - where synthetic enzymes with substrate specificity are selected for catalytic activity, binding and regulation. In the broad field of in vitro display, developments such as the incorporation of unnatural amino acids and the production of cell toxic proteins expand the diverse spectrum of future applications for IVC.
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Affiliation(s)
- Achim Rothe
- CSIRO Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
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