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Fujii S, Matsuura T, Yomo T. In vitro directed evolution of alpha-hemolysin by liposome display. Biophysics (Nagoya-shi) 2015; 11:67-72. [PMID: 27493517 PMCID: PMC4736788 DOI: 10.2142/biophysics.11.67] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 12/01/2022] Open
Abstract
We have developed a method to enable in vitro directed evolution that can be applied to membrane proteins. This method, termed liposome display, uses liposomes as compartments in which membrane proteins are synthesized and as scaffolds for membrane protein integration. Thus, the synthesized membrane proteins are displayed on the surface of the liposome and exhibit their functions. A randomly mutated DNA library of the membrane protein was generated, encapsulated in the liposomes at the single-molecule level, and used to generate a liposome library. Liposomes displaying the desired membrane protein function were selected, thus accumulating the DNA molecule encoding the desired membrane protein. We have applied this method to alpha-hemolysin, a membrane protein derived from Staphylococcus aureus. Alpha-hemolysin forms a nanopore in the membrane, which allows the penetration of small molecules. We aimed to improve this nanopore activity by using the liposome display method. Consequently, alpha-hemolysin evolved and attained a higher specific affinity for the liposome membrane. In this review, we describe the essential characteristics of liposome display and the properties of the evolved alpha-hemolysin obtained by this method.
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Affiliation(s)
- Satoshi Fujii
- Japan Science and Technology (JST), ERATO, Yomo Dynamical Micro-scale Reaction Environment Project, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Japan Science and Technology (JST), ERATO, Yomo Dynamical Micro-scale Reaction Environment Project, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Japan Science and Technology (JST), ERATO, Yomo Dynamical Micro-scale Reaction Environment Project, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-1 E-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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52
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Gagoski D, Mureev S, Giles N, Johnston W, Dahmer-Heath M, Škalamera D, Gonda TJ, Alexandrov K. Gateway-compatible vectors for high-throughput protein expression in pro- and eukaryotic cell-free systems. J Biotechnol 2014; 195:1-7. [PMID: 25529348 DOI: 10.1016/j.jbiotec.2014.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/06/2014] [Accepted: 12/11/2014] [Indexed: 12/16/2022]
Abstract
Although numerous techniques for protein expression and production are available the pace of genome sequencing outstrips our ability to analyze the encoded proteins. To address this bottleneck, we have established a system for parallelized cloning, DNA production and cell-free expression of large numbers of proteins. This system is based on a suite of pCellFree Gateway destination vectors that utilize a Species Independent Translation Initiation Sequence (SITS) that mediates recombinant protein expression in any in vitro translation system. These vectors introduce C or N terminal EGFP and mCherry fluorescent and affinity tags, enabling direct analysis and purification of the expressed proteins. To maximize throughput and minimize the cost of protein production we combined Gateway cloning with Rolling Circle DNA Amplification. We demonstrate that as little as 0.1 ng of plasmid DNA is sufficient for template amplification and production of recombinant human protein in Leishmania tarentolae and Escherichia coli cell-free expression systems. Our experiments indicate that this approach can be applied to large gene libraries as it can be reliably performed in multi-well plates. The resulting protein expression pipeline provides a valuable new tool for applications of the post genomic era.
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Affiliation(s)
- Dejan Gagoski
- Institute for Molecular Bioscience, University of Queensland, Australia
| | - Sergey Mureev
- Institute for Molecular Bioscience, University of Queensland, Australia
| | - Nichole Giles
- Institute for Molecular Bioscience, University of Queensland, Australia
| | - Wayne Johnston
- Institute for Molecular Bioscience, University of Queensland, Australia
| | - Mareike Dahmer-Heath
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Dubravka Škalamera
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Thomas J Gonda
- School of Pharmacy, University of Queensland, Brisbane, Australia; University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience, University of Queensland, Australia.
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Diem MD, Hyun L, Yi F, Hippensteel R, Kuhar E, Lowenstein C, Swift EJ, O'Neil KT, Jacobs SA. Selection of high-affinity Centyrin FN3 domains from a simple library diversified at a combination of strand and loop positions. Protein Eng Des Sel 2014; 27:419-29. [PMID: 24786107 DOI: 10.1093/protein/gzu016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative scaffold molecules represent a class of proteins important to the study of protein design and mechanisms of protein-protein interactions, as well as for the development of therapeutic proteins. Here, we describe the generation of a library built upon the framework of a consensus FN3 domain sequence resulting in binding proteins we call Centyrins. This new library employs diversified positions within the C-strand, CD-loop, F-strand and FG-loop of the FN3 domain. CIS display was used to select high-affinity Centyrin variants against three targets; c-MET, murine IL-17A and rat TNFα and scanning mutagenesis studies were used to define the positions of the library most important for target binding. Contributions from both the strand and loop positions were noted, although the pattern was different for each molecule. In addition, an affinity maturation scheme is described that resulted in a significant improvement in the affinity of one selected Centyrin variant. Together, this work provides important data contributing to our understanding of potential FN3 binding interfaces and a new tool for generating high-affinity scaffold molecules.
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Affiliation(s)
- Michael D Diem
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Linus Hyun
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Fang Yi
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Randi Hippensteel
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Elise Kuhar
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Cassandra Lowenstein
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Edward J Swift
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Karyn T O'Neil
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Steven A Jacobs
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
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55
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Abstract
Protein engineering is at an exciting stage because designed protein-protein interactions are being used in many applications. For instance, three designed proteins are now in clinical trials. Although there have been many successes over the last decade, protein engineering still faces numerous challenges. Often, designs do not work as anticipated and they still require substantial redesign. The present review focuses on the successes, the challenges and the limitations of rational protein design today.
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56
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ProxiMAX randomization: a new technology for non-degenerate saturation mutagenesis of contiguous codons. Biochem Soc Trans 2014; 41:1189-94. [PMID: 24059507 PMCID: PMC3782830 DOI: 10.1042/bst20130123] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Back in 2003, we published ‘MAX’ randomization, a process of non-degenerate saturation mutagenesis using exactly 20 codons (one for each amino acid) or else any required subset of those 20 codons. ‘MAX’ randomization saturates codons located in isolated positions within a protein, as might be required in enzyme engineering, or else on one face of an α-helix, as in zinc-finger engineering. Since that time, we have been asked for an equivalent process that can saturate multiple contiguous codons in a non-degenerate manner. We have now developed ‘ProxiMAX’ randomization, which does just that: generating DNA cassettes for saturation mutagenesis without degeneracy or bias. Offering an alternative to trinucleotide phosphoramidite chemistry, ProxiMAX randomization uses nothing more sophisticated than unmodified oligonucleotides and standard molecular biology reagents. Thus it requires no specialized chemistry, reagents or equipment, and simply relies on a process of saturation cycling comprising ligation, amplification and digestion for each cycle. The process can encode both unbiased representation of selected amino acids or else encode them in predefined ratios. Each saturated position can be defined independently of the others. We demonstrate accurate saturation of up to 11 contiguous codons. As such, ProxiMAX randomization is particularly relevant to antibody engineering.
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57
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Houlihan G, Gatti-Lafranconi P, Kaltenbach M, Lowe D, Hollfelder F. An experimental framework for improved selection of binding proteins using SNAP display. J Immunol Methods 2014; 405:47-56. [DOI: 10.1016/j.jim.2014.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/15/2013] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
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58
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Stafford RL, Matsumoto ML, Yin G, Cai Q, Fung JJ, Stephenson H, Gill A, You M, Lin SH, Wang WD, Masikat MR, Li X, Penta K, Steiner AR, Baliga R, Murray CJ, Thanos CD, Hallam TJ, Sato AK. In vitro Fab display: a cell-free system for IgG discovery. Protein Eng Des Sel 2014; 27:97-109. [PMID: 24586053 PMCID: PMC3966677 DOI: 10.1093/protein/gzu002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Selection technologies such as ribosome display enable the rapid discovery of novel antibody fragments entirely in vitro. It has been assumed that the open nature of the cell-free reactions used in these technologies limits selections to single-chain protein fragments. We present a simple approach for the selection of multi-chain proteins, such as antibody Fab fragments, using ribosome display. Specifically, we show that a two-chain trastuzumab (Herceptin) Fab domain can be displayed in a format which tethers either the heavy or light chain to the ribosome while retaining functional antigen binding. Then, we constructed synthetic Fab HC and LC libraries and performed test selections against carcinoembryonic antigen (CEA) and vascular endothelial growth factor (VEGF). The Fab selection output was reformatted into full-length immunoglobulin Gs (IgGs) and directly expressed at high levels in an optimized cell-free system for immediate screening, purification and characterization. Several novel IgGs were identified using this cell-free platform that bind to purified CEA, CEA positive cells and VEGF.
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Affiliation(s)
- Ryan L Stafford
- Sutro Biopharma, Inc., 310 Utah Ave Suite 150, South San Francisco, CA 94080, USA
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59
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Teplyakov A, Obmolova G, Malia TJ, Luo J, Jacobs SA, Chan W, Domingo D, Baker A, O'Neil KT, Gilliland GL. C-terminal β-strand swapping in a consensus-derived fibronectin Type III scaffold. Proteins 2014; 82:1359-69. [PMID: 24375666 DOI: 10.1002/prot.24502] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 12/09/2013] [Accepted: 12/17/2013] [Indexed: 11/07/2022]
Abstract
The crystal structures of six different fibronectin Type III consensus-derived Tencon domains, whose solution properties exhibit no, to various degrees of, aggregation according to SEC, have been determined. The structures of the five variants showing aggregation reveal 3D domain swapped dimers. In all five cases, the swapping involves the C-terminal β-strand resulting in the formation of Tencon dimers in which the target-binding surface is blocked. All of the variants differ in sequence in the FG loop, which is the hinge loop in the β-strand-swapped dimers. The six tencon variants have between 0 and 5 residues inserted between positions 77 and 78 in the FG loop. Analysis of the structures suggests that a non-glycine residue at position 77 and insertions of <4 residues may destabilize the β-turn in the FG loop promoting β-strand swapping. Swapped dimers with an odd number of inserted residues may be less stable, particularly if they contain proline residues, because they cannot form perfect β-bridges in the FG regions that link the swapped dimers. The Tencon β-swapped variants with the longest FG sequences are observed to form higher order hexameric or helical oligomeric structures in the crystal correlating well with the aggregation properties of these domains observed in solution. Understanding the structural basis for domain-swapped dimerization and oligomerization will support engineering efforts of the Tencon domain to produce variants with desired biophysical properties.
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Affiliation(s)
- Alexey Teplyakov
- Janssen Research & Development, LLC, Biotechnology Center of Excellence, 1400 McKean Road, Spring House, Pennsylvania, 19477
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60
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Biomolecular Display Technology. Anim Biotechnol 2014. [DOI: 10.1016/b978-0-12-416002-6.00020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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61
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Justo GZ, Suarez ER, Melo C, Lima MA, Nader HB, Pinhal MAS. From Combinatorial Display Techniques to Microarray Technology: New Approaches to the Development and Toxicological Profiling of Targeted Nanomedicines. Nanotoxicology 2014. [DOI: 10.1007/978-1-4614-8993-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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62
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Understanding the role of cross-arm binding efficiency in the activity of monoclonal and multispecific therapeutic antibodies. Methods 2014; 65:95-104. [DOI: 10.1016/j.ymeth.2013.07.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 07/08/2013] [Accepted: 07/09/2013] [Indexed: 01/09/2023] Open
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63
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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64
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Abstract
In vitro methods have enabled the rapid and efficient evolution of proteins and successful generation of novel and highly functional proteins. However, the available methods consider only globular proteins (e.g., antibodies, enzymes) and not membrane proteins despite the biological and pharmaceutical importance of the latter. In this study, we report the development of a method called liposome display that can evolve the properties of membrane proteins entirely in vitro. This method, which involves in vitro protein synthesis inside liposomes, which are cell-sized phospholipid vesicles, was applied to the pore-forming activity of α-hemolysin, a membrane protein derived from Staphylococcus aureus. The obtained α-hemolysin mutant possessed only two point mutations but exhibited a 30-fold increase in its pore-forming activity compared with the WT. Given the ability to synthesize various membrane proteins and modify protein synthesis and functional screening conditions, this method will allow for the rapid and efficient evolution of a wide range of membrane proteins.
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65
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Wada A. Development of Next-Generation Peptide Binders Using In vitro Display Technologies and Their Potential Applications. Front Immunol 2013; 4:224. [PMID: 23914189 PMCID: PMC3730117 DOI: 10.3389/fimmu.2013.00224] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/29/2013] [Indexed: 12/02/2022] Open
Abstract
During the last decade, a variety of monoclonal antibodies have been developed and used as molecular targeting drugs in medical therapies. Although antibody drugs tend to have intense pharmacological activities and negligible side effects, several issues in their development and prescription remain to be resolved. Synthetic peptides with affinities and specificities for a desired target have received significant attention as alternatives to antibodies. In vitro display technologies are powerful methods for the selection of such peptides from combinatorial peptide libraries. Various types of peptide binders are being selected with such technologies for use in a wide range of fields from bioscience to medicine. This mini review article focuses on the current state of in vitro display selection of synthetic peptide binders and compares the selected peptides with natural peptides/proteins to provide a better understanding of the target affinities and inhibitory activities derived from their amino acid sequences and structural frameworks. The potential of synthetic peptide binders as alternatives to antibody drugs in therapeutic applications is also reviewed.
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66
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Skirgaila R, Pudzaitis V, Paliksa S, Vaitkevicius M, Janulaitis A. Compartmentalization of destabilized enzyme-mRNA-ribosome complexes generated by ribosome display: a novel tool for the directed evolution of enzymes. Protein Eng Des Sel 2013; 26:453-61. [DOI: 10.1093/protein/gzt017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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67
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Ishizawa T, Kawakami T, Reid PC, Murakami H. TRAP Display: A High-Speed Selection Method for the Generation of Functional Polypeptides. J Am Chem Soc 2013; 135:5433-40. [DOI: 10.1021/ja312579u] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Takahiro Ishizawa
- Department of Life Sciences,
Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Takashi Kawakami
- Department of Life Sciences,
Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Patrick C. Reid
- PeptiDream Inc., 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Hiroshi Murakami
- Department of Life Sciences,
Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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68
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Patel S, Mathonet P, Jaulent AM, Ullman CG. Selection of a high-affinity WW domain against the extracellular region of VEGF receptor isoform-2 from a combinatorial library using CIS display. Protein Eng Des Sel 2013; 26:307-15. [PMID: 23378640 DOI: 10.1093/protein/gzt003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
WW domains are small β-sheet motifs that are involved in intracellular signalling through the recognition of proline-rich or phosphorylated linear peptide sequences. Here, we describe modification of this motif to provide a framework for engineering the side chains exposed on its concave surface. This non-natural scaffold incorporates an additional tryptophan, has a shorter loop 1 and supports modification of 25% of the natural protein to form a novel affinity reagent. We demonstrate the utility of this structure by selecting a high-affinity binder to the extracellular region of human vascular endothelial growth factor receptor isoform 2 (VEGFR-2) from a library of modifications, using a cell-free molecular display platform, CIS display. The isolate has low nanomolar affinity to VEGFR-2 and inhibits binding of human VEGF to its receptor with nanomolar activity. The structure is amenable to cyclisation to improve its proteolytic stability and has advantages over larger protein scaffolds in that it can be synthesised chemically to high yields offering potential for therapeutic and non-therapeutic applications.
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Affiliation(s)
- Seema Patel
- Isogenica Ltd, Little Chesterford, Essex CB10 1XL, UK
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69
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Zhong X, Kieras E, Sousa E, D'Antona A, Baber JC, He T, Desharnais J, Wood L, Luxenberg D, Stahl M, Kriz R, Lin L, Somers W, Fitz LJ, Wright JF. Pyroglutamate and O-linked glycan determine functional production of anti-IL17A and anti-IL22 peptide-antibody bispecific genetic fusions. J Biol Chem 2013; 288:1409-19. [PMID: 23184956 PMCID: PMC3543023 DOI: 10.1074/jbc.m112.417717] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/13/2012] [Indexed: 01/05/2023] Open
Abstract
Protein biosynthesis and extracellular secretion are essential biological processes for therapeutic protein production in mammalian cells, which offer the capacity for correct folding and proper post-translational modifications. In this study, we have generated bispecific therapeutic fusion proteins in mammalian cells by combining a peptide and an antibody into a single open reading frame. A neutralizing peptide directed against interleukin-17A (IL17A) was genetically fused to the N termini of an anti-IL22 antibody, through either the light chain, the heavy chain, or both chains. Although the resulting fusion proteins bound and inhibited IL22 with the same affinity and potency as the unmodified anti-IL22 antibody, the peptide modality in the fusion scaffold was not active in the cell-based assay due to the N-terminal degradation. When a glutamine residue was introduced at the N terminus, which can be cyclized to form pyroglutamate in mammalian cells, the IL17A neutralization activity of the fusion protein was restored. Interestingly, the mass spectroscopic analysis of the purified fusion protein revealed an unexpected O-linked glycosylation modification at threonine 5 of the anti-IL17A peptide. The subsequent removal of this post-translational modification by site-directed mutagenesis drastically enhanced the IL17A binding affinity and neutralization potency for the resulting fusion protein. These results provide direct experimental evidence that post-translational modifications during protein biosynthesis along secretory pathways play critical roles in determining the structure and function of therapeutic proteins produced by mammalian cells. The newly engineered peptide-antibody genetic fusion is promising for therapeutically targeting multiple antigens in a single antibody-like molecule.
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Affiliation(s)
- Xiaotian Zhong
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Elizabeth Kieras
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Eric Sousa
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Aaron D'Antona
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - J. Christian Baber
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Tao He
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | | | - Lauren Wood
- Pfizer CovX Research, San Diego, California 92121
| | - Deborah Luxenberg
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Mark Stahl
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Ronald Kriz
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Laura Lin
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Will Somers
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Lori J. Fitz
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
| | - Jill F. Wright
- From the Pfizer BioTherapeutics Research and Development, Cambridge, Massachusetts 02140 and
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70
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Mier W, Krämer S, Zitzmann S, Altmann A, Leotta K, Schierbaum U, Schnölzer M, Eisenhut M, Haberkorn U. PEGylation enables the specific tumor accumulation of a peptide identified by phage display. Org Biomol Chem 2013; 11:2706-11. [DOI: 10.1039/c3ob27475f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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71
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Abstract
In the past decade, in vitro evolution techniques have been used to improve the performance or alter the activity of a number of different enzymes and have generated enzymes de novo. In this review, we provide an overview of the available in vitro methods, their application, and some general considerations for enzyme engineering in vitro. We discuss the advantages of in vitro over in vivo approaches and focus on ribosome display, mRNA display, DNA display technologies, and in vitro compartmentalization (IVC) methods. This review aims to help researchers determine which approach is best suited for their own experimental needs and to highlight that in vitro methods offer a promising route for enzyme engineering.
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Affiliation(s)
- Misha V Golynskiy
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, USA
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72
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Protein Engineering as an Enabling Tool for Synthetic Biology. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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73
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Genetically encoded libraries of nonstandard peptides. J Nucleic Acids 2012; 2012:713510. [PMID: 23097693 PMCID: PMC3477784 DOI: 10.1155/2012/713510] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/12/2012] [Indexed: 11/17/2022] Open
Abstract
The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.
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74
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Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes. J Nucleic Acids 2012; 2012:923214. [PMID: 22957209 PMCID: PMC3431101 DOI: 10.1155/2012/923214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/10/2012] [Indexed: 11/17/2022] Open
Abstract
Directed evolution of proteins is a technique used to modify protein functions through "Darwinian selection." In vitro compartmentalization (IVC) is an in vitro gene screening system for directed evolution of proteins. IVC establishes the link between genetic information (genotype) and the protein translated from the information (phenotype), which is essential for all directed evolution methods, by encapsulating both in a nonliving microcompartment. Herein, we introduce a new liposome-based IVC system consisting of a liposome, the protein synthesis using recombinant elements (PURE) system and a fluorescence-activated cell sorter (FACS) used as a microcompartment, in vitro protein synthesis system, and high-throughput screen, respectively. Liposome-based IVC is characterized by in vitro protein synthesis from a single copy of a gene in a cell-sized unilamellar liposome and quantitative functional evaluation of the synthesized proteins. Examples of liposome-based IVC for screening proteins such as GFP and β-glucuronidase are described. We discuss the future directions for this method and its applications.
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75
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Kozlov IA, Thomsen ER, Munchel SE, Villegas P, Capek P, Gower AJ, Pond SJK, Chudin E, Chee MS. A highly scalable peptide-based assay system for proteomics. PLoS One 2012; 7:e37441. [PMID: 22701568 PMCID: PMC3373263 DOI: 10.1371/journal.pone.0037441] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022] Open
Abstract
We report a scalable and cost-effective technology for generating and screening high-complexity customizable peptide sets. The peptides are made as peptide-cDNA fusions by in vitro transcription/translation from pools of DNA templates generated by microarray-based synthesis. This approach enables large custom sets of peptides to be designed in silico, manufactured cost-effectively in parallel, and assayed efficiently in a multiplexed fashion. The utility of our peptide-cDNA fusion pools was demonstrated in two activity-based assays designed to discover protease and kinase substrates. In the protease assay, cleaved peptide substrates were separated from uncleaved and identified by digital sequencing of their cognate cDNAs. We screened the 3,011 amino acid HCV proteome for susceptibility to cleavage by the HCV NS3/4A protease and identified all 3 known trans cleavage sites with high specificity. In the kinase assay, peptide substrates phosphorylated by tyrosine kinases were captured and identified by sequencing of their cDNAs. We screened a pool of 3,243 peptides against Abl kinase and showed that phosphorylation events detected were specific and consistent with the known substrate preferences of Abl kinase. Our approach is scalable and adaptable to other protein-based assays.
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Affiliation(s)
- Igor A Kozlov
- Prognosys Biosciences Inc., La Jolla, California, United States of America.
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76
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Development of anti-infectives using phage display: biological agents against bacteria, viruses, and parasites. Antimicrob Agents Chemother 2012; 56:4569-82. [PMID: 22664969 DOI: 10.1128/aac.00567-12] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The vast majority of anti-infective therapeutics on the market or in development are small molecules; however, there is now a nascent pipeline of biological agents in development. Until recently, phage display technologies were used mainly to produce monoclonal antibodies (MAbs) targeted against cancer or inflammatory disease targets. Patent disputes impeded broad use of these methods and contributed to the dearth of candidates in the clinic during the 1990s. Today, however, phage display is recognized as a powerful tool for selecting novel peptides and antibodies that can bind to a wide range of antigens, ranging from whole cells to proteins and lipid targets. In this review, we highlight research that exploits phage display technology as a means of discovering novel therapeutics against infectious diseases, with a focus on antimicrobial peptides and antibodies in clinical or preclinical development. We discuss the different strategies and methods used to derive, select, and develop anti-infectives from phage display libraries and then highlight case studies of drug candidates in the process of development and commercialization. Advances in screening, manufacturing, and humanization technologies now mean that phage display can make a significant contribution in the fight against clinically important pathogens.
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77
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Lu WC, Ellington AD. In vitro selection of proteins via emulsion compartments. Methods 2012; 60:75-80. [PMID: 22491026 DOI: 10.1016/j.ymeth.2012.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 12/23/2011] [Accepted: 03/09/2012] [Indexed: 11/25/2022] Open
Abstract
In vitro compartmentalization (IVC) is a method to generate numerous, small, aqueous compartments (up to 10(10) compartments per ml) by mixing water, surfactants, and oil. The water phase is surrounded by surfactants and an oil phase, and to a first approximation each water-in-oil compartment is like an artificial cell. By introducing single genes into compartments that are competent for transcription and translation, these cell-like compartments can synthesize RNA protein variants in libraries. Screening or selecting for function has in turn led to schemes for the directed evolution of biomolecules. However, IVC selections can cover larger library sizes, and provide greater control over selection conditions and stringencies. The key issue in designing and executing IVC selections is how to couple genotype and phenotype, and in this review we have organized and presented a variety of mechanisms by which proteins and RNA can attach to or amplify their own templates following emulsification and selection.
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Affiliation(s)
- Wei-Cheng Lu
- Institute of Cellular and Molecule Biology, University of Texas at Austin, TX 78712, USA
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78
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Weinstock MT, Francis JN, Redman JS, Kay MS. Protease-resistant peptide design-empowering nature's fragile warriors against HIV. Biopolymers 2012; 98:431-42. [PMID: 23203688 PMCID: PMC3548907 DOI: 10.1002/bip.22073] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/05/2012] [Accepted: 04/04/2012] [Indexed: 01/29/2023]
Abstract
Peptides have great potential as therapeutic agents, but their use is often limited by susceptibility to proteolysis and their resulting in vivo fragility. In this review, we focus on peptidomimetic approaches to produce protease-resistant peptides with the potential for greatly improved clinical utility. We focus on the use of mirror-image (D-peptide) and ß-peptides as two leading approaches with distinct design principles and challenges. Application to the important and difficult problem of inhibiting HIV entry illustrates the current state-of-the-art in peptidomimetic technologies. We also summarize future directions for this field and highlight remaining obstacles to widespread use of protease-resistant peptides.
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Affiliation(s)
- Matthew T Weinstock
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
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79
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Ullman CG, Frigotto L, Cooley RN. In vitro methods for peptide display and their applications. Brief Funct Genomics 2011; 10:125-34. [PMID: 21628313 DOI: 10.1093/bfgp/elr010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The presentation of recombinant peptide libraries linked to their coding sequence can be referred to as 'peptide display'. Phage display is the most widely practiced peptide display technology but more recent alternatives such as CIS display, ribosome display and mRNA display offer advantages over phage for speed, library size and the display of unnatural amino acids. These have provided researchers with tools to address some of the failings of peptides such as their low affinity, low stability and inability to cross biological membranes. In this review, we assess some of the recent advances in peptide display and its application.
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Affiliation(s)
- Christopher G Ullman
- Isogenica Ltd., The Mansion, Chesterford Research Park, Little Chesterford, Essex, UK.
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80
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Petrovskaya LE, Shingarova LN, Dolgikh DA, Kirpichnikov MP. Alternative scaffold proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:581-91. [DOI: 10.1134/s1068162011050141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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81
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Naimuddin M, Kubo T. Display of disulfide-rich proteins by complementary DNA display and disulfide shuffling assisted by protein disulfide isomerase. Anal Biochem 2011; 419:33-9. [PMID: 21867670 DOI: 10.1016/j.ab.2011.07.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 07/07/2011] [Accepted: 07/27/2011] [Indexed: 10/17/2022]
Abstract
We report an efficient system to produce and display properly folded disulfide-rich proteins facilitated by coupled complementary DNA (cDNA) display and protein disulfide isomerase-assisted folding. The results show that a neurotoxin protein containing four disulfide linkages can be displayed in the folded state. Furthermore, it can be refolded on a solid support that binds efficiently to its natural acetylcholine receptor. Probing the efficiency of the display proteins prepared by these methods provided up to 8-fold higher enrichment by the selective enrichment method compared with cDNA display alone, more than 10-fold higher binding to its receptor by the binding assays, and more than 10-fold higher affinities by affinity measurements. Cotranslational folding was found to have better efficiency than posttranslational refolding between the two investigated methods. We discuss the utilities of efficient display of such proteins in the preparation of superior quality proteins and protein libraries for directed evolution leading to ligand discovery.
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Affiliation(s)
- Mohammed Naimuddin
- Janusys Corporation, Saitama Industrial Technology Center, Skip City, Kawaguchi, Saitama 333-0844, Japan.
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82
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Wang W, Hara S, Liu M, Aigaki T, Shimizu S, Ito Y. Polypeptide aptamer selection using a stabilized ribosome display. J Biosci Bioeng 2011; 112:515-7. [PMID: 21813322 DOI: 10.1016/j.jbiosc.2011.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 12/01/2022]
Abstract
A newly developed ribosome display protocol was applied to the in vitro selection of polypeptide aptamers to small molecular weight chemicals, 6-[hydroxy(4-nitrobenzyl)phosphonyl]hexanoic acid and vitamin B12, chosen from a peptide library of random sequences. New peptide sequences binding to the targets were found after six rounds of this protocol.
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Affiliation(s)
- Wei Wang
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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83
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Kaltenbach M, Stein V, Hollfelder F. SNAP dendrimers: multivalent protein display on dendrimer-like DNA for directed evolution. Chembiochem 2011; 12:2208-16. [PMID: 21780273 DOI: 10.1002/cbic.201100240] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Indexed: 01/25/2023]
Abstract
Display systems connect a protein with the DNA encoding it. Such systems (e.g., phage or ribosome display) have found widespread application in the directed evolution of protein binders and constitute a key element of the biotechnological toolkit. In this proof-of-concept study we describe the construction of a system that allows the display of multiple copies of a protein of interest in order to take advantage of avidity effects during affinity panning. To this end, dendrimer-like DNA is used as a scaffold with docking points that can join the coding DNA with multiple protein copies. Each DNA construct is compartmentalised in water-in-oil emulsion droplets. The corresponding protein is expressed, in vitro, inside the droplets as a SNAP-tag fusion. The covalent bond between DNA and the SNAP-tag is created by reaction with dendrimer-bound benzylguanine (BG). The ability to form dendrimer-like DNA straightforwardly from oligonucleotides bearing BG allowed the comparison of a series of templates differing in size, valency and position of BG. In model selections the most efficient constructs show recoveries of up to 0.86 % and up to 400-fold enrichments. The comparison of mono- and multivalent constructs suggests that the avidity effect enhances enrichment by up to fivefold and recovery by up to 25-fold. Our data establish a multivalent format for SNAP-display based on dendrimer-like DNA as the first in vitro display system with defined tailor-made valencies and explore a new application for DNA nanostructures. These data suggest that multivalent SNAP dendrimers have the potential to facilitate the selection of protein binders especially during early rounds of directed evolution, allowing a larger diversity of candidate binders to be recovered.
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Affiliation(s)
- Miriam Kaltenbach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
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84
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Design and development of peptides and peptide mimetics as antagonists for therapeutic intervention. Future Med Chem 2011; 2:1813-22. [PMID: 21428804 DOI: 10.4155/fmc.10.259] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The concept of peptides as therapeutic agents has been historically disregarded by the pharmaceutical industry on account of their susceptibility to degradation, their size and consequent limitations in methods of delivery. Recently, however, there has been a surge of interest in peptides and their mimetics as potential antagonists for therapeutic intervention. This is in part due to the increased half-life and oral availability that has been achieved for a number of peptide-based systems, the introduction and acceptance of alternative delivery methods, and the prevalence of proteomics to identify countless protein-protein interaction targets. The use of peptides and molecules that mimic their function therefore has great potential to effectively target a range of proteins that are pathogenically implicated in numerous diseases.
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85
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Dübel S, Stoevesandt O, Taussig MJ, Hust M. Generating recombinant antibodies to the complete human proteome. Trends Biotechnol 2010; 28:333-9. [PMID: 20538360 DOI: 10.1016/j.tibtech.2010.05.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
In vitro antibody generation technologies have now been available for two decades. Research reagents prepared via phage display are becoming available and several recent studies have demonstrated that these technologies are now sufficiently advanced to facilitate generation of a comprehensive renewable resource of antibodies for any protein encoded by the approximately 22,500 human protein-coding genes. Antibody selection in vitro offers properties not available in animal-based antibody generation methods. By adjusting the biochemical milieu during selection, it is possible to control the antigen conformation recognized, the antibody affinity or unwanted cross-reactivity. For larger-scale antibody generation projects, the handling, transport and storage logistics and bacterial production offer cost benefits. Because the DNA sequence encoding the antibody is available, modifications, such as site-specific in vivo biotinylation and multimerization, are only a cloning step away. This opinion article summarizes opportunities for the generation of antibodies for proteome research using in vitro technologies.
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Affiliation(s)
- Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry and Biotechnology, D-38106 Braunschweig, Germany.
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86
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Eldridge B, Cooley RN, Odegrip R, McGregor DP, FitzGerald KJ, Ullman CG. An in vitro selection strategy for conferring protease resistance to ligand binding peptides. Protein Eng Des Sel 2009; 22:691-8. [DOI: 10.1093/protein/gzp052] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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87
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Oyston PCF, Fox MA, Richards SJ, Clark GC. Novel peptide therapeutics for treatment of infections. J Med Microbiol 2009; 58:977-987. [DOI: 10.1099/jmm.0.011122-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As antibiotic resistance increases worldwide, there is an increasing pressure to develop novel classes of antimicrobial compounds to fight infectious disease. Peptide therapeutics represent a novel class of therapeutic agents. Some, such as cationic antimicrobial peptides and peptidoglycan recognition proteins, have been identified from studies of innate immune effector mechanisms, while others are completely novel compounds generated in biological systems. Currently, only selected cationic antimicrobial peptides have been licensed, and only for topical applications. However, research using new approaches to identify novel antimicrobial peptide therapeutics, and new approaches to delivery and improving stability, will result in an increased range of peptide therapeutics available in the clinic for broader applications.
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Affiliation(s)
- P. C. F. Oyston
- Microbiology, Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - M. A. Fox
- Microbiology, Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - S. J. Richards
- Microbiology, Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - G. C. Clark
- Microbiology, Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
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88
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Stein V, Hollfelder F. An efficient method to assemble linear DNA templates for in vitro screening and selection systems. Nucleic Acids Res 2009; 37:e122. [PMID: 19617373 PMCID: PMC2764453 DOI: 10.1093/nar/gkp589] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A method is presented to assemble a gene of interest into a linear DNA template with all the components necessary for in vitro transcription and translation in ∼90 min. Assembly is achieved using a coupled uracil excision–ligation strategy based on USER Enzyme and T4 DNA ligase, which allows the simultaneous and seamless assembly of three different PCR products. The method is suitable for screening and selection systems of very high throughput as up to 1011 molecules can be efficiently assembled and purified in reaction volumes of 100 μl. The method is exemplified with the gene coding for a mutant version of O6-alkylguanine alkyltransferase, which is efficiently assembled with an N-terminal peptide tag and its 5′- and 3′-untranslated regions that include a T7 promoter, ribosome binding site and T7 terminator. The utility of the method is further corroborated by assembling error-prone PCR libraries and regenerating templates following model affinity selections. This fast and robust method should find widespread application in directed evolution for the assembly of gene libraries and the regeneration of linear DNA templates between successive screening and selection cycles.
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Affiliation(s)
- Viktor Stein
- Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
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89
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Grönwall C, Ståhl S. Engineered affinity proteins—Generation and applications. J Biotechnol 2009; 140:254-69. [DOI: 10.1016/j.jbiotec.2009.01.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 12/05/2008] [Accepted: 01/26/2009] [Indexed: 12/11/2022]
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90
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Osada E, Shimizu Y, Akbar BK, Kanamori T, Ueda T. Epitope Mapping Using Ribosome Display in a Reconstituted Cell-Free Protein Synthesis System. ACTA ACUST UNITED AC 2009; 145:693-700. [DOI: 10.1093/jb/mvp027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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91
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Reiersen H, Berntsen G, Stassar M, Cochlovius B. Screening human antibody libraries against carcinoma cells by affinity purification and polymerase chain reaction. J Immunol Methods 2008; 330:44-56. [DOI: 10.1016/j.jim.2007.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 09/26/2007] [Accepted: 10/25/2007] [Indexed: 11/16/2022]
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92
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Stein V, Sielaff I, Johnsson K, Hollfelder F. A Covalent Chemical Genotype–Phenotype Linkage for in vitro Protein Evolution. Chembiochem 2007; 8:2191-4. [DOI: 10.1002/cbic.200700459] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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93
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Löfblom J, Sandberg J, Wernérus H, Ståhl S. Evaluation of staphylococcal cell surface display and flow cytometry for postselectional characterization of affinity proteins in combinatorial protein engineering applications. Appl Environ Microbiol 2007; 73:6714-21. [PMID: 17873070 PMCID: PMC2074959 DOI: 10.1128/aem.01432-07] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
For efficient generation of high-affinity protein-based binding molecules, fast and reliable downstream characterization platforms are needed. In this work, we have explored the use of staphylococcal cell surface display together with flow cytometry for affinity characterization of candidate affibody molecules directly on the cell surface. A model system comprising three closely related affibody molecules with different affinities for immunoglobulin G and an albumin binding domain with affinity for human serum albumin was used to investigate advantages and differences compared to biosensor technology in a side-by-side manner. Equilibrium dissociation constant (K(D)) determinations as well as dissociation rate analysis were performed using both methods, and the results show that the on-cell determinations give both K(D) and dissociation rate values in a very fast and reproducible manner and that the relative affinities are very similar to the biosensor results. Interestingly, the results also show that there are differences between the absolute affinities determined with the two different technologies, and possible explanations for this are discussed. This work demonstrates the advantages of cell surface display for directed evolution of affinity proteins in terms of fast postselectional, on-cell characterization of candidate clones without the need for subcloning and subsequent protein expression and purification but also demonstrates that it is important to be aware that absolute affinities determined using different methods often vary substantially and that such comparisons therefore could be difficult.
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Affiliation(s)
- John Löfblom
- School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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94
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Blethrow JD, Tang C, Deng C, Krutchinsky AN. Modular mass spectrometric tool for analysis of composition and phosphorylation of protein complexes. PLoS One 2007; 2:e358. [PMID: 17406682 PMCID: PMC1832223 DOI: 10.1371/journal.pone.0000358] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 03/18/2007] [Indexed: 11/18/2022] Open
Abstract
The combination of high accuracy, sensitivity and speed of single and multiple-stage mass spectrometric analyses enables the collection of comprehensive sets of data containing detailed information about complex biological samples. To achieve these properties, we combined two high-performance matrix-assisted laser desorption ionization mass analyzers in one modular mass spectrometric tool, and applied this tool for dissecting the composition and post-translational modifications of protein complexes. As an example of this approach, we here present studies of the Saccharomyces cerevisiae anaphase-promoting complexes (APC) and elucidation of phosphorylation sites on its components. In general, the modular concept we describe could be useful for assembling mass spectrometers operating with both matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) ion sources into powerful mass spectrometric tools for the comprehensive analysis of complex biological samples.
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Affiliation(s)
- Justin D. Blethrow
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Chao Tang
- XProteo Inc, New York, New York, United States of America
| | - Changhui Deng
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Andrew N. Krutchinsky
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
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95
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Bertschinger J, Grabulovski D, Neri D. Selection of single domain binding proteins by covalent DNA display. Protein Eng Des Sel 2007; 20:57-68. [PMID: 17242027 DOI: 10.1093/protein/gzl055] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Selection technologies such as phage and ribosome display, which provide a physical linkage between genetic information and encoded polypeptide, are important tools for the engineering of proteins for diagnostic and therapeutic applications. We have recently described a selection strategy called covalent DNA display, in which individual proteins are covalently linked to the cognate encoding DNA template in separate droplets of a water-in-oil emulsion. We here report on the optimization of several experimental steps in covalent DNA display technology, such as the elution conditions and the PCR strategy used for the amplification of selected DNA templates. A PCR assembly strategy was developed, which allows the amplification of the DNA templates over repeated rounds of selection. In addition, we could demonstrate that approximately 50% of the DNA templates form a covalent adduct with the corresponding proteins in the compartments of a water-in-oil emulsion. In model selection experiments, differences in recovery efficiency <100 000 per round of selection could be observed when comparing a specific binding polypeptide with a binder of irrelevant specificity. Furthermore, the optimized protocol was successfully applied for the selection of single domain proteins, capable of specific binding to mouse serum albumin (MSA). A mutant derived from the SH3 domain of the Fyn kinase, with millimolar affinity to MSA, was affinity matured using covalent DNA display and yielded several MSA binding FynSH3 variants with dissociation constants in the 100 nM range.
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Affiliation(s)
- Julian Bertschinger
- Institute of Pharmaceutical Sciences, ETH Hönggerberg, Wolfgang-Pauli-Strasse 10, HCI G394, CH-8093 Zurich, Switzerland.
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96
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Ohashi H, Shimizu Y, Ying BW, Ueda T. Efficient protein selection based on ribosome display system with purified components. Biochem Biophys Res Commun 2006; 352:270-6. [PMID: 17113037 DOI: 10.1016/j.bbrc.2006.11.017] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 11/07/2006] [Indexed: 11/17/2022]
Abstract
Using the PURE (Protein synthesis Using Recombinant Elements) system, we developed an efficient and highly controllable ribosome display method for selection of functional protein. The PURE system is composed of purified factors and enzymes that are responsible for gene expression in Escherichia coli. We performed the detailed analyses and optimization of the ribosome display system and demonstrated the formation of stable mRNA/ribosome/polypeptide ternary complexes. As complex formation is fundamental to successful ribosome display, these improvements resulted in a dramatic increase in the mRNA recovery rate. As a result, a approximately 12,000-fold enrichment of single-chain antibody (scFv) cDNA was achieved in a single round of selection. Specific selection of scFv mRNA from a 1:10(10) dilution in competitor mRNA was achieved with only three rounds of affinity selection. These findings, together with the results in the accompanying paper [T. Matsuura, H. Yanagida, J. Ushioda, I. Urabe, T. Yomo, Nascent chain, RNA, and ribosome complexes generated by pure translation system (see the accompanying paper).], demonstrate that the PURE system can provide a basis for reliable and reproducible ribosome display.
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Affiliation(s)
- Hiroyuki Ohashi
- The Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB-401, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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Matsuura T, Yomo T. In vitro evolution of proteins. J Biosci Bioeng 2006; 101:449-56. [PMID: 16935245 DOI: 10.1263/jbb.101.449] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Accepted: 05/08/2006] [Indexed: 11/17/2022]
Abstract
Consecutive rounds of diversification and selection of the fittest is believed to be the main driving force for the evolution of life. For the evolution of life to proceed, all living cells are surrounded by a lipid bilayer that separates their own genes from the external environment and from those of other organisms. In this way, the genetic information of an individual is replicated on the basis of their phenotype; thus the enrichment of the fittest will occur. Hence, evolution is based on linkage between genotype and phenotype owing to the surrounding of the genetic material with a barrier. The linkage between genotype and phenotype is also known to be essential for the directed evolution of proteins. Indeed, systems for molecular evolution, including phage display, ribosome display, and in vitro compartmentalization, all satisfy this requirement in different ways. These systems have been shown to be powerful tools for high-throughput screening for the functions of proteins, screening as many as <10(12) molecules in 1 d. These selection systems in combination with various gene libraries yield proteins with improved or altered biophysical properties, and may even allow the generation of proteins with novel functions.
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Affiliation(s)
- Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Abstract
Display technologies are fundamental to the isolation of specific high-affinity binding proteins for diagnostic and therapeutic applications in cancer, neurodegenerative, and infectious diseases as well as autoimmune and inflammatory disorders. Applications extend into the broad field of antibody (Ab) engineering, synthetic enzymes, proteomics, and cell-free protein synthesis. Recently, in vitro display technologies have come to prominence due to the isolation of high-affinity human antibodies by phage display, the development of novel scaffolds for ribosome display, and the discovery of novel protein-protein interactions. In vitro display represents an emerging and innovative technology for the rapid isolation and evolution of high-affinity peptides and proteins. So far, only one clinical drug candidate produced by in vitro display technology has been approved by the FDA for use in humans, but several are in clinical or preclinical testing. This review highlights recent advances in various engineered biopharmaceutical products isolated by in vitro display with a focus on the commercial developments.
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Affiliation(s)
- Achim Rothe
- CSIRO Molecular and Health Technologies, Parkville, Victoria, Australia
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Abstract
Cell-free translation systems have developed significantly over the last two decades and improvements in yield have resulted in their use for protein production in the laboratory. These systems have protein engineering applications, such as the production of proteins containing unnatural amino acids and development of proteins exhibiting novel functions. Recently, it has been suggested that cell-free translation systems might be used as the fundamental basis for cell-like systems. We review recent progress in the field of cell-free translation systems and describe their use as tools for protein production and engineering.
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Affiliation(s)
- Yoshihiro Shimizu
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan
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Affiliation(s)
- John W Kehoe
- Biosciences Division, Argonne National Laboratory, Building 202, Argonne, Illinois 60439, USA
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