1
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Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins. Sci Rep 2023; 13:1339. [PMID: 36693880 PMCID: PMC9873692 DOI: 10.1038/s41598-023-27710-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approach to select the ensemble of folded proteins from an initial library. The thermostable CheY protein from Thermotoga maritima was chosen as scaffold. Four loops of CheY were diversified to create a new binding surface. The subset of the library giving rise to folded proteins was first selected using a natural protein partner of the template scaffold. Then, a gene shuffling approach based on a single restriction enzyme was used to recombine DNA sequences encoding these filtrated variants. Taken together, the filtration strategy and the shuffling of the filtrated sequences were shown to enrich the library in folded and stable sequences while maintaining a large diversity in the final library (Lib-Cheytins 2.1). Binders of the Oplophorus luciferase Kaz domain were then selected by phage display from the final library, showing affinities in the μM range. One of the best variants induced a loss of 92% of luminescent activity, suggesting that this Cheytin preferentially binds to the Kaz active site.
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2
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Phage Displayed Domain Antibodies (dAb) for Detection of Allergenic Pistachio Proteins in Foods. Foods 2020; 9:foods9091230. [PMID: 32899286 PMCID: PMC7554873 DOI: 10.3390/foods9091230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 11/16/2022] Open
Abstract
Pistachio nuts (Pistacia vera) have been consumed by past and present-day civilizations because of their organoleptic characteristics and potential health benefits. However, they can also produce moderate to severe IgE-mediated reactions in allergic individuals. In this work, we report the isolation of the first recombinant antibodies against pistachio nut, produced without animal immunization, to be used in immunoassays for detection of allergenic pistachio in food products. Several phage display biopanning strategies were evaluated to screen the human-based domain antibody library (dAb) in search for pistachio-specific probes. The clone producing the PVF4 phage-dAb was finally selected, and it does not cross-react with cashew despite the phylogenetic proximity with pistachio. Western blot and matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-TOF/TOF) analysis demonstrated that this clone recognised a unique band of ∼22 kDa related to the basic subunit of pistachio 11S globulin (allergen Pis v 2). The PVF4 phage-dAb allowed detection of pistachio in a food matrix with a limit of detection (LOD) of 3983 mg kg−1 in an indirect phage-enzyme-linked immunosorbent assay (ELISA). The ELISA method developed was used to assess applicability of the PVF4 phage-dAb for analysis of 77 commercial food products.
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3
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Sui Z, Liu M, Wang W, Chen H, Wang G, An R, Liang X, Komiyama M. Efficient Preparation of Large-Sized Rings of Single-Stranded DNA through One-Pot Ligation of Multiple Fragments. Chem Asian J 2019; 14:3251-3254. [PMID: 31400067 DOI: 10.1002/asia.201900963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/07/2019] [Indexed: 12/26/2022]
Abstract
Circular single-stranded DNA (c-ssDNA) has significant applications in DNA detection, the development of nucleic acid medicine, and DNA nanotechnology because it shows highly unique features in mobility, dynamics, and topology. However, in most cases, the efficiency of c-ssDNA preparation is very low because polymeric byproducts are easily formed due to intermolecular reaction. Herein, we report a one-pot ligation method to efficiently prepare large c-ssDNA. By ligating several short fragments of linear single-stranded DNA (l-ssDNA) in one-pot by using T4 DNA ligase, longer l-ssDNAs intermediates are formed and then rapidly consumed by the cyclization. Since the intramolecular cyclization reaction is much faster than intermolecular polymerization, the formation of polymeric products is suppressed and the dominance of intramolecular cyclization is promoted. With this simple approach, large-sized single-stranded c-ssDNAs (e.g., 200-nt) were successfully synthesized in high selectivity and yield.
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Affiliation(s)
- Zhe Sui
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Mengqing Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Weinan Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
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4
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Henry KA, Kim DY, Kandalaft H, Lowden MJ, Yang Q, Schrag JD, Hussack G, MacKenzie CR, Tanha J. Stability-Diversity Tradeoffs Impose Fundamental Constraints on Selection of Synthetic Human V H/V L Single-Domain Antibodies from In Vitro Display Libraries. Front Immunol 2017; 8:1759. [PMID: 29375542 PMCID: PMC5763143 DOI: 10.3389/fimmu.2017.01759] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/27/2017] [Indexed: 11/18/2022] Open
Abstract
Human autonomous VH/VL single-domain antibodies (sdAbs) are attractive therapeutic molecules, but often suffer from suboptimal stability, solubility and affinity for cognate antigens. Most commonly, human sdAbs have been isolated from in vitro display libraries constructed via synthetic randomization of rearranged VH/VL domains. Here, we describe the design and characterization of three novel human VH/VL sdAb libraries through a process of: (i) exhaustive biophysical characterization of 20 potential VH/VL sdAb library scaffolds, including assessment of expression yield, aggregation resistance, thermostability and tolerance to complementarity-determining region (CDR) substitutions; (ii) in vitro randomization of the CDRs of three VH/VL sdAb scaffolds, with tailored amino acid representation designed to promote solubility and expressibility; and (iii) systematic benchmarking of the three VH/VL libraries by panning against five model antigens. We isolated ≥1 antigen-specific human sdAb against four of five targets (13 VHs and 7 VLs in total); these were predominantly monomeric, had antigen-binding affinities ranging from 5 nM to 12 µM (average: 2–3 µM), but had highly variable expression yields (range: 0.1–19 mg/L). Despite our efforts to identify the most stable VH/VL scaffolds, selection of antigen-specific binders from these libraries was unpredictable (overall success rate for all library-target screens: ~53%) with a high attrition rate of sdAbs exhibiting false positive binding by ELISA. By analyzing VH/VL sdAb library sequence composition following selection for monomeric antibody expression (binding to protein A/L followed by amplification in bacterial cells), we found that some VH/VL sdAbs had marked growth advantages over others, and that the amino acid composition of the CDRs of this set of sdAbs was dramatically restricted (bias toward Asp and His and away from aromatic and hydrophobic residues). Thus, CDR sequence clearly dramatically impacts the stability of human autonomous VH/VL immunoglobulin domain folds, and sequence-stability tradeoffs must be taken into account during the design of such libraries.
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Affiliation(s)
- Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Dae Young Kim
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Hiba Kandalaft
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Michael J Lowden
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Qingling Yang
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Joseph D Schrag
- Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - C Roger MacKenzie
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.,School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.,School of Environmental Sciences, University of Guelph, Guelph, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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5
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Kim DY, Hussack G, Kandalaft H, Tanha J. Mutational approaches to improve the biophysical properties of human single-domain antibodies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1983-2001. [DOI: 10.1016/j.bbapap.2014.07.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/05/2014] [Accepted: 07/11/2014] [Indexed: 01/06/2023]
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6
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Nishi M, Jian N, Yamamoto K, Seto H, Nishida Y, Tonoyama Y, Shimizu N, Nishi Y. Ligation-based assembly for constructing mouse synthetic scFv libraries by chain shuffling with in vivo-amplified VH and VL fragments. J Immunol Methods 2014; 412:53-69. [PMID: 25010461 DOI: 10.1016/j.jim.2014.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/26/2014] [Accepted: 06/25/2014] [Indexed: 11/24/2022]
Abstract
In vitro assembly of two or three PCR fragments using primers is a common method of constructing scFv fragments for display on the surface of phage. However, mismatch annealing often occurs during in this step, leading to cloning and display of incomplete Fab or scFv fragments. To overcome this limitation, we developed a ligation-based two-fragment assembly (LTFA) protocol that involved separately cloning VH and Vκ fragments into the high-copy-number plasmid pUC18. The VH and Vκ fragments had randomized complementarity-determining region 3 (CDR3) and were joined with a peptidyl linker composed of (G4S)3. Using this approach, complete sequences of scFv fragments were successfully constructed, and the sequencing of 83 scFv clones revealed that none of the sequences, including the linker region, contained deletions or mutations. In contrast, linker sequences generated using a conventional two-fragment PCR assembly (TFPA) protocol often contained sequence anomalies, including large truncations. Using the LTFA protocol, a final library size of 1.0×10(8)cfu was achieved. Examination of the amino acid profiles of the generated scFv fragments within the randomized regions introduced using degenerate codons did not detect any bias from that expected based on stochastic distribution. After several cycles of panning with this library, antigen-specific scFvs against two reference antigens, hen egg lysozyme and streptavidin were detected. In addition, scFvs with specificity against peptidyl antigens in the loop region of the Medaka ortholog of human C6orf89, which encodes a histone deacetylase enhancer that interacts with the bombesin receptor, were also obtained. The LTFA protocol developed here is robust and allows for the easy construction of integral scFv fragments compared with conventional TFPA. Utilizing LTFA, other CDRs can be readily combined. This approach also allows for the in vitro maturation of scFv fragments by separately introducing randomization in CDRs or using error-prone PCR for the amplification of pre-selected sequences as a template scaffold.
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Affiliation(s)
- Michiru Nishi
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho Nagaham, Shiga 526-0829, Japan
| | - Nan Jian
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho Nagaham, Shiga 526-0829, Japan
| | - Keiko Yamamoto
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho Nagaham, Shiga 526-0829, Japan
| | - Haruyo Seto
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho Nagaham, Shiga 526-0829, Japan
| | - Yuichi Nishida
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho Nagaham, Shiga 526-0829, Japan
| | - Yasuhiro Tonoyama
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho Nagaham, Shiga 526-0829, Japan; Advanced Research Center for Genome Super Power, Keio University, 2 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Nobuyoshi Shimizu
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho Nagaham, Shiga 526-0829, Japan; Advanced Research Center for Genome Super Power, Keio University, 2 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Yoshisuke Nishi
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho Nagaham, Shiga 526-0829, Japan.
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7
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Shahsavarian MA, Le Minoux D, Matti KM, Kaveri S, Lacroix-Desmazes S, Boquet D, Friboulet A, Avalle B, Padiolleau-Lefèvre S. Exploitation of rolling circle amplification for the construction of large phage-display antibody libraries. J Immunol Methods 2014; 407:26-34. [PMID: 24681277 DOI: 10.1016/j.jim.2014.03.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/06/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Phage display antibody libraries have proven to have a significant role in the discovery of therapeutic antibodies and polypeptides with desired biological and physicochemical properties. Obtaining a large and diverse phage display antibody library, however, is always a challenging task. Various steps of this technique can still undergo optimization in order to obtain an efficient library. In the construction of a single chain fragment variable (scFv) phage display library, the cloning of the scFv fragments into a phagemid vector is of crucial importance. An efficient restriction enzyme digestion of the scFv DNA leads to its proper ligation with the phagemid followed by its successful cloning and expression. Here, we are reporting a different approach to enhance the efficiency of the restriction enzyme digestion step. We have exploited rolling circle amplification (RCA) to produce a long strand of DNA with tandem repeats of scFv sequences, which is found to be highly susceptible to restriction digestion. With this important modification, we are able to construct a large phage display antibody library of naive SJL/J mice. The size of the library is estimated as ~10(8) clones. The number of clones containing a scFv fragment is estimated at 90%. Hence, the present results could considerably aid the utilization of the phage-display technique in order to get an efficiently large antibody library.
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Affiliation(s)
- Melody A Shahsavarian
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, CS 60319, 60203 Compiègne, France
| | - Damien Le Minoux
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, CS 60319, 60203 Compiègne, France
| | - Kalyankumar M Matti
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, CS 60319, 60203 Compiègne, France
| | - Srini Kaveri
- Centre de Recherche des Cordeliers, Université Pierre et Marie Curie-Paris6, UMR S 872, Paris F-75006, France; Université Paris Descartes, UMR 872, Paris F-75006, France; INSERM, UMR 872, Paris F-75006, France; International Associated Laboratory IMPACT, Institut National de la Santé et de la Recherche Médicale-France and Indian Council of Medical Research-India, National Institute of Immunohaemotology, Mumbai, India
| | - Sébastien Lacroix-Desmazes
- Centre de Recherche des Cordeliers, Université Pierre et Marie Curie-Paris6, UMR S 872, Paris F-75006, France; Université Paris Descartes, UMR 872, Paris F-75006, France; INSERM, UMR 872, Paris F-75006, France; International Associated Laboratory IMPACT, Institut National de la Santé et de la Recherche Médicale-France and Indian Council of Medical Research-India, National Institute of Immunohaemotology, Mumbai, India
| | - Didier Boquet
- Laboratoire d'Ingénierie des Anticorps pour la Santé (LIAS), iBiTecS, SPI, Commissariat à l'Energie Atomique, 91191 Gif sur Yvette, France
| | - Alain Friboulet
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, CS 60319, 60203 Compiègne, France
| | - Bérangère Avalle
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, CS 60319, 60203 Compiègne, France
| | - Séverine Padiolleau-Lefèvre
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, CS 60319, 60203 Compiègne, France.
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8
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Esteban O, Christ D, Stock D. Purification of molecular machines and nanomotors using phage-derived monoclonal antibody fragments. Methods Mol Biol 2013; 996:203-17. [PMID: 23504426 DOI: 10.1007/978-1-62703-354-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Molecular machines and nanomotors are sophisticated biological assemblies that convert potential energy stored either in transmembrane ion gradients or in ATP into kinetic energy. Studying these highly dynamic biological devices by X-ray crystallography is challenging, as they are difficult to produce, purify, and crystallize. Phage display technology allows us to put a handle on these molecules in the form of highly specific antibody fragments that can also stabilize conformations and allow versatile labelling for electron microscopy, immunohistochemistry, and biophysics experiments.Here, we describe a widely applicable protocol for selecting high-affinity monoclonal antibody fragments against a complex molecular machine, the A-type ATPase from T. thermophilus that allows fast and simple purification of this transmembrane rotary motor from its wild-type source. The approach can be readily extended to other integral membrane proteins and protein complexes as well as to soluble molecular machines and nanomotors.
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Affiliation(s)
- Olga Esteban
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza, Spain
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9
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Phage display antibodies for diagnostic applications. Biologicals 2013; 41:209-16. [DOI: 10.1016/j.biologicals.2013.04.001] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/29/2013] [Accepted: 04/02/2013] [Indexed: 11/23/2022] Open
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10
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Reverdatto S, Rai V, Xue J, Burz DS, Schmidt AM, Shekhtman A. Combinatorial library of improved peptide aptamers, CLIPs to inhibit RAGE signal transduction in mammalian cells. PLoS One 2013; 8:e65180. [PMID: 23785412 PMCID: PMC3681763 DOI: 10.1371/journal.pone.0065180] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/23/2013] [Indexed: 01/28/2023] Open
Abstract
Peptide aptamers are small proteins containing a randomized peptide sequence embedded into a stable protein scaffold, such as Thioredoxin. We developed a robust method for building a Combinatorial Library of Improved Peptide aptamers (CLIPs) of high complexity, containing ≥3×1010 independent clones, to be used as a molecular tool in the study of biological pathways. The Thioredoxin scaffold was modified to increase solubility and eliminate aggregation of the peptide aptamers. The CLIPs was used in a yeast two-hybrid screen to identify peptide aptamers that bind to various domains of the Receptor for Advanced Glycation End products (RAGE). NMR spectroscopy was used to identify interaction surfaces between the peptide aptamers and RAGE domains. Cellular functional assays revealed that in addition to directly interfering with known binding sites, peptide aptamer binding distal to ligand sites also inhibits RAGE ligand-induced signal transduction. This finding underscores the potential of using CLIPs to select allosteric inhibitors of biological targets.
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Affiliation(s)
- Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - Vivek Rai
- Langone Medical Center, New York University, New York, New York, United States of America
| | - Jing Xue
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - David S. Burz
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - Ann Marie Schmidt
- Langone Medical Center, New York University, New York, New York, United States of America
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
- * E-mail:
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11
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Dudgeon K, Rouet R, Christ D. Rapid prediction of expression and refolding yields using phage display. Protein Eng Des Sel 2013; 26:671-4. [DOI: 10.1093/protein/gzt019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Dudgeon K, Rouet R, Famm K, Christ D. Selection of human VH single domains with improved biophysical properties by phage display. Methods Mol Biol 2012; 911:383-97. [PMID: 22886264 DOI: 10.1007/978-1-61779-968-6_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Human antibody variable heavy (VH) domains tend to display poor biophysical properties when expressed in isolation. Consequently, the domains are often characterized by low expression levels, high levels of aggregation, and increased "stickiness." Here, we describe methods that allow the engineering of human VH domains with improved biophysical properties by phage display. The engineered domains withstand challenging conditions, such as high temperature and acidic pH. Engineered human single domains are a promising new class of antibody fragments and represent robust research tools and building blocks for the generation of antibody therapeutics.
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Affiliation(s)
- Kip Dudgeon
- Garvan Institute of Medical Research, Darlinghurst/Sydney, NSW, Australia
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13
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General strategy for the generation of human antibody variable domains with increased aggregation resistance. Proc Natl Acad Sci U S A 2012; 109:10879-84. [PMID: 22745168 DOI: 10.1073/pnas.1202866109] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The availability of stable human antibody reagents would be of considerable advantage for research, diagnostic, and therapeutic applications. Unfortunately, antibody variable heavy and light domains (V(H) and V(L)) that mediate the interaction with antigen have the propensity to aggregate. Increasing their aggregation resistance in a general manner has proven to be a difficult and persistent problem, due to the high level of sequence diversity observed in human variable domains and the requirement to maintain antigen binding. Here we outline such an approach. By using phage display we identified specific positions that clustered in the antigen binding site (28, 30-33, 35 in V(H) and 24, 49-53, 56 in V(L)). Introduction of aspartate or glutamate at these positions endowed superior biophysical properties (non-aggregating, well-expressed, and heat-refoldable) onto domains derived from common human germline families (V(H)3 and V(κ)1). The effects of the mutations were highly positional and independent of sequence diversity at other positions. Moreover, crystal structures of mutant V(H) and V(L) domains revealed a surprising degree of structural conservation, indicating compatibility with V(H)/V(L) pairing and antigen binding. This allowed the retrofitting of existing binders, as highlighted by the development of robust high affinity antibody fragments derived from the breast cancer therapeutic Herceptin. Our results provide a general strategy for the generation of human antibody variable domains with increased aggregation resistance.
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14
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Rouet R, Dudgeon K, Christ D. Generation of human single domain antibody repertoires by Kunkel mutagenesis. Methods Mol Biol 2012; 907:195-209. [PMID: 22907352 DOI: 10.1007/978-1-61779-974-7_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Human antibody single domains are a promising new class of antibody fragments. Here we describe methods for the cloning of human V(H) and V(L) genes into phage and phagemid vectors. Furthermore, we provide detailed protocols for the generation of single domain antibody libraries by Kunkel mutagenesis and the analysis of diversity by DNA sequencing and superantigen binding.
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Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Darlinghurst/Sydney, NSW, Australia
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15
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Enhanced error-prone RCA mutagenesis by concatemer resolution. Plasmid 2011; 66:47-51. [DOI: 10.1016/j.plasmid.2011.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 03/21/2011] [Accepted: 03/24/2011] [Indexed: 11/20/2022]
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16
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Lowe D, Dudgeon K, Rouet R, Schofield P, Jermutus L, Christ D. Aggregation, stability, and formulation of human antibody therapeutics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2011; 84:41-61. [DOI: 10.1016/b978-0-12-386483-3.00004-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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17
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Urvoas A, Guellouz A, Valerio-Lepiniec M, Graille M, Durand D, Desravines DC, van Tilbeurgh H, Desmadril M, Minard P. Design, Production and Molecular Structure of a New Family of Artificial Alpha-helicoidal Repeat Proteins (αRep) Based on Thermostable HEAT-like Repeats. J Mol Biol 2010; 404:307-27. [DOI: 10.1016/j.jmb.2010.09.048] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 09/15/2010] [Accepted: 09/21/2010] [Indexed: 01/07/2023]
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18
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Lee CMY, McGuire H, Basten A, King C, Christ D. Expression, purification and characterization of recombinant interleukin-21. J Immunol Methods 2010; 362:185-9. [PMID: 20800065 DOI: 10.1016/j.jim.2010.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 06/28/2010] [Accepted: 08/17/2010] [Indexed: 10/19/2022]
Abstract
Interleukin-21 (IL-21) is a key regulator of the immune system. However, studies of this cytokine have so far been hampered by the limited availability of recombinant protein preparations. Here we describe a method based on refolding of inclusion bodies expressed in E. coli by rapid dilution. The method was applied to human and murine IL-21 proteins, which were further purified by affinity chromatography and gel-filtration. The proteins are pure and highly active as determined by endotoxin and cell proliferation assays. The availability of milligram quantities of protein enabled us to generate monoclonal antibody fragments against the cytokine and will aid in further structural, biochemical and physiological analyses.
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Affiliation(s)
- Carol M Y Lee
- Garvan Institute of Medical Research, Darlinghurst/Sydney, Australia
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Protein-protein interactions and selection: generation of molecule-binding proteins on the basis of tertiary structural information. FEBS J 2010; 277:2006-14. [PMID: 20412054 DOI: 10.1111/j.1742-4658.2010.07627.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Antibodies and their fragments are attractive binding proteins because their high binding strength is generated by several hypervariable loop regions, and because high-quality libraries can be prepared from the vast gene clusters expressed by mammalian lymphocytes. Recent explorations of new genome sequences and protein structures have revealed various small, nonantibody scaffold proteins. Accurate structural descriptions of protein-protein interactions based on X-ray and NMR analyses allow us to generate binding proteins by using grafting and library techniques. Here, we review approaches for generating binding proteins from small scaffold proteins on the basis of tertiary structural information. Identification of binding sites from visualized tertiary structures supports the transfer of function by peptide grafting. The local library approach is advantageous as a go-between technique for grafted foreign peptide sequences and small scaffold proteins. The identification of binding sites also supports the construction of efficient libraries with a low probability of denatured variants, and, in combination with the design for library diversity, opens the way to increasing library density and randomized sequence lengths without decreasing density. Detailed tertiary structural analyses of protein-protein complexes allow accurate description of epitope locations to enable the design of and screening for multispecific, high-affinity proteins recognizing multiple epitopes in target molecules.
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An Y, Wu W, Lv A. A PCR-after-ligation method for cloning of multiple DNA inserts. Anal Biochem 2010; 402:203-5. [PMID: 20363207 DOI: 10.1016/j.ab.2010.03.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 03/29/2010] [Accepted: 03/30/2010] [Indexed: 11/25/2022]
Abstract
Here we present a novel and simple PCR-after-ligation method for efficient assembly of multiple DNA inserts. After initial ligation of multiple inserts and vector, the ligation mixture is used as template for a PCR using a pair of primers flanking the cloning sites on the vector. The fragment with correct size is gel purified and inserted into the vector by conventional two-way ligation. With this method, a recombinant plasmid containing four DNA inserts was correctly constructed. As a control, all of the constructs obtained directly from DNA ligation were found to be self-ligation of the vector.
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Affiliation(s)
- Yingfeng An
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, People's Republic of China
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21
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Cell-free cloning using multiply-primed rolling circle amplification with modified RNA primers. Biotechniques 2009; 47:609-15. [PMID: 19594445 DOI: 10.2144/000113155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The predominant method for DNA cloning is by propagation in biological hosts, but this method has limitations because certain sequences are difficult to clone using any combination of available hosts or vectors. Recently, multiply-primed rolling circle amplification (MPRCA) has been applied to overcome the problems of the DNA cloning via host cells. However, when MPRCA is used to amplify from minute quantities of DNA template, the products are mostly by-product DNA molecules generated by false priming and primer dimer formation. This study demonstrates that MPRCA using random RNA primers[#x02014]instead of DNA primers[#x02014]blocked the synthesis of by-products and succeeded in amplifying one copy of a circular DNA molecule more than 1012-fold to give microgram quantities of amplification product without using submicroliter reaction volumes. Furthermore, a ligation strategy was elaborated to circularize only the desired DNA sequence and eliminate undesired ligation-products. A combination of these methods was able to amplify and ligate a large construct without undesired DNA sequences and at microgram quantities within one day. Therefore, these methods have the possibility to improve DNA cloning techniques that have been restricted by the limitations of PCR methods or by the host cell.
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Arbabi-Ghahroudi M, MacKenzie R, Tanha J. Selection of non-aggregating VH binders from synthetic VH phage-display libraries. Methods Mol Biol 2009; 525:187-216, xiii. [PMID: 19252860 DOI: 10.1007/978-1-59745-554-1_10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The particular interest in VH antibody fragments stems from the fact that they can rival their "naturally occurring" single-domain antibody (sdAb) counterparts (camelid VHHs and shark VNARs) with regard to such desirable characteristics as stability, solubility, expression, and ability to penetrate cryptic epitopes and outperform them in terms of less immunogenicity, a much valued property in human immunotherapy applications. However, human VHs are typically prone to aggregation. Various approaches for developing non-aggregating human VHs with binding specificities have relied on a combination of recombinant DNA technology and phage-display technology. VH gene libraries are constructed synthetically by randomizing the CDRs of a single VH scaffold fused to a gene encoding a phage coat protein. Recombinant phage expressing the resulting VH libraries in fusion with the pIII protein is propagated in Escherichia coli. Monoclonal phage displaying VHs with specificities for target antigens are isolated from the libraries by a process called panning. The exertion of stability pressure in addition to binding pressure during panning ensures that the isolated VH binders are also non-aggregating. The genes encoding the desired VHs selected from the libraries are packaged within the phage particles, linking genotype and phenotype, hence making possible the identification of the selected VHs through identifying its physically linked genotype. Here, we describe the application of recombinant DNA and phage-display technologies for the construction of a phage-displayed human VH library, the panning of the library against a protein, and the expression, purification, and characterization of non-aggregating VHs isolated by panning.
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Affiliation(s)
- Mehdi Arbabi-Ghahroudi
- National Research Council of Canada, Institute for Biological Sciences, Ottawa, Ontario, Canada
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Dudgeon K, Famm K, Christ D. Sequence determinants of protein aggregation in human VH domains. Protein Eng Des Sel 2008; 22:217-20. [DOI: 10.1093/protein/gzn059] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lee CMY, Iorno N, Sierro F, Christ D. Selection of human antibody fragments by phage display. Nat Protoc 2007; 2:3001-8. [DOI: 10.1038/nprot.2007.448] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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