Abstract
Phage display (PD) is a powerful method and has been extensively used to generate monoclonal antibodies and identify epitopes, mimotopes, and protein interactions. More recently, the combination of next-generation sequencing (NGS) with PD (NGPD) has revolutionized the capabilities of the method by creating large data sets of sequences from affinity selection-based approaches (biopanning) otherwise challenging to obtain. NGPD can monitor motif enrichment, allow tracking of the selection process over consecutive rounds, and highlight unspecific binders. To tackle the wealth of data obtained, bioinformatics tools have been developed that allow for identifying specific binding sequences (binders) that can then be validated. Here, we provide a detailed account of the use of NGPD experiments to identify ubiquitin-specific protease peptide ligands.
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References
Mevissen TET, Komander D (2017) Mechanisms of deubiquitinase specificity and regulation. Annu Rev Biochem 86:159–192
Sowa ME, Bennett EJ, Gygi SP, Harper JW (2009) Defining the human deubiquitinating enzyme interaction landscape. Cell 138:389–403
Remenyi A, Good MC, Lim WA (2006) Docking interactions in protein kinase and phosphatase networks. Curr Opin Struct Biol 16:676–685
Pozhidaeva AK et al (2015) Structural characterization of interaction between human ubiquitin-specific protease 7 and immediate-early protein ICP0 of herpes simplex Virus-1. J Biol Chem 290:22907–22918
Zhang ZM et al (2015) An allosteric interaction links USP7 to Deubiquitination and chromatin targeting of UHRF1. Cell Rep 12:1400–1406
Cheng J et al (2015) Molecular mechanism for the substrate recognition of USP7. Protein Cell 6:849–852
Ngubane NA et al (2013) High-throughput sequencing enhanced phage display identifies peptides that bind mycobacteria. PLoS One 8:e77844
AC’t Hoen P et al (2012) Phage display screening without repetitious selection rounds. Anal Biochem 421:622–631
Spiliotopoulos A et al (2019) Discovery of peptide ligands targeting a specific ubiquitin-like domain-binding site in the deubiquitinase USP11. J Biol Chem 294:424–436
Fagerlund A, Myrset AH, Kulseth MA (2008) Construction and characterization of a 9-mer phage display pVIII-library with regulated peptide density. Appl Microbiol Biotechnol 80:925–936
Noren KA, Noren CJ (2001) Construction of high-complexity combinatorial phage display peptide libraries. Methods 23:169–178
Heinis C, Rutherford T, Freund S, Winter G (2009) Phage-encoded combinatorial chemical libraries based on bicyclic peptides. Nat Chem Biol 5:502–507
Tharp JM et al (2020) An amber obligate active site-directed ligand evolution technique for phage display. Nat Commun 11:1392
Qi H et al (2021) Antibody binding epitope mapping (AbMap) of hundred antibodies in a single run. Mol Cell Proteomics 20:100059
Ting JP et al (2018) Utilization of peptide phage display to investigate hotspots on IL-17A and what it means for drug discovery. PLoS One 13:e0190850
Cao J et al (2021) Phage-display based discovery and characterization of peptide ligands against WDR5. Molecules 26:1225
Gubeli RJ et al (2021) In vitro-evolved peptides bind monomeric actin and mimic actin-binding protein thymosin-beta4. ACS Chem Biol 16:820–828
Ashkenazy H et al (2021) Motifier: an IgOme profiler based on peptide motifs using machine learning. J Mol Biol 433:167071
Felici F, Castagnoli L, Musacchio A, Jappelli R, Cesareni G (1991) Selection of antibody ligands from a large library of oligopeptides expressed on a multivalent exposition vector. J Mol Biol 222:301–310
Shen W, Le S, Li Y, Hu F (2016) SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One 11:e0163962
FastX-Toolkit. http://hannonlab.cshl.edu/fastx_toolkit/
Dodt M, Roehr JT, Ahmed R, Dieterich C (2012) FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms. Biology (Basel) 1:895–905
Tange O (2011) GNU parallel - the command-line power tool. USENIX Mag 2011:32–47
Acknowledgments
This work was supported by the University of Nottingham and the Biotechnology and Biological Sciences Research Council (BBSRC) doctoral training studentships [grant number BB/M008770/1].
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Spiliotopoulos, A. et al. (2023). Next-Generation Phage Display to Identify Peptide Ligands of Deubiquitinases. In: Maupin-Furlow, J., Edelmann, M.J. (eds) Deubiquitinases. Methods in Molecular Biology, vol 2591. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2803-4_12
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DOI: https://doi.org/10.1007/978-1-0716-2803-4_12
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