Abstract
Protein–protein interactions are essential to cellular functions and signaling pathways. We recently combined bioinformatics and custom oligonucleotide arrays to construct custom-made peptide-phage libraries for screening peptide–protein interactions, an approach we call proteomic peptide-phage display (ProP-PD). In this chapter, we describe protocols for phage display for the identification of natural peptide binders for a given protein. We finally describe deep sequencing for the analysis of the proteomic peptide-phage display.
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References
Stumpf MPH, Thorne T, De Silva E et al (2008) Estimating the size of the human interactome. Proc Natl Acad Sci U S A 105:6959–6964
Davey NE, Van Roey K, Weatheritt RJ et al (2012) Attributes of short linear motifs. Mol BioSyst 8:268–281
Chene P (2004) Inhibition of the p53-MDM2 interaction: targeting a protein–protein interface. Mol Cancer Res 2:20–28
Kang MH, Reynolds CP (2009) Bcl-2 inhibitors: targeting mitochondrial apoptotic pathways in cancer therapy. Clin Cancer Res 15:1126–1132
Liu M, Li C, Pazgier M et al (2010) D-peptide inhibitors of the p53-MDM2 interaction for targeted molecular therapy of malignant neoplasms. Proc Natl Acad Sci USA 107:14321–14326
Shangary S, Wang S (2009) Small-molecule inhibitors of the MDM2-p53 protein–protein interaction to reactivate p53 function: a novel approach for cancer therapy. Annu Rev Pharmacol Toxicol 49:223–241
Ivarsson Y, Arnold R, Mclaughlin M et al (2014) Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes. Proc Natl Acad Sci U S A 111:2542–2547
Arkin MR, Wells JA (2004) Small-molecule inhibitors of protein–protein interactions: progressing towards the dream. Nat Rev Drug Discov 3:301–317
Davey NE, Travé G, Gibson TJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36:159–169
Bork P, Jensen LJ, Von Mering C et al (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol 14:292–299
Ryan DP, Matthews JM (2005) Protein–protein interactions in human disease. Curr Opin Struct Biol 15:441–446
Kosuri S, Church GM (2014) Large-scale de novo DNA synthesis: technologies and applications. Nat Methods 11:499–507
Larman HB, Zhao Z, Laserson U et al (2011) Autoantigen discovery with a synthetic human peptidome. Nat Biotechnol 29:535–541
Caruthers MH, Beaucage SL, Becker C et al (1983) Deoxyoligonucleotide synthesis via the phosphoramidite method. Gene Amplif Anal 3:1–26
Caruthers MH (1985) Gene synthesis machines: DNA chemistry and its uses. Science 230:281–285
Caruthers MH, Barone AD, Beaucage SL et al (1987) Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method. Methods Enzymol 154:287–313
Kosuri S, Eroshenko N, Leproust EM et al (2010) Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol 28:1295–1299
Matzas M, Stahler PF, Kefer N et al (2010) High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol 28:1291–1294
Mclaughlin ME, Sidhu SS (2013) Chapter fifteen - engineering and analysis of peptide-recognition domain specificities by phage display and deep sequencing. In: Amy EK (ed) Method enzymol. Academic, London, pp 327–349
Fuh G, Pisabarro MT, Li Y et al (2000) Analysis of PDZ domain-ligand interactions using carboxyl-terminal phage display. J Biol Chem 275:21486–21491
Held HA, Sidhu SS (2004) Comprehensive mutational analysis of the M13 major coat protein: improved scaffolds for C-terminal phage display. J Mol Biol 340:587–597
Malik P, Terry TD, Gowda LR et al (1996) Role of capsid structure and membrane protein processing in determining the size and copy number of peptides displayed on the major coat protein of filamentous bacteriophage. J Mol Biol 260:9–21
Tonikian R, Zhang Y, Boone C et al (2007) Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat Protoc 2:1368–1386
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Seo, MH., Nim, S., Jeon, J., Kim, P.M. (2017). Large-Scale Interaction Profiling of Protein Domains Through Proteomic Peptide-Phage Display Using Custom Peptidomes. In: Uttamchandani, M., Yao, S. (eds) Small Molecule Microarrays. Methods in Molecular Biology, vol 1518. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6584-7_14
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DOI: https://doi.org/10.1007/978-1-4939-6584-7_14
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