Abstract
The Src Homology 2 (SH2) domain is an emerging biotechnology with applications in basic science, drug discovery, and even diagnostics. The SH2 domains rapid uptake into different areas of research is a direct result of the wealth of information generated on its biochemical, biological, and biophysical role in mammalian cell biology. Functionally, the SH2 domain binds and recognizes specific phosphotyrosine (pTyr) residues in the cell to mediate protein–protein interactions (PPIs) that govern signal transduction networks. These signal transduction networks are responsible for relaying growth and stress state signals to the cell’s nucleus, ultimately effecting a change in cell biology. Protein engineers have been able to increase the affinity of SH2 domains for pTyr while also tailoring the domains’ specificity to unique amino acid sequences flanking the pTyr residue. In this way, it has been possible to develop unique SH2 variants for use in affinity-purification coupled to mass spectrometry (AP-MS) experiments, microscopy, or even synthetic biology. This chapter outlines methods to tailor the affinity and specificity of virtually any human SH2 domain using a combination of rational engineering and phage-display approaches.
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Abbreviations
- PTM:
-
Posttranslational modification
- pTyr:
-
Phosphotyrosine
- SH2:
-
Src-Homology 2
References
Waksman G, Kominos D, Robertson SC et al (1992) Crystal structure of the phosphotyrosine recognition domain of SH2 of v-src complexed with tyrosine-phosphorylated peptides. Nature 358:646–653
Kaneko T, Huang H, Zhao B et al (2010) Loops govern SH2 domain specificity by controlling access to binding pockets. Sci Signal 3:ra34. https://doi.org/10.1126/scisignal.2000796
Hause RJ, Leung KK, Barkinge JL et al (2012) Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors. PLoS One 7:e44471. https://doi.org/10.1371/journal.pone.0044471
Haslam NJ, Shields DC (2012) Peptide-binding domains: are limp handshakes safest? Sci Signal 5:pe40. https://doi.org/10.1126/scisignal.2003372
Thibault P, Michnick SW, Kanshin E et al (2015) A cell-signaling network temporally resolves specific versus promiscuous phosphorylation. Cell Rep 10:1202–1214. https://doi.org/10.1016/j.celrep.2015.01.052
Liu BA, Engelmann BW, Nash PD (2012) The language of SH2 domain interactions defines phosphotyrosine-mediated signal transduction. FEBS Lett 586:2597–2605. https://doi.org/10.1016/j.febslet.2012.04.054
Lim WA, Pawson T (2010) Phosphotyrosine signaling: evolving a new cellular communication system. Cell 142:661–667. https://doi.org/10.1016/j.cell.2010.08.023.Phosphotyrosine
Li L, Tibiche C, Fu C et al (2012) The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. Genome Res 22:1222–1230. https://doi.org/10.1101/gr.128819.111
Doll S, Gnad F, Mann M (2019) The case for proteomics and phospho-proteomics in personalized cancer medicine. Proteomics Clin Appl 13:1800113. https://doi.org/10.1002/prca.201800113
Kaneko T, Huang H, Cao X et al (2012) Superbinder SH2 domains act as antagonists of cell signaling. Sci Signal 5:ra68. https://doi.org/10.1126/scisignal.2003021
Martyn GD, Veggiani G, Kusebauch U et al (2022) Engineered SH2 domains for targeted phosphoproteomics. ACS Chem Biol 17:1472–1484. https://doi.org/10.1021/acschembio.2c00051
Schneider M, Lane L, Boutet E et al (2009) The UniprotKB/Swiss-Prot knowledgebase and its plant proteome annotation program. J Proteome 72:567–573. https://doi.org/10.1016/j.jprot.2008.11.010.The
Papadopoulos JS, Agarwala R (2007) COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23:1073–1079. https://doi.org/10.1093/bioinformatics/btm076
Waterhouse AM, Procter JB, Martin DMA et al (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189–1191. https://doi.org/10.1093/bioinformatics/btp033
Burley SK, Berman HM, Bhikadiya C et al (2019) RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res 47:D464–D474. https://doi.org/10.1093/nar/gky1004
Schrodinger L, DeLano W (2020) PyMol. Retrieved from http://www.pymol.org/pymol
Liu BA, Ogiue-Ikeda M, Machida K (2017) Expression and production of SH2 domain proteins. In: SH2 domains: methods and protocols. Springer Nature, pp 117–162
Tinti M, Kiemer L, Costa S et al (2013) The SH2 domain interaction landscape. Cell Rep 3:1293–1305. https://doi.org/10.1016/j.celrep.2013.03.001.The
Jones RB, Gordus A, Krall JA, MacBeath G (2006) A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439:168–174. https://doi.org/10.1038/nature04177
Huang H, Li L, Wu C et al (2007) Defining the specificity space of the human Src homology 2 domain. Mol Cell Proteomics 7:768–784. https://doi.org/10.1074/mcp.M700312-MCP200
Veggiani G, Huang H, Yates BP et al (2019) Engineered SH2 domains with tailored specificities and enhanced affinities for phosphoproteome analysis. Protein Sci 28:403–413. https://doi.org/10.1002/pro.3551
Liu H, Huang H, Voss C et al (2019) Surface loops in a single SH2 domain are capable of encoding the spectrum of specificity of the SH2 family. Mol Cell Proteomics 18:372–382. https://doi.org/10.1074/mcp.RA118.001123
Kunkel TA (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A 82:488–492. https://doi.org/10.1073/pnas.82.2.488
Tonikian R, Zhang Y, Boone C, Sidhu SS (2007) Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat Protoc 2:1368–1386. https://doi.org/10.1038/nprot.2007.151
Huang H, Kaneko T, Sidhu SS, Li SSC (2017) Creation of phosphotyrosine superbinders by directed evolution of an SH2 domain. In: Machida K, Liu BA (eds) SH2 domains methods and protocols, 1555th edn. Springer Nature, New York, pp 225–254
Hu J, Hubbard SR (2005) Structural characterization of a novel Cbl phosphotyrosine recognition motif in the APS family of adapter proteins. J Biol Chem 280:18943–18949. https://doi.org/10.1074/jbc.M414157200
Ng C, Jackson RA, Buschdorf JP et al (2008) Structural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates. EMBO J 27:804–816. https://doi.org/10.1038/emboj.2008.18
Stein A, Aloy P (2008) Contextual specificity in peptide-mediated protein interactions. PLoS One 3:e2524. https://doi.org/10.1371/journal.pone.0002524
Wagner MJ, Stacey MM, Liu BA, Pawson T (2013) Molecular mechanisms of SH2- and PTB-domain-containing proteins in receptor tyrosine kinase signaling. Cold Spring Harb Perspect Biol 5. https://doi.org/10.1101/cshperspect.a008987
Nuttall SD, Walsh RB (2008) Display scaffolds: protein engineering for novel therapeutics. Curr Opin Pharmacol 8:609–615. https://doi.org/10.1016/j.coph.2008.06.007
Bostrom J, Lee CV, Haber L, Fuh G (2009) Improving antibody binding affinity and specificity for therapeutic development. In: Therapeutic antibodies: methods and protocols. Springer, pp 353–376
Hattori T, Koide S (2019) Next-generation antibodies for post-translational modifications. Curr Opin Struct Biol 51:141–148. https://doi.org/10.1016/j.sbi.2018.04.006.Next-generation
Machida K, Liu BA (2017) SH2 domains: methods and protocols. In: Methods in molecular biology, 1555th edn. Springer Nature, New York, pp 1–546
Bian Y, Li L, Dong M et al (2016) Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder. Nat Chem Biol 12:959–966. https://doi.org/10.1038/nchembio.2178
Tong J, Cao B, Martyn GD et al (2017) Protein-phosphotyrosine proteome profiling by superbinder-SH2 domain affinity purification mass spectrometry, sSH2-AP-MS. Proteomics 17:1600360. https://doi.org/10.1002/pmic.201600360
Freeman J, Kriston-vizi J, Seed B, Ketteler R (2012) A high-content imaging workflow to study Grb2 signaling complexes by expression cloning. J Vis Exp 68:e4382. https://doi.org/10.3791/4382
Noguchi T, Ishiba H, Honda K et al (2017) Synthesis of Grb2 SH2 domain proteins for mirror-image screening systems. Bioconjug Chem 28:609–619. https://doi.org/10.1021/acs.bioconjchem.6b00692
Sun J, Lei L, Tsai CM et al (2017) Engineered proteins with sensing and activating modules for automated reprogramming of cellular functions. Nat Commun 8:477. https://doi.org/10.1038/s41467-017-00569-6
Findlay GM, Smith MJ, Lanner F et al (2013) Interaction domains of Sos1/Grb2 are finely tuned for cooperative control of embryonic stem cell fate. Cell 152:1008–1020. https://doi.org/10.1016/j.cell.2013.01.056
Barnea G, Strapps W, Herrada G et al (2008) The genetic design of signaling cascades to record receptor activation. PNAS 105:64–69
Farrell MV, Nunez AC, Yang Z et al (2022) Protein-PAINT: Superresolution microscopy with signaling proteins. Sci Signal 15:eabg9782
The Uniprot Consortium, Bateman A (2019) UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 47:D506–D515. https://doi.org/10.1093/nar/gky1049
Silva D, Santos G, Barroca M, Collins T (2017) Inverse PCR for point mutation introduction. In: Methods in molecular biology. Springer, pp 87–100
Fujimoto K, Fukuda T, Marumoto R (1988) Expression and secretion of human epidermal growth factor by Escherichia coli using enterotoxin signal sequences. J Biotechnol 8:77–86
Thie H, Schirrmann T, Paschke M et al (2008) SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli. New Biotechnol 25:49–54. https://doi.org/10.1016/j.nbt.2008.01.001
Lawrie J, Niu W, Guo J (2019) Engineering of a sulfotyrosine-recognizing small protein scaffold for the study of protein tyrosine O-sulfation. In: Methods in enzymology. Elsevier, pp 67–89
Warner HR, Duncan BK, Garrett C, Neuhard J (1981) Synthesis and metabolism of uracil-containing deoxyribonucleic acid in Escherichia coli. J Bacteriol 145:687–695. https://doi.org/10.1128/jb.145.2.687-695.1981
Sidhu SS, Lowman HB, Cunningham BC, Wells JA (2000) Phage display for selection of novel binding peptides. Methods Enzymol 328:333–363
Ju T, Niu W, Guo J (2016) Evolution of Src homology 2 (SH2) domain to recognize sulfotyrosine. ACS Chem Biol 11:2551–2557. https://doi.org/10.1021/acschembio.6b00555
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Martyn, G.D., Veggiani, G., Sidhu, S.S. (2023). Engineering SH2 Domains with Tailored Specificities and Affinities. In: Carlomagno, T., Köhn, M. (eds) SH2 Domains. Methods in Molecular Biology, vol 2705. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3393-9_17
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