Abstract
Yeast surface display is a powerful protein engineering technology that is extensively used to improve various properties of proteins, including affinity, specificity, and stability or even to add novel functions (usually ligand binding). Apart from its robustness and versatility as an engineering tool, yeast display offers a further critical advantage: Once the selection campaign is finished, usually resulting in an oligoclonal pool, these enriched protein variants can be analyzed individually on the surface of yeast without the need for any sub-cloning, soluble expression, and purification. Here, we provide detailed protocols for determining both the affinity and the thermal stability of yeast displayed proteins. In addition, we discuss the advantages, challenges, and potential pitfalls associated with affinity and stability analysis using yeast surface display.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Cherf GM, Cochran JR (2015) Applications of yeast surface display for protein engineering. Methods Mol Biol 1319:155–175. https://doi.org/10.1007/978-1-4939-2748-7_8
Boder ET, Wittrup KD (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15:553–557. https://doi.org/10.1038/nbt0697-553
Pepper LR, Cho YK, Boder ET, Shusta EV (2008) A decade of yeast surface display technology: where are we now? Comb Chem High Throughput Screen 11(2):127–134. https://doi.org/10.2174/138620708783744516
Angelini A, Chen TF, de Picciotto S, Yang NJ, Tzeng A, Santos MS, Van Deventer JA, Traxlmayr MW, Wittrup KD (2015) Protein engineering and selection using yeast surface display. Methods Mol Biol 1319:3–36. https://doi.org/10.1007/978-1-4939-2748-7_1
Decanniere K, Transue TR, Desmyter A, Maes D, Muyldermans S, Wyns L (2001) Degenerate interfaces in antigen-antibody complexes. J Mol Biol 313(3):473–478. https://doi.org/10.1006/jmbi.2001.5075
Gai SA, Wittrup KD (2007) Yeast surface display for protein engineering and characterization. Curr Opin Struct Biol 17(4):467–473. https://doi.org/10.1016/j.sbi.2007.08.012
Lipovsek D, Antipov E, Armstrong KA, Olsen MJ, Klibanov AM, Tidor B, Wittrup KD (2007) Selection of horseradish peroxidase variants with enhanced enantioselectivity by yeast surface display. Chem Biol 14(10):1176–1185. https://doi.org/10.1016/j.chembiol.2007.09.008
Traxlmayr MW, Faissner M, Stadlmayr G, Hasenhindl C, Antes B, Ruker F, Obinger C (2012) Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast. Biochim Biophys Acta 1824(4):542–549. https://doi.org/10.1016/j.bbapap.2012.01.006
Traxlmayr MW, Obinger C (2012) Directed evolution of proteins for increased stability and expression using yeast display. Arch Biochem Biophys 526(2):174–180. https://doi.org/10.1016/j.abb.2012.04.022
Traxlmayr MW, Kiefer JD, Srinivas RR, Lobner E, Tisdale AW, Mehta NK, Yang NJ, Tidor B, Wittrup KD (2016) Strong enrichment of aromatic residues in binding sites from a charge-neutralized hyperthermostable Sso7d scaffold library. J Biol Chem 291(43):22496–22508. https://doi.org/10.1074/jbc.M116.741314
Zajc CU, Dobersberger M, Schaffner I, Mlynek G, Puhringer D, Salzer B, Djinovic-Carugo K, Steinberger P, De Sousa LA, Yang NJ, Obinger C, Holter W, Traxlmayr MW, Lehner M (2020) A conformation-specific ON-switch for controlling CAR T cells with an orally available drug. Proc Natl Acad Sci U S A 117(26):14926–14935. https://doi.org/10.1073/pnas.1911154117
Kauke MJ, Traxlmayr MW, Parker JA, Kiefer JD, Knihtila R, McGee J, Verdine G, Mattos C, Wittrup KD (2017) An engineered protein antagonist of K-Ras/B-Raf interaction. Sci Rep 7(1):5831. https://doi.org/10.1038/s41598-017-05889-7
Koide A, Gilbreth RN, Esaki K, Tereshko V, Koide S (2007) High-affinity single-domain binding proteins with a binary-code interface. Proc Natl Acad Sci U S A 104(16):6632–6637. https://doi.org/10.1073/pnas.0700149104
Lipovsek D, Lippow SM, Hackel BJ, Gregson MW, Cheng P, Kapila A, Wittrup KD (2007) Evolution of an interloop disulfide bond in high-affinity antibody mimics based on fibronectin type III domain and selected by yeast surface display: molecular convergence with single-domain camelid and shark antibodies. J Mol Biol 368(4):1024–1041. https://doi.org/10.1016/j.jmb.2007.02.029
Razai A, Garcia-Rodriguez C, Lou J, Geren IN, Forsyth CM, Robles Y, Tsai R, Smith TJ, Smith LA, Siegel RW, Feldhaus M, Marks JD (2005) Molecular evolution of antibody affinity for sensitive detection of botulinum neurotoxin type A. J Mol Biol 351(1):158–169. https://doi.org/10.1016/j.jmb.2005.06.003
Boder ET, Midelfort KS, Wittrup KD (2000) Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci U S A 97(20):10701–10705. https://doi.org/10.1073/pnas.170297297
Midelfort KS, Wittrup KD (2006) Context-dependent mutations predominate in an engineered high-affinity single chain antibody fragment. Protein Sci 15(2):324–334. https://doi.org/10.1110/ps.051842406
Uchanski T, Zogg T, Yin J, Yuan D, Wohlkonig A, Fischer B, Rosenbaum DM, Kobilka BK, Pardon E, Steyaert J (2019) An improved yeast surface display platform for the screening of nanobody immune libraries. Sci Rep 9(1):382. https://doi.org/10.1038/s41598-018-37212-3
Akiba H, Tamura H, Kiyoshi M, Yanaka S, Sugase K, Caaveiro JMM, Tsumoto K (2019) Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep 9(1):15481. https://doi.org/10.1038/s41598-019-50722-y
De Genst E, Silence K, Decanniere K, Conrath K, Loris R, Kinne J, Muyldermans S, Wyns L (2006) Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies. Proc Natl Acad Sci U S A 103(12):4586–4591. https://doi.org/10.1073/pnas.0505379103
Chao G, Lau WL, Hackel BJ, Sazinsky SL, Lippow SM, Wittrup KD (2006) Isolating and engineering human antibodies using yeast surface display. Nat Protoc 1(2):755–768. https://doi.org/10.1038/nprot.2006.94
Hunter SA, Cochran JR (2016) Cell-binding assays for determining the affinity of protein-protein interactions: technologies and considerations. Methods Enzymol 580:21–44. https://doi.org/10.1016/bs.mie.2016.05.002
Julian MC, Lee CC, Tiller KE, Rabia LA, Day EK, Schick AJ III, Tessier PM (2015) Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies. Protein Eng Des Sel 28(10):339–350. https://doi.org/10.1093/protein/gzv050
Julian MC, Li L, Garde S, Wilen R, Tessier PM (2017) Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability. Sci Rep 7:45259. https://doi.org/10.1038/srep45259
Teufl M, Zajc CU, Traxlmayr MW (2022) Engineering Strategies to Overcome the Stability−Function Trade-2 Off in Proteins. ACS Synth Biol. https://doi.org/10.1021/acssynbio.1c00512
Hackel BJ, Ackerman ME, Howland SW, Wittrup KD (2010) Stability and CDR composition biases enrich binder functionality landscapes. J Mol Biol 401(1):84–96. https://doi.org/10.1016/j.jmb.2010.06.004
Hasenhindl C, Traxlmayr MW, Wozniak-Knopp G, Jones PC, Stadlmayr G, Rüker F, Obinger C (2013) Stability assessment on a library scale: a rapid method for the evaluation of the commutability and insertion of residues in C-terminal loops of the CH3 domains of IgG1-Fc. Protein Eng Des Sel 26(10):675–682. https://doi.org/10.1093/protein/gzt041
Ahmad S, Kamal MZ, Sankaranarayanan R, Rao NM (2008) Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight. J Mol Biol 381(2):324–340. https://doi.org/10.1016/j.jmb.2008.05.063
Orr BA, Carr LM, Wittrup KD, Roy EJ, Kranz DM (2003) Rapid method for measuring ScFv thermal stability by yeast surface display. Biotechnol Prog 19(2):631–638. https://doi.org/10.1021/bp0200797
Gera N, Hussain M, Rao BM (2013) Protein selection using yeast surface display. Methods 60(1):15–26. https://doi.org/10.1016/j.ymeth.2012.03.014
Boder ET, Wittrup KD (1998) Optimal screening of surface-displayed polypeptide libraries. Biotechnol Prog 14(1):55–62. https://doi.org/10.1021/bp970144q
Laurent E, Sieber A, Salzer B, Wachernig A, Seigner J, Lehner M, Geyeregger R, Kratzer B, Jager U, Kunert R, Pickl WF, Traxlmayr MW (2021) Directed evolution of stabilized monomeric CD19 for monovalent CAR interaction studies and monitoring of CAR-T cell patients. ACS Synth Biol 10(5):1184–1198. https://doi.org/10.1021/acssynbio.1c00010
Acknowledgments
This work was supported by the Austrian Science Fund (FWF Project W1224—Doctoral Program on Biomolecular Technology of Proteins—BioToP) and by the Federal Ministry for Digital and Economic Affairs of Austria and the National Foundation for Research, Technology and Development of Austria to the Christian Doppler Research Association (Christian Doppler Laboratory for Next Generation CAR T Cells).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
1 Electronic Supplementary Material
Supplemental Excel Sheet 1
(XLSX 219Â kb)
Supplemental Excel Sheet 2
(XLSX 195Â kb)
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Zajc, C.U., Teufl, M., Traxlmayr, M.W. (2022). Affinity and Stability Analysis of Yeast Displayed Proteins. In: Traxlmayr, M.W. (eds) Yeast Surface Display. Methods in Molecular Biology, vol 2491. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2285-8_9
Download citation
DOI: https://doi.org/10.1007/978-1-0716-2285-8_9
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-2284-1
Online ISBN: 978-1-0716-2285-8
eBook Packages: Springer Protocols