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. 2025:2937:81-109.
doi: 10.1007/978-1-0716-4591-8_5.

Epitope Mapping Using Yeast Display and Next Generation Sequencing

Thomas Van Blarcom  1 , Andrea Rossi  1 , Davide Foletti  1   2 , Purnima Sundar  1 , Steven Pitts  1   2 , Zea Melton  1 , Dilduz Telman  1 , Lora Zhao  1 , Wai Ling Cheung  1   3 , Jan Berka  1   4 , Wenwu Zhai  1   5 , Pavel Strop  1   6 , Jaume Pons  1   7 , Arvind Rajpal  1   6 , Javier Chaparro-Riggers  8
Affiliations

Epitope Mapping Using Yeast Display and Next Generation Sequencing

Thomas Van Blarcom et al. Methods Mol Biol. 2025.

Abstract

Monoclonal antibodies are the largest class of therapeutic proteins due in part to their ability to bind an antigen with a high degree of affinity and specificity. A precise determination of their epitope is important for gaining insight into their therapeutic mechanism of action and to help differentiate antibodies that bind the same antigen. Here we describe a method to precisely and efficiently map the epitopes of multiple antibodies in parallel over the course of just several weeks. This approach is based on a combination of rational library design, yeast surface display, and next-generation DNA sequencing and provides quantitative insight into the epitope residues most critical for the antibody-antigen interaction. As an example, we will use this method to map the epitopes of several antibodies that neutralize alpha toxin from Staphylococcus aureus.

Keywords: Alpha toxin; Antibody; Antigen; Epitope mapping; FACS; Library design; Next-generation sequencing; Staphylococcus aureus; Yeast display.

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References

    1. Chao G, Cochran JR, Wittrup KD (2004) Fine epitope mapping of anti-epidermal growth factor receptor antibodies through random mutagenesis and yeast surface display. J Mol Biol 342(2):539–550. https://doi.org/10.1016/j.jmb.2004.07.053 - DOI - PubMed
    1. Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A (2004) A structural perspective on protein-protein interactions. Curr Opin Struct Biol 14(3):313–324. https://doi.org/10.1016/j.sbi.2004.04.006 - DOI - PubMed
    1. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velazquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dotsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A (2012) A method for integrative structure determination of protein-protein complexes. Bioinformatics 28(24):3282–3289. https://doi.org/10.1093/bioinformatics/bts628 - DOI - PubMed - PMC
    1. Abdiche YN, Miles A, Eckman J, Foletti D, Van Blarcom TJ, Yeung YA, Pons J, Rajpal A (2014) High-throughput epitope binning assays on label-free array-based biosensors can yield exquisite epitope discrimination that facilitates the selection of monoclonal antibodies with functional activity. PLoS One 9(3):e92451. https://doi.org/10.1371/journal.pone.0092451 - DOI - PubMed - PMC
    1. Jin L, Fendly BM, Wells JA (1992) High resolution functional analysis of antibody-antigen interactions. J Mol Biol 226(3):851–865 - DOI - PubMed

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