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Updated: Sep 17, 2025

Protein Engineering by Yeast Surface Display
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Epitope Mapping Using Yeast Display and Next Generation Sequencing.

Thomas Van Blarcom1, Andrea Rossi1, Davide Foletti1,2

  • 1Rinat, Pfizer Inc., South San Francisco, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 2, 2025
PubMed
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This summary is machine-generated.

We developed a rapid method to precisely map antibody binding sites, or epitopes. This technique uses yeast display and DNA sequencing to identify critical residues for antibody-antigen interactions, aiding therapeutic protein development.

Area of Science:

  • Biochemistry
  • Immunology
  • Protein Engineering

Background:

  • Monoclonal antibodies are key therapeutic proteins due to high affinity and specificity for antigens.
  • Precisely determining antibody epitopes is crucial for understanding therapeutic mechanisms and distinguishing antibodies.
  • Current epitope mapping methods can be time-consuming and lack efficiency for multiple antibodies.

Purpose of the Study:

  • To develop and validate a novel, efficient, and parallel method for precise epitope mapping of multiple antibodies.
  • To gain quantitative insights into the critical residues involved in antibody-antigen interactions.
  • To demonstrate the method's utility by mapping epitopes of antibodies neutralizing Staphylococcus aureus alpha toxin.

Main Methods:

  • A combination of rational library design and yeast surface display was employed.
Keywords:
Alpha toxinAntibodyAntigenEpitope mappingFACSLibrary designNext-generation sequencingStaphylococcus aureusYeast display

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  • Next-generation DNA sequencing was utilized for high-throughput analysis.
  • The method enables parallel mapping of multiple antibody epitopes within weeks.

    • Main Results:

    • The described method precisely and efficiently maps antibody epitopes in parallel.
    • Quantitative data on critical epitope residues for antibody-antigen binding is provided.
    • The approach was successfully applied to map epitopes of antibodies targeting Staphylococcus aureus alpha toxin.

    Conclusions:

    • This novel method offers a significant advancement in epitope mapping efficiency and precision.
    • The technique provides valuable insights for antibody engineering and therapeutic development.
    • The approach is broadly applicable for characterizing antibody-antigen interactions across various targets.