Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing

Caitlin A. Kowalsky, Matthew S. Faber, Aritro Nath, Hailey E. Dann, Vince W. Kelly, Li Liu, Purva Shanker, Ellen K. Wagner, Jennifer A. Maynard, Christina Chan, Timothy A. Whitehead

Research output: Contribution to journalArticlepeer-review

59 Scopus citations


Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Herewe show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. Inall threecases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps canbe prepared at a rate of four per day.

Original languageEnglish (US)
Pages (from-to)26457-26470
Number of pages14
JournalJournal of Biological Chemistry
Issue number44
StatePublished - Oct 30 2015

Bibliographical note

Publisher Copyright:
© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.


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