Mapping the Epitope Interactions of Trastuzumab Via Plasma Induced Modification of Biomolecules (PLIMB)

Abstract

Epitope mapping is the process of identifying the site(s) of an antigen where an antibody binds. Knowledge of epitopes facilitates drug design and patent applications; hence it is a key element of vaccine and drug development. Hydroxyl radical protein footprinting coupled with mass spectrometry offers opportunities to map antibody-binding regions of antigens with greater simplicity and increased throughput over x-ray crystallography. We report here the use of hydroxyl radical protein footprinting via Plasma Induced Modification of Biomolecules (PLIMB) to characterize the epitopes of trastuzumab (Herceptin) bound to receptor tyrosine-protein kinase erbB-2 (HER2). The protein samples were exposed to plasma for hydroxyl radical labeling, the labeled sites were identified using mass spectrometry, and the data was analyzed using Byos (Protein Metrics). The PLIMB data is compared to previously published results that determined the epitope of trastuzumab using x-ray crystallography.