Suppressing allostery in epitope mapping experiments using millisecond hydrogen / deuterium exchange mass spectrometry

Localization of the interface between the candidate antibody and its antigen target, commonly known as epitope mapping, is a critical component of the development of therapeutic monoclonal antibodies. With the recent availability of commercial automated systems, hydrogen / deuterium eXchange (HDX) is rapidly becoming the tool for mapping epitopes preferred by researchers in both industry and academia. However, this approach has a significant drawback in that it can be confounded by ‘allosteric’ structural and dynamic changes that result from the interaction, but occur far from the point(s) of contact. Here, we introduce a ‘kinetic’ millisecond HDX workflow that suppresses allosteric effects in epitope mapping experiments. The approach employs a previously introduced microfluidic apparatus that enables millisecond HDX labeling times with on-chip pepsin digestion and electrospray ionization. The ‘kinetic’ workflow also differs from conventional HDX-based epitope mapping in that the antibody is introduced to the antigen at the onset of HDX labeling. Using myoglobin / anti-myoglobin as a model system, we demonstrate that at short ‘kinetic’ workflow labeling times (i.e., 200 ms), the HDX signal is already fully developed at the ‘true’ epitope, but is still largely below the significance threshold at allosteric sites. Identification of the ‘true’ epitope is supported by computational docking predictions and allostery modeling using the rigidity transmission allostery algorithm.