Antibody epitope mapping at single residue resolution for unpurified antigens

Abstract

Abstract The vast majority of antigen-antibody interactions rely upon binding to conformational epitopes, which are composed of amino acids that are discontinuous in the protein sequence but are brought together upon three-dimensional protein folding. This character has made conformational epitopes particularly difficult to map because they are only formed in the native structure of the antigen protein. X-ray crystallography is a gold-standard method for mapping conformational epitopes at high-resolution, but it only works for highly purified antigens and is time consuming, and is not applicable when crystals of antigen-antibody complex are unavailable. Here we present a novel middle-down HDX-MS technology with subzero temperature separation that effectively tackles these limitations. It successfully mapped the conformational epitopes in a VPF growth factor targeted by a therapeutic antibody, in a complex protein mixture where the antigen content is as low as 10%. It provided single amino acid resolution by online gas-phase fragmentation on the LC-MS time scale. It also uses directly the whole antibody, pre-digestion of the antibody to Fab fragments is no longer needed. In conclusion, the subzero temperature separation based HDX-MS technology represents an alternative high-resolution epitope mapping approach to X-ray crystallography, and is also a fast and cost-effective solution for new antibody and vaccine development. Its potential in paratope mapping, as well as epitope mapping for other difficult targets and bispecific antibodies will be discussed.