Determination of Protein Monoclonal-Antibody Epitopes by a Combination of Structural Proteomics Methods

Structural proteomics techniques are useful for the determinationof protein interaction interfaces. Each technique provides orthogonalstructural information on the structure and the location of proteininteraction sites. Here, we have characterized a monoclonal antibodyepitope for a protein antigen by a combination of differential photoreactivesurface modification (SM), cross-linking (CL), differential hydrogen-deuteriumexchange (HDX), and epitope extraction/excision. We found that experimentaldata from different approaches agree with each other in determiningthe epitope of the monoclonal antibody on the protein antigens usingthe HIV-1 p24-mAb E complex as an illustrative example. A combinationof these multiple structural proteomics approaches results in a detailedpicture of the interaction of the proteins and increases confidencein the determination of the final structure of the protein interactioninterface. Data are available via ProteomeXchange with identifierPXD040902.