Mapping of discontinuous conformational epitopes by amide hydrogen/deuterium exchange mass spectrometry and computational docking

• DOI: 10.1002/jmr.1169
• Publication Date: 2012-03-08T16:28:22Z
• Authors: Deepangi Pandit; Steven J. Tuske; Stephen J Coales; Sook Yen E; Anita Liu; Jessica E. Lee; Jeffrey A. Morrow; Jennifer F. Nemeth; Yoshitomo Hamuro
• Keywords: Models, Molecular; 0301 basic medicine; Interleukin-13; Surface Properties; Amino Acid Motifs; Interleukin-17; Molecular Sequence Data; Antibodies, Monoclonal; Cytochromes c; Deuterium Exchange Measurement; Hydrogen Bonding; Peptide Fragments; 03 medical and health sciences; Structural Homology, Protein; Humans; Computer Simulation; Amino Acid Sequence; Binding Sites, Antibody; Protein Structure, Quaternary; Antibodies, Immobilized; Epitope Mapping; Protein Binding

Understanding antigen–antibody interactions at the sub‐molecular level is of particular interest for scientific, regulatory, and intellectual property reasons, especially with increasing demand for monoclonal antibody therapeutic agents. Although various techniques are available for the determination of an epitope, there is no widely applicable, high‐resolution, and reliable method available. Here, a combination approach using amide hydrogen/deuterium exchange coupled with proteolysis and mass spectrometry (HDX‐MS) and computational docking was applied to investigate antigen–antibody interactions. HDX‐MS is a widely applicable, medium‐resolution, medium‐throughput technology that can be applied to epitope identification. First, the epitopes of cytochrome c–E8, IL‐13–CNTO607, and IL‐17A–CAT‐2200 interactions identified using the HDX‐MS method were compared with those identified by X‐ray co‐crystal structures. The identified epitopes are in good agreement with those identified using high‐resolution X‐ray crystallography. Second, the HDX‐MS data were used as constraints for computational docking. More specifically, the non‐epitope residues of an antigen identified using HDX‐MS were designated as binding ineligible during computational docking. This approach, termed HDX‐DOCK, gave more tightly clustered docking poses than stand‐alone docking for all antigen–antibody interactions examined and improved docking results significantly for the cytochrome c–E8 interaction. Copyright © 2012 John Wiley & Sons, Ltd.