title: Mapping of discontinuous conformational epitopes by amide hydrogen/deuterium exchange mass spectrometry and computational docking.
abstract: 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.
authors.affiliation: ExSAR Corporation, Monmouth Junction, NJ 08852, USA.
authors.forename: Deepangi
authors.initials: D
authors.lastname: Pandit
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Tuske
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Coales
authors.forename: Sook Yen
authors.initials: SY
authors.lastname: E
authors.forename: Anita
authors.initials: A
authors.lastname: Liu
authors.forename: Jessica E
authors.initials: JE
authors.lastname: Lee
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Morrow
authors.forename: Jennifer F
authors.initials: JF
authors.lastname: Nemeth
authors.forename: Yoshitomo
authors.initials: Y
authors.lastname: Hamuro
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D055910:Antibodies, Immobilized / Q000737:chemistry*; D000911:Antibodies, Monoclonal / Q000737:chemistry*; D001666:Binding Sites, Antibody; D003198:Computer Simulation; D045304:Cytochromes c / Q000737:chemistry / Q000276:immunology; D041961:Deuterium Exchange Measurement; D018604:Epitope Mapping; D006801:Humans; D006860:Hydrogen Bonding; D018793:Interleukin-13 / Q000737:chemistry / Q000276:immunology; D020381:Interleukin-17 / Q000737:chemistry / Q000276:immunology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000302:isolation & purification; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D040681:Structural Homology, Protein; D013499:Surface Properties
chemical_list: D055910:Antibodies, Immobilized; D000911:Antibodies, Monoclonal; D018793:Interleukin-13; D020381:Interleukin-17; D010446:Peptide Fragments; D045304:Cytochromes c