title: Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties.
abstract: Protein-peptide interactions are a common occurrence and essential for numerous cellular processes, and frequently explored in broad applications within biology, medicine, and proteomics. Therefore, understanding the molecular mechanism(s) of protein-peptide recognition, specificity, and binding interactions will be essential. In this study, we report the first detailed analysis of antibody-peptide interaction characteristics, by combining large-scale experimental peptide binding data with the structural analysis of eight human recombinant antibodies and numerous peptides, targeting tryptic mammalian and eukaryote proteomes. The results consistently revealed that promiscuous peptide-binding interactions, that is, both specific and degenerate binding, were exhibited by all antibodies, and the discovery was corroborated by orthogonal data, indicating that this might be a general phenomenon for low-affinity antibody-peptide interactions. The molecular mechanism for the degenerate peptide-binding specificity appeared to be executed through the use of 2-3 semi-conserved anchor residues in the C-terminal part of the peptides, in analogue to the mechanism utilized by the major histocompatibility complex-peptide complexes. In the long-term, this knowledge will be instrumental for advancing our fundamental understanding of protein-peptide interactions, as well as for designing, generating, and applying peptide specific antibodies, or peptide-binding proteins in general, in various biotechnical and medical applications.
authors.affiliation: Department of Immunotechnology, Lund University, Lund, Sweden.
authors.forename: Niclas
authors.initials: N
authors.lastname: Olsson
authors.forename: Stefan
authors.initials: S
authors.lastname: Wallin
authors.forename: Peter
authors.initials: P
authors.lastname: James
authors.forename: Carl A K
authors.initials: CA
authors.lastname: Borrebaeck
authors.forename: Christer
authors.initials: C
authors.lastname: Wingren
mesh_terms: D000595:Amino Acid Sequence; D000918:Antibody Specificity; D000939:Epitopes / Q000737:chemistry / Q000276:immunology*; D006801:Humans; D013058:Mass Spectrometry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000276:immunology*; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000276:immunology; D057127:Single-Chain Antibodies / Q000737:chemistry* / Q000276:immunology*
chemical_list: D000939:Epitopes; D010455:Peptides; D011994:Recombinant Proteins; D057127:Single-Chain Antibodies