Abstract
Adaptive immunity is based on antigen-specific lymphocyte responses, with inparticular B cells secreting seric immunoglobulins (IG) involved in the opsonization of bacteriaand the neutralization of viruses. At the heart of these mechanisms is the formation of IG -Ag complexes, which challenge our understanding in terms of binding affinity and interactionspecificity.In this work, we dissect the interfaces of IG - Ag complexes with high resolution crystal structures,making a stride towards a better understanding of binding affinity and interaction specificity. First,we present global interface statistics clearly distinguishing ligand types (proteins, peptides, chem-ical compounds), and stressing the role of side chains. Second, we analyze the relative positions ofCDR with and without antigen, exhibiting a remarkably conserved pattern involving seven seamsbetween CDR. We also show that this generic pattern exhibits specific properties as a function ofthe ligand type. Finally, we present binding affinity predictions of unprecedented accuracy, with amedian absolute error of 1.02 kcal/mol.We anticipate that our findings will be of broad interest, not only in studying immune responsesat the structural level, but also in bio-engineering and IG design, with IG used extensively indiagnostics and as well as therapeutic agents.