Dissecting Interfaces of Antibody -Antigen Complexes: from Ligand Specific Features to Binding Affinity Predictions

Abstract : Adaptive immunity is based on antigen-specific lymphocyte responses, with in particular B cells secreting seric immunoglobulins (IG) involved in the opsonization of bacteria and 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 interaction specificity. 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 of CDR with and without antigen, exhibiting a remarkably conserved pattern involving seven seams between CDR. We also show that this generic pattern exhibits specific properties as a function of the ligand type. Finally, we present binding affinity predictions of unprecedented accuracy, with a median absolute error of 1.02 kcal/mol. We anticipate that our findings will be of broad interest, not only in studying immune responses at the structural level, but also in bio-engineering and IG design, with IG used extensively in diagnostics and as well as therapeutic agents.
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[Research Report] RR-8770, Inria Sophia Antipolis. 2015, pp.61
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Simon Marillet, Marie-Paule Lefranc, Pierre Boudinot, Frédéric Cazals. Dissecting Interfaces of Antibody -Antigen Complexes: from Ligand Specific Features to Binding Affinity Predictions. [Research Report] RR-8770, Inria Sophia Antipolis. 2015, pp.61. 〈hal-01191462〉

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