Exploring the intricacies of antigen-antibody interfaces: Effects of binding-induced conformational changes and...

Antibodies are cornerstone molecules in immunity and biotechnology. Understanding the structural basis of specific antigen-antibody recognition is pivotal for informed antibody engineering and affinity optimization. However, the functional significance of binding-induced conformational changes, the principles governing binding interface organization, and the relationship between interface features and affinity remain incompletely understood. Here, we uncover the structural logic underlying antigen-antibody binding through integrated, multilevel analyses of large-scale structural datasets. Quantitative analyses reveal that binding-induced conformational rearrangements, although subtle, are functionally directed adjustments that refine interfacial complementarity. At the ensemble level, these adjustments significantly enhance electrostatic complementarity, whereas the optimization of geometric fit becomes evident upon stratification, revealing context-specific modes of refinement across different interface-area regimes. While the heavy chain typically dominates the binding, the total interface area is the more reliable correlate of affinity, with light and heavy chains contributing similarly by expanding the binding interface. Further analysis reveals the preferences of individual CDRs for specific interaction types. We also define six distinct interaction fingerprints of antigen-antibody binding, highlighting area-efficient and area-inefficient complexes with signature interaction profiles. Collectively, these findings delineate the mechanistic landscape of antigen-antibody binding and offer a roadmap for rational antibody engineering.