Designing antibodies with precise specificity to antigens remains a primary challenge in biology and medicine. To uncover the structural principles governing antibody-antigen recognition in the complementarity determining regions (CDR), knob-socket (KS) analysis was applied to 1,004 antibody-antigen co-crystal structures. The KS analysis simplifies complex multi-body packing interactions into repetitive patterns of residue groups and allows the characterization of the packing motifs as well as their amino acid composition that contribute to binding specificity and affinity of an antibody with its antigen. CDRs are essentially coil conformations interacting at the quaternary structure level. However, CDR packing is quite different from tertiary coil packing in globular proteins, which is dominated by nonpolar residues such as leucine arranged in 3+1 knob-sockets, where 3 coil residues form a socket that packs another knob residue from another secondary structure . Antibody CDR packing favors polar residues—such as serine and tyrosine as well as glycine—and are predominantly packed in a 2+1+1 motif. In this case, a 3 residue socket on either the antibody or antigen consists of 2 residues from one secondary structure and a separate residue from another secondary structure packs a quaternary knob residue from the opposing domain. This difference emphasizes that antibody-antigen recognition is mediated by a unique mechanism and amino acid residue preferences to achieve binding specificity. Furthermore, categorization by CDR types (CDR1, CDR2, and CDR3) and chains (heavy vs. light) identifies the different contributions to antibody-antigen binding, where a majority of interactions are from the 3rd CDR. These findings provide a structural framework for understanding antibody recognition and specificity at the quaternary level that offers insights to guide rational antibody design and engineering for future therapeutic and diagnostic applications.
Thao et al. (Sun,) studied this question.