Identification of differences in the specificity-determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires

Abstract

Studies of antibodies of known three-dimensional structure have revealed that insertion and deletion of amino acids at the hypervariable loops change the canonical structures, thus generating differences in the antigen-binding site topography. Such differences determine the size of the antigen with which the antibody interacts. Here, 59 unique antibodies determined at a resolution of 3.0 A or below, including 19 in complex with proteins, 18 with peptides and 22 with haptens, were analyzed to identify and characterize differences in the residues that are directly involved in the interaction with antigen, so-called specificity-determining residues (SDRs). It was found that antibodies use a similar number of SDRs to recognize proteins and peptides but contact haptens with five SDRs less. By using a score of SDR usage, differences in the location of the SDRs, depending on the type of antigen recognized, were then identified with precision. An analysis of the surface generated by the SDRs usage indicates that the differences found correlate well with the size of the antigen. Anti-protein antibodies have the largest SDR surface, with SDRs of high usage located in the edge of the surface. The SDR surface of anti-hapten antibodies is the smallest, with hot spots of contacts in the interior of the binding surface and buried in the V(L):V(H) interface. The SDR surface of anti-peptide antibodies has a size in between anti-protein and anti-hapten antibodies, with the SDRs of high usage located in the interior of the antigen-binding site but do not buried as in anti-hapten antibodies. These findings led to a fine-tuning of the model correlating differences in the antigen-binding site topography with its preference to recognize antigens of different size. Therefore, it is discussed how this knowledge should help to design antibody repertoires biased toward the recognition of antigens of predefined size.