Canonical Structure Repertoire of the Antigen-binding Site of Immunoglobulins Suggests Strong Geometrical Restrictions Associated to the Mechanism of Immune Recognition

Abstract

Is the structural repertoire of immunoglobulins free to adopt an almost infinite number of conformations to build the diversity of the immune response or does it take advantage of only a few conformations? In this paper we study this question by applying the canonical structure model to characterize the structural repertoire of immunoglobulins. The results found, indicate that only ten combinations out of the 300 possible different canonical structure classes (combinations of canonical structures), make up 87% of 381 sequences analyzed. This suggests that the structural repertoire of immunoglobulins is restricted to the preferential use of a small number of canonical structure classes. The possible functional significance of these results was studied by analyzing the correspondence between the observed canonical structural repertoire implicit in Ig sequences and the types of antigens recognized. Two different sets of canonical structure classes were distinguished: one with preference for some specific types of antigens like proteins, polysaccharides or haptens, and the other with multi-specific binding capabilities. Analysis of antibodies of known three-dimensional structure shows that for two specific classes, the canonical conformations of H2 and L1 determine the geometrical characteristics of the antigen-binding site, while at least in one multi-specific class, the changes in the general geometry of the antigen-binding site are produced by different conformations of H3. Implications of these results for the molecular recognition process mediated by immunoglobulins are discussed.