J. Mol. Biol. (1995) 254, 497–504 Canonical Structure Repertoire of the Antigen-binding Site of Immunoglobulins Suggests Strong Geometrical Restrictions Associated to the Mechanism of Immune Recognition Enrique Vargas-Madrazo 1 *, Francisco Lara-Ochoa 2 and Juan Carlos Almagro 2 * Is the structural repertoire of immunoglobulins free to adopt an almost 1 Instituto de Investigaciones infinite number of conformations to build the diversity of the immune Biolo ´gicas, Universidad response or does it take advantage of only a few conformations? In this Veracruzana, J. Barrera 54 M. A. Mun ˜oz, Xalapa paper we study this question by applying the canonical structure model to Veracruz, Mexico characterize the structural repertoire of immunoglobulins. The results found, indicate that only ten combinations out of the 300 2 Instituto de Quı ´mica possible different canonical structure classes (combinations of canonical Universidad Nacional structures), make up 87% of 381 sequences analyzed. This suggests that the Auto ´noma de Me ´xico structural repertoire of immunoglobulins is restricted to the preferential Circuito Exterior, Ciudad use of a small number of canonical structure classes. The possible Universitaria, C.P. 04510 functional significance of these results was studied by analyzing the Me ´xico, D.F. 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.  1995 Academic Press Limited Keywords: canonical structure; canonical structure class; antigen-antibody complex; molecular recognition *Corresponding author Introduction Antibody molecules are highly antigen-specific receptors of the immune system. Antigen-antibody interaction involves the antibody variable domains V H and V L , each composed of a two -sheet framework (Amzel & Poljak, 1979). The antigen- binding site is composed of six hypervariable loops; three from V H and three from V L denoted H1, H2, H3 and L1, L2, L3, respectively (Wu & Kabat, 1970; Poljak et al ., 1973). Analysis of antibodies of known three-dimen- sional structure has revealed a small number of main-chain conformations or canonical structures for H1 and H2 as well as for L1, L2, L3 (Chothia & Lesk, 1987; Chothia et al ., 1989; Tramontano et al ., 1990). A canonical structure is determined by the loop size and by the presence of certain residues at key positions in both the loop and the framework regions (Chothia & Lesk, 1987; Chothia et al ., 1989; Tramontano et al ., 1990). Based on these rules relating the amino acid sequence and the three- dimensional structure of the hypervariable loops, Abbreviations used: Ig, immunoglobulin; VL, variable light domain; VH, variable heavy domain; H1, H2 and H3, first, second and third hypervariable loop of the heavy chain, respectively; L1, L2 and L3; first, second and third hypervariable loop of the light chain, respectively; PDB, Brookhaven Protein Data Bank. 0022–2836/95/480497–08 $12.00/0  1995 Academic Press Limited