Antibodies Can Exploit Molecular Crowding to Bind New Antigens at Noncanonical Paratope Positions

Despite having limited number of antibody molecules, it is still unclear how immune system recognizes surfeit of antigens. A novel mechanism of antigen recognition was deciphered from the crystallographic analysis of scFv 2D10 bound to disaccharide moiety. High-resolution crystal structure of the complex reveals unusual binding of scFv 2D10 with α1-6 mannobiose resembling supramolecular assemblies. The disaccharide interacts with the scFv 2D10 at two sites independent of canonical sugar binding positions, in two chemically distinct environments. At site A, α1-6 mannobiose lies on two-fold symmetry axis interacting through π-stacking and water network. However, at site B, α1-6 mannobiose exists in two orientations related by quasi-symmetry with direct hydrogen bonds. Although individual one on one interactions are low at both sites, symmetry related molecules contribute significantly for stable binding of the disaccharides, indicated by 2–4 fold lower binding energies. These interactions are facilitated due to relatively high concentrations of receptor and ligand. We propose that the molecular crowding leading to supramolecular associations acts as a specificity determinant and could be naturally exploited to bind diverse antigens. This previously uncharacterized property will considerably enhance the recognition repertoire of antibodies and therefore allows the humoral response to deal with the threat posed by plethora of antigens.