Analysis of nanobody paratopes reveals greater diversity than classical antibodies.

Abstract

Nanobodies (Nbs) are a class of antigen binding protein derived from camelid immune systems, which achieve equivalent binding affinities and specificities to classical antibodies (Abs) despite being comprised of only a single variable domain. Here we use a dataset of 156 unique Nb:antigen complex structures to characterise nanobody-antigen binding, and draw comparison to a set of 156 unique Ab:antigen structures. We analyse residue composition and interactions at the antigen interface, together with structural features of the paratopes of both datasets. Our analysis finds that the set of nanobody structures displays much greater paratope diversity, in terms of the structural segments involved in the paratope, the residues used at these positions to contact the antigen, and furthermore the type of contacts made with the antigen. Our findings suggest a different relationship between contact propensity and sequence variability from that observed for antibody VH domains. The distinction between sequence positions that control interaction specificity and those that form the domain scaffold is much less clear cut for nanobodies, and furthermore H3 loop positions play a much more dominant role in determining interaction specificity.