Nanobodies versus canonical antibodies: an updated comparison of their binding modes

Abstract

Heavy-chain only antibodies, produced by the adaptive immune systems of camelids and cartilaginous fish, complement canonical antibodies comprising both heavy and light chain variable domains. Using an integrated interface model that unifies interfacial atoms--including solvent molecules, contacts, buried surface areas, and interface curvature measures, we shed light on two aspects of antibody binding that have so far remained elusive when comparing single domain (SdAb) and double domain (DdAb) antibodies. First, contrary to previous reports of smaller SdAb interfaces, we show that SdAb achieve an interface size comparable to that of DdAb despite using a single variable domain and fewer interface residues, a consequence of a geometric pattern driven by convexity and curvature effects. Second, we show that SdAb exhibit a broader diversity of binding modes than previously reported, with a prominent role played by FR regions. Finally, we discuss the thermodynamic implications of these findings for the design of high-affinity single domain antibodies, with particular relevance to protein engineering and design.