Antigen recognition by single-domain antibodies: structural latitudes and constraints

Abstract

Single-domain antibodies (sdAbs), the autonomous variable domains of heavy chain-only antibodies produced naturally by camelid ungulates and cartilaginous fishes, have evolved to bind antigen using only three complementarity-determining region (CDR) loops rather than the six present in conventional VH:VL antibodies. It has been suggested, based on limited evidence, that sdAbs may adopt paratope structures that predispose them to preferential recognition of recessed protein epitopes, but poor or non-recognition of protuberant epitopes and small molecules. Here, we comprehensively surveyed the evidence in support of this hypothesis. We found some support for a global structural difference in the paratope shapes of sdAbs compared with those of conventional antibodies: sdAb paratopes have smaller molecular surface areas and diameters, more commonly have non-canonical CDR1 and CDR2 structures, and have elongated CDR3 length distributions, but have similar amino acid compositions and are no more extended (interatomic distance measured from CDR base to tip) than conventional antibody paratopes. Comparison of X-ray crystal structures of sdAbs and conventional antibodies in complex with cognate antigens showed that sdAbs and conventional antibodies bury similar solvent-exposed surface areas on proteins and form similar types of non-covalent interactions, although these are more concentrated in the compact sdAb paratope. Thus, sdAbs likely have privileged access to distinct antigenic regions on proteins, but only owing to their small molecular size and not to general differences in molecular recognition mechanism. The evidence surrounding the purported inability of sdAbs to bind small molecules was less clear. The available data provide a structural framework for understanding the evolutionary emergence and function of autonomous heavy chain-only antibodies.

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

“…Indeed, we found only minor differences in paratope motif spaces used by mouse and humans (>50% overlap, Suppl Fig. 4C, 14) and it was recently shown that neither CDR/FR length nor the distribution of interface residues in human and murine antibodies differ substantially (Collis et al, 2003;Henry and MacKenzie, 2018;Wang et al, 2018).…”

“…Comparing motifs between TCR and antibodyantigen motifs would shed light on mechanistic similarities and differences in antibody and TCR antigen-interaction (Antunes et al, 2018;Bradley and Thomas, 2019;Dash et al, 2017;Glanville et al, 2017;Gowthaman and Pierce, 2018;Hellman et al, 2019Hellman et al, , 2019Lanzarotti et al, 2018;Ostmeyer et al, 2019;Riley and Baker, 2018;Turner et al, 2006). Furthermore, it remains to be investigated in how far the motif-based rules uncovered here for VH-VL-antigen complexes are transferable to scFV, nanobody, and other novel antibody constructs (Henry and MacKenzie, 2018;Mitchell and Colwell, 2018). Finally, we wish to state that, while one of the main aims of this paper was to advance our quantitative understanding of antibody-antibody recognition, the second main aim was to develop computational approaches that may help study antibody-antigen interaction in the years to come.…”

Structural Aspects of the Allergen-Antibody Interaction

“…Heavy chain only antibodies are present in nature and are produced by camelids and sharks. The paratopes formed by the single chain antibodies have a very similar amino acid composition to that observed in conventional antibodies ( 77 , 78 ). The heavy chain only antibodies, and especially their V H domains, are relatively easy to produce and their biophysical, as well as structural properties, allow for easy application in biotechnology and therapeutics ( 77 , 79 ).…”

“…The paratopes formed by the single chain antibodies have a very similar amino acid composition to that observed in conventional antibodies ( 77 , 78 ). The heavy chain only antibodies, and especially their V H domains, are relatively easy to produce and their biophysical, as well as structural properties, allow for easy application in biotechnology and therapeutics ( 77 , 79 ). Single domain antibodies (specific for lysozyme) were isolated years before discovery of heavy chain antibodies in camelids ( 76 ), and were proposed as alternative to conventional monoclonal antibodies.…”

The structure of myeloid cell‐specific TNF inhibitors affects their biological properties

“…Single variable domains of heavy chain antibodies (also called V H Hs or nanobodies) are the antigen‐binding proteins [1]. Despite their small size (~15 kDa), these single domain binding units demonstrate high affinities and antigen‐binding specificities [2]. Although VHHs were discovered almost 25 years ago, studies based on their application are relevant to clinical research and provide opportunity to improve existing antibody‐based therapies.…”