Conformational features and interaction mechanisms of V(H)H antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction

The β‐hairpin conformation is regarded as an important basic motif to form and regulate protein–protein interactions. Single‐domain V(H)H antibodies are potential therapeutic and diagnostic tools, and the third complementarity‐determining regions of the heavy chains (CDR3s) of these antibodies are critical for antigen recognition. Although the sequences and conformations of the CDR3s are diverse, CDR3s sometimes adopt β‐hairpin conformations. However, characteristic features and interaction mechanisms of β‐hairpin CDR3s remain to be fully elucidated. In this study, we investigated the molecular recognition of the anti‐HigB2 V(H)H antibody Nb8, which has a CDR3 that forms a β‐hairpin conformation. The interaction was analyzed by evaluation of alanine‐scanning mutants, molecular dynamics simulations, and hydrogen/deuterium exchange mass spectrometry. These experiments demonstrated that positions 93 and 94 (Chothia numbering) in framework region 3, which is right outside CDR3 by definition, play pivotal roles in maintaining structural stability and binding properties of Nb8. These findings will facilitate the design and optimization of single‐domain antibodies.