Structural Insights into the Stability and Recognition Mechanism of the Antiquinalphos Nanobody for the Detection of Quinalphos in Foods

Nanobodies (Nbs) have great potential in immunoassaysdue to theirexceptional physicochemical properties. With the immortal nature ofNbs and the ability to manipulate their structures using protein engineering,it will become increasingly valuable to understand what structuralfeatures of Nbs drive high stability, affinity, and selectivity. Here,we employed an anti-quinalphos Nb as a model to illustrate the structuralbasis of Nbs' distinctive physicochemical properties and therecognition mechanism. The results indicated that the Nb-11A-ligandcomplexes exhibit a tunnel binding mode formed byCDR1, CDR2, and FR3. The orientation and hydrophobicity of small ligandsare the primary determinants of their diverse affinities to Nb-11A.In addition, the primary factors contributing to Nb-11A's limitedstability at high temperatures and in organic solvents are the rearrangementof the hydrogen bonding network and the enlargement of the bindingcavity. Importantly, Ala 97 and Ala 34 at the active cavity'sbottom and Arg 29 and Leu 73 at its entrance play vital roles in haptenrecognition, which were further confirmed by mutant Nb-F3. Thus, ourfindings contribute to a deeper understanding of the recognition andstability mechanisms of anti-hapten Nbs and shed new light on therational design of novel haptens and directed evolution to producehigh-performance antibodies.

Automated summary

This study elucidates the structural basis of the unique physicochemical properties and recognition mechanism of Nanobodies (Nbs) using an anti-quinalphos Nb as a model. The Nb-11A-ligand complexes exhibit a tunnel binding mode formed by CDR1, CDR2, and FR3. The affinity of small ligands to Nb-11A is primarily determined by their orientation and hydrophobicity. Furthermore, the rearrangement of the hydrogen bonding network and enlargement of the binding cavity contribute to limited stability of Nb-11A at high temperatures and in organic solvents. Key residues at the active cavity's bottom and entrance play vital roles in hapten recognition.