Conformation-Selective Binding Domains of Intramolecular Chemically Induced Protein Dimerisation Systems.

Chemically induced protein dimerisation (CID) is a widely used approach for detecting and actuating small-molecule-protein interactions. Here, we demonstrate that CID systems can be used as building blocks for higher-order ligand-controlled protein systems. To this end, we converted classical FK506- and cyclosporine A-controlled CIDs into single-chain pseudo-allosteric proteins. These systems displayed 15- and 50-fold gains in ligand affinity compared with the parental components operating in trans. Using these fusion proteins as baits in mRNA display, we identified FN3con binding domains that recognise the holo state of each bait with subnanomolar affinity and >100-fold selectivity over the apo form. Integration of the binding domains and intramolecular CIDs into two-component enzymatic protein biosensors enabled quantification of the cognate ligands with low-nanomolar limits of detection (LODs). ELISA assays based on the developed systems displayed mid-picomolar LODs and accurately quantified FK506 and cyclosporine A in unprocessed blood samples from transplant patients with accuracy comparable to that of LC-MS/MS. This work establishes a generalisable strategy for harnessing the affinity gains of intramolecular CID systems to create gain-of-signal assays for small molecules and ions.