Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles

Binding protein generation relies on laborious screening cascades that process candidate molecules individually. To break with this paradigm, we developed NestLink, a binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. NestLink builds on genetically fused barcoding peptides, termed flycodes, which are designed for maximal detectability by mass spectrometry and serve as unique molecular identifiers for accurate deep sequencing. We applied NestLink to overcome current limitations of binder generation. Rare binders against an integral membrane protein were identified directly in the cellular environment of a human pathogen. Hundreds of binder candidates were simultaneously ranked according to kinetic parameters. Adverse effects of target immobilization were overcome by selecting nanobodies against an ABC transporter entirely in solution. NestLink may provide a basis for the selection of tailored binder characteristics directly in tissues or in living organisms.