Peptide ligase–mediated display: A cell-free platform for tunable selection of affinity peptides

Herein, we report a bead-surface protein display method based on a peptidyl transferase reaction, termed peptide ligase-mediated display (PL display). This technique enables the covalent linkage of genotypic DNA and phenotypic protein variants on beads via a minimal nine-amino acid linker in a fully cell-free system. Using this method, hemagglutinin (HA)-tag sequences introduced at a 0.01% frequency were completely isolated in a single round of selection via fluorescence-activated cell sorting (FACS) against an anti-HA-tag antibody. Furthermore, consensus sequences that bind to the anti-HA-tag antibody were enriched from a random peptide library with a sequence diversity of 1.7 × 10⁶ in two rounds of selection using FACS. This quantitative affinity selection platform using PL display is applicable under diverse conditions, as it is not constrained by cellular physiological properties, fluctuations in gene expression, or the structural and functional limitations of linker proteins involved in genotype-phenotype linkage. These advantages arise from the use of a fully cell-free system and covalent linkage with a minimal linker.