High-throughput characterization of protein–protein interactions by reprogramming yeast mating

Abstract

Significance De novo design of protein binders often requires experimental screening to select functional variants from a design library. We have achieved high-throughput, quantitative characterization of protein–protein binding interactions without requiring purified recombinant proteins, by linking interaction strength with yeast mating. Using a next-generation sequencing output, we have characterized protein networks consisting of thousands of pairwise interactions in a single tube and have demonstrated the effect of changing the binding environment. This approach addresses an existing bottleneck in protein binder design by enabling the high-throughput and quantitative characterization of binding strength between designed protein libraries and multiple target proteins in a fully defined environment.