Emergence of specific binding and catalysis from a designed generalist binding protein.

The evolution of binding and catalysis played a central role in the emergence of life. While natural proteins have finely tuned affinities for their primary ligands, they also bind weakly and promiscuously to other molecules, which serve as starting points for stepwise, incremental evolution of entirely new specificities. Thus, modern proteins emerged from the joint exploration of sequence and structural space. The ability of natural proteins to bind promiscuously to small molecule fragments has been widely evaluated using methods including crystallographic fragment screening. However, this approach had not been applied to proteins. Here, we apply this method to explore the promiscuity of a small molecule-binding protein ABLE. As in Nature, we found ABLE was capable of forming weak complexes, which were found to be excellent starting points for evolving entirely new functions, including a binder of a turn-on fluorophore and a highly efficient and specific Kemp eliminase enzyme. This work shows how Nature and protein designers can take advantage of promiscuous binding interactions to evolve new proteins with specialized functions.