Characterization of the Functional Diversity and Evolvability of Chimeric Enzymes Assembled by Structure-Guided SCHEMA Recombination

Abstract

In nature proteins evolve by a combination of point mutagenesis and recombination. This process has generated hundreds of fascinating and structurally complex protein folds capable of performing a myriad of important and diverse biochemical functions. This has inspired protein engineers to mimic natural protein evolution in the library to construct synthetic proteins with new or improved properties. Here I show that homologous protein recombination can be used in the library to engineer novel enzymes with new catalytic activities and altered substrate specificities. I also propose that homologous recombination can be used in the laboratory to overcome the challenge of improving the native activities of wild-type proteins. In nature recombination may have helped proteins escape local maxima of the fitness landscape by introducing many homologous mutations to which proteins are highly tolerant. Protein engineers can possibly use it for the same purpose. I validate this hypothesis computationally with highly simplified protein models, and I attempt an experimental verification of this theory with cellulases.