Epistasis shapes the fitness landscape of an allosteric specificity switch

Abstract

Epistasis is a major determinant in the emergence of novel protein function. In allosteric proteins, direct interactions between inducer-binding mutations propagate through the allosteric network, manifesting as epistasis at the level of biological function. Elucidating this relationship between local interactions and their global effects is essential to understanding evolution of allosteric proteins. We integrate computational design, structural and biophysical analysis to characterize the emergence of novel inducer specificity in an allosteric transcription factor. Adaptive landscapes of different inducers of the engineered mutant show that a few strong epistatic interactions constrain the number of viable sequence pathways, revealing ridges in the fitness landscape leading to new specificity. Crystallographic evidence shows a single mutation drives specificity by reshaping the binding pocket. Comparison of biophysical and functional landscapes emphasizes the nonlinear relationship between local inducer affinity and global function (allostery). Our results highlight the functional and evolutionary complexity of allosteric proteins.