Genetic and biophysical causes of historical protein evolution

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My lab develops and applies new approaches at the interface of molecular evolution and protein biochemistry . We have played a lead role in developing ancestral protein reconstruction (APR) with molecular experiments as a powerful strategy to decisively identify the genetic, biophysical, and evolutionary mechanisms by which extant proteins evolved new functions. We recently expanded this approach by conducting the first studies to use deep mutational scanning of massive protein libraries to characterize the distribution of functions in the sequence space around ancestral proteins; this allows us to compare the trajectories taken during history to the vast number of alternative paths that could have been taken, thus providing insight into the roles of functional optimization, neutral chance, epistasis, and historical contingency in shaping the trajectories and outcomes of protein evolution. In the next 5 years, we will further develop these approaches and apply them to two major problem areas: 1) Evolution of complex protein features. Many proteins assemble into specific multimeric complexes and are functionally regulated by binding to allosteric effectors. These features usually many interacting residues, so it has been difficult to identify the evolutionary genetic and biochemical mechanisms by which they originate during evolution. We will use APR and vertebrate hemoglobin as an ideal model system to dissect the particular historical mutations and consequent changes in physical properties that cause this essential protein to acquire multimerization and allostery from a simpler precursor. 2) Comprehensive assessment of the functional, fitness, and epistatic effects of substitutions during long-term protein evolution. Targeted experiments have shown that mutations often epistatically modify the effects of other mutations in the same protein; theory and case studies suggest these dependencies can make evolutionary paths and outcomes contingent on chance events. There have been no comprehensive studies, however, to characterize the extent of epistasis among the full set of substitutions that occurred during history, their effects on evolutionary processes, or the temporal dynamics by which these effects emerge. We will use high-throughput protein library assays on ancestral proteins to measure the functional and fitness effects and epistatic interactions of all substitution that occurred across long, well-resolved historical trajectories, determine how shifts in these effects over time affected evolutionary processes, and analyze how underlying biophysical mechanisms mediated these effects. As in our past work, we expect these new strategies to generate strongly supported new knowledge concerning the mechanisms and forces that drive protein evolution, and that our approaches will be adopted by other groups to deepen our evolutionary and biochemical understanding of other protein families.