Ancient Thioredoxins Evolved to Modern Day Stability-Function Requirement by Altering Native State Ensemble

Thioredoxins (Thrxs) - small globular proteins that reduce other proteins - are ubiquitous in all forms of life, from archaea to mammals. Although ancestral Thioredoxins share sequential and structural similarity with the modern day (extant) homologs, they exhibit significantly different functional activity and stability. We investigate this puzzle by comparative studies of their (ancient and modern day Thrxs’) native state ensemble, as quantified by the Dynamic Flexibility Index (DFI), a metric for the relative resilience of an amino acid to perturbations in the rest of the protein. Clustering proteins using DFI profiles strongly resembles an alternate classification scheme based on their activity and stability. The DFI profiles of the extant proteins are substantially different around the α3, α4 helices and catalytic regions. Likewise, allosteric coupling of the active site with the rest of the protein is different between ancient and extant Thrxs, possibly explaining the decreased catalytic activity at low pH with evolution. At a global level, we note that the population of low flexibility (called hinges) and high flexibility sites increases with evolution. The heterogeneity (quantified by the variance) in DFI distribution increases with the decrease in the melting temperature typically associated with the evolution of ancient proteins to their modern-day counterparts.