Conserved energetic changes drive function in an ancient protein fold

Abstract

While the ongoing revolution in structural biology offers an unprecedented understanding of the relationship between protein structure and function, it also confirms a puzzling, widely applicable principle: protein domains with highly conserved three-dimensional folds can perform radically disparate biochemical functions. To gain insight to this fundamental structural enigma, we mapped the energetic landscapes of a family of bacterial transcription factors and their anciently diverged structural homologs, the periplasmic binding proteins. Using hydrogen exchange/mass spectrometry, bioinformatics, X-ray crystallography, and molecular dynamics, we uncovered an unexpected contrast: despite binding the same sugars, the two families evolved unique "energetic blueprints" to support their distinct functional requirements. To test if differences in energetic ensembles have functional consequences, we rationally redesigned the protein fold for tunable ligand-driven transcriptional responses. Strikingly, energy-driven protein engineering produced synthetic transcription factors with the theoretically anticipated ligand-induced transcriptional outputs. Thus, decoding energetic blueprints among conserved protein folds provides a novel explanation for diverse functional adaptations, paves an alternative roadmap for protein design, and offers a new approach for engineering challenging drug targets.