Surveying the Sequence Space Landscape of Fold-Switching Proteins

Abstract

A central tenet of biology is that globular proteins have a unique three-dimensional structure under physiological conditions. Over the past 15 years, however, a growing number of proteins have been shown to switch folds, i.e. remodel their secondary and tertiary structures in response to cellular stimuli, leading to biologically relevant functional changes. Previously, we identified 96 of these fold-switching proteins in the Protein Data Bank (PDB). We also found evidence suggesting that their natural abundance likely exceeds their PDB abundance. Thus, we sought to identify other putative fold switchers with only one solved conformation. To do this, we identified two characteristic features of our ∼100 fold-switching proteins—incorrect secondary structure predictions and likely independent folding cooperativity—and searched the PDB for other proteins with similar features. Reassuringly, this method identified the fold-switching regions of 13/15 proteins, each with one solved structure and experimental support for an alternative conformation (p < 2.0∗10−5, hypergeometric test). We are now using a modified version of this method to estimate the size of sequence space for a family of fold-switching proteins. Specifically, we have mapped out sequence space for an E. coli protein known to switch folds and functions (RfaH) and its paralog that maintains a single fold and function (NusG). Preliminary experimental results suggest that our computational method successfully identifies both fold switchers and non-fold switchers in bacterial phyla distantly related to E. coli. Thus, the fold-switching mechanism appears to be conserved among distantly-related bacterial species, highlighting its biological relevance and suggesting that fold switching could be an evolutionarily robust mechanism.