Identification and Prediction 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) [1]. We also found evidence suggesting that their natural abundance likely exceeds their PDB representation. To gauge how pervasive fold switchers might be in nature, we sought to explore their evolutionary conservation and sequence properties by developing a bioinformatics-based method to predict previously unidentified fold switchers from their genomic sequences. We used this method to perform blind predictions on regions of protein sequence space known to contain both fold switchers and non-fold switchers. This space comprises ∼7000 non-redundant sequences from a family of bacterial transcription factors known as RfaH and NusG. RfaH regulates protein expression by functioning as both a transcription factor with an alpha-helical fold and a translation factor with a beta-barrel fold. In contrast, NusG maintains its beta-barrel fold and functions as a transcription factor. Upon mapping RfaH/NusG sequence space, we predicted the propensities of several sequences therein to switch folds. Our predictions, validated by several experimental methods, suggest that fold switching is conserved among distantly-related bacterial phyla, highlighting its evolutionary robustness. Furthermore, preliminary evidence indicates that sequence constraints are looser for fold-switching sequences than for non-fold-switching ones, suggesting that many uncharacterized genomic sequences could potentially switch folds. [1] Porter and Looger (2018) Proc Natl Acad Sci USA 115:5968-5973