Many dissimilar NusG protein domains switch between alpha-helix and beta-sheet folds

Folded proteins are assumed to be built upon fixed scaffolds of secondary structure, alpha-helices and beta-sheets. Experimentally determined structures of >58,000 non-redundant proteins support this assumption, though it has recently been challenged by similar to 100 fold-switching proteins. Though ostensibly rare, these proteins raise the question of how many uncharacterized proteins have shapeshifting-rather than fixed-secondary structures. Here, we use a comparative sequence-based approach to predict fold switching in the universally conserved NusG transcription factor family, one member of which has a 50-residue regulatory subunit experimentally shown to switch between alpha-helical and beta-sheet folds. Our approach predicts that 24% of sequences in this family undergo similar alpha-helix (sic) beta-sheet transitions. While these predictions cannot be reproduced by other state-of-the-art computational methods, they are confirmed by circular dichroism and nuclear magnetic resonance spectroscopy for 10 out of 10 sequence-diverse variants. This work suggests that fold switching may be a pervasive mechanism of transcriptional regulation in all kingdoms of life.