Many dissimilar protein domains switch between α-helix and β-sheet folds

Hundreds of millions of structured proteins sustain life through chemical interactions and catalytic reactions1. Though dynamic, these proteins are assumed to be built upon fixed scaffolds of secondary structure, -helices and {beta}-sheets. Experimentally determined structures of over >58,000 non-redundant proteins support this assumption, though it has recently been challenged by [~]100 fold-switching proteins2. These "metamorphic3" proteins, though ostensibly rare, raise the question of how many uncharacterized proteins have shapeshifting-rather than fixed-secondary structures. To address this question, we developed a comparative sequence-based approach that predicts fold-switching proteins from differences in secondary structure propensity. We applied this approach to the universally conserved NusG transcription factor family of [~]15,000 proteins, one of which has a 50-residue regulatory subunit experimentally shown to switch between -helical and {beta}-sheet folds4. Our approach predicted that 25% of the sequences in this family undergo similar -helix {rightleftharpoons} {beta}-sheet transitions, a frequency two orders of magnitude larger than previously observed. Our predictions evade state-of-the-art computational methods but were confirmed experimentally by circular dichroism and nuclear magnetic resonance spectroscopy for all 10 assiduously chosen dissimilar variants. These results suggest that fold switching is a pervasive mechanism of transcriptional regulation in all kingdoms of life and imply that numerous uncharacterized proteins may also switch folds.