PT - JOURNAL ARTICLE AU - Lauren L. Porter AU - Allen K. Kim AU - Swechha Rimal AU - Loren L. Looger AU - Ananya Majumdar AU - Brett D. Mensh AU - Mary Starich TI - Many dissimilar protein domains switch between α-helix and β-sheet folds AID - 10.1101/2021.06.10.447921 DP - 2022 Jan 01 TA - bioRxiv PG - 2021.06.10.447921 4099 - http://biorxiv.org/content/early/2022/03/17/2021.06.10.447921.short 4100 - http://biorxiv.org/content/early/2022/03/17/2021.06.10.447921.full AB - 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, α-helices and β-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 α-helical and β-sheet folds4. Our approach predicted that 25% of the sequences in this family undergo similar α-helix ⇌ β-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.Competing Interest StatementThe authors have declared no competing interest.