1. Many dissimilar NusG protein domains switch between α-helix and β-sheet folds
- Author
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Porter, Lauren L, Kim, Allen K, Rimal, Swechha, Looger, Loren L, Majumdar, Ananya, Mensh, Brett D, Starich, Mary R, and Strub, Marie-Paule
- Subjects
Biochemistry and Cell Biology ,Bioinformatics and Computational Biology ,Biological Sciences ,Biotechnology ,Genetics ,Generic health relevance ,Amino Acid Sequence ,Protein Conformation ,alpha-Helical ,Protein Conformation ,beta-Strand ,Protein Domains ,Transcription Factors - Abstract
Folded proteins are assumed to be built upon fixed scaffolds of secondary structure, α-helices and β-sheets. Experimentally determined structures of >58,000 non-redundant proteins support this assumption, though it has recently been challenged by ~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 α-helical and β-sheet folds. Our approach predicts that 24% of sequences in this family undergo similar α-helix ⇌ β-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.
- Published
- 2022