1. Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation.
- Author
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Chen W, Lu W, Wolynes PG, and Komives EA
- Subjects
- Animals, Avidin chemistry, Binding Sites, Biotin chemistry, DNA metabolism, Fluorescence Resonance Energy Transfer, Gene Expression Regulation, Humans, Immobilized Proteins chemistry, Immobilized Proteins genetics, Immobilized Proteins metabolism, Interferons chemistry, Interferons metabolism, Inverted Repeat Sequences, Mice, Molecular Dynamics Simulation, NF-KappaB Inhibitor alpha chemistry, NF-KappaB Inhibitor alpha metabolism, Protein Binding, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Protein Interaction Domains and Motifs, Single Molecule Imaging methods, Transcription Factor RelA chemistry, Transcription Factor RelA metabolism, DNA genetics, Interferons genetics, NF-KappaB Inhibitor alpha genetics, Transcription Factor RelA genetics, Transcription, Genetic
- Abstract
Binding and unbinding of transcription factors to DNA are kinetically controlled to regulate the transcriptional outcome. Control of the release of the transcription factor NF-κB from DNA is achieved through accelerated dissociation by the inhibitor protein IκBα. Using single-molecule FRET, we observed a continuum of conformations of NF-κB in free and DNA-bound states interconverting on the subseconds to minutes timescale, comparable to in vivo binding on the seconds timescale, suggesting that structural dynamics directly control binding kinetics. Much of the DNA-bound NF-κB is partially bound, allowing IκBα invasion to facilitate DNA dissociation. IκBα induces a locked conformation where the DNA-binding domains of NF-κB are too far apart to bind DNA, whereas a loss-of-function IκBα mutant retains the NF-κB conformational ensemble. Overall, our results suggest a novel mechanism with a continuum of binding modes for controlling association and dissociation of transcription factors., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2021
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