Visualization of the nanospring dynamics of the IκBα ankyrin repeat domain in real time

I kappa B alpha is a crucial regulator of NF kappa B transcription. NF kappa B-mediated gene activation is robust because levels of free I kappa B alpha are kept extremely low by rapid, ubiquitin-independent degradation of newly synthesized I kappa B alpha. I kappa B alpha has a weakly folded ankyrin repeat 5-6 (AR5-6) region that is critical in establishing its short intracellular half-life. The AR5-6 region of I kappa B alpha folds upon binding to NF kappa B. The NF kappa B-bound I kappa B alpha has a long half-life and requires ubiquitin-targeted degradation. We present single molecule FRET evidence that the native state of I kappa B alpha transiently populates an intrinsically disordered state characterized by a more extended structure and fluctuations on the millisecond time scale. Binding to NF kappa B or introduction of stabilizing mutations in AR 6 suppressed the fluctuations, whereas higher temperature or small amounts of urea increased them. The results reveal that intrinsically disordered protein regions transition between collapsed and extended conformations under native conditions.