DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB

We recently discovered that I kappa B alpha enhances the rate of release of nuclear factor kappa B (NF kappa B) from DNA target sites in a process we have termed molecular stripping. Coarse-grained molecular dynamics simulations of the stripping pathway revealed two mechanisms for the enhanced release rate: the negatively charged PEST region of I kappa B alpha electrostatically repels the DNA, and the binding of I kappa B alpha appears to twist the NF kappa B heterodimer so that the DNA can no longer bind. Here, we report amide hydrogen/deuterium exchange data that reveal long-range allosteric changes in the NF kappa B (RelA-p50) heterodimer induced by DNA or I kappa B alpha binding. The data suggest that the two Ig-like subdomains of each Rel-homology region, which are connected by a flexible linker in the heterodimer, communicate in such a way that when DNA binds to the N-terminal DNA-binding domains, the nuclear localization signal becomes more highly exchanging. Conversely, when I kappa B alpha binds to the dimerization domains, amide exchange throughout the DNA-binding domains is decreased as if the entire domain is becoming globally stabilized. The results help understand how the subtle mechanism of molecular stripping actually occurs. (C) 2017 Elsevier Ltd. All rights reserved.