Conformational Dynamics in NF-κB Transcriptional Regulation

Abstract

The NF-κB family of transcription factor is a central mediator of immune and imflammatory responses. NF-κB functions as a dimer and recognize DNA through the two N-terminal domains (NTDs). Previous hydrogen-deuterium exchange mass spectrometry, stopped-flow experiments and molecular dynamics simulations suggested the two NTDs can undergo relative motions which plays an important role in the kinetics of DNA association and dissociation. Here we showed by single-molecule FRET the direct evidence of relative domain motions in the NF-κB RelA-p50 dimer. Surprisingly, the two NTDs underwent slow heterogeneous motions on the timescale of seconds to minutes. These motions are scaled down when NF-κB is bound to DNA and allosterically altered by the inhibitor protein IκBα, which is known to accelerate DNA dissociation and prevent DNA binding. A new DNA-bound conformation unexpected from crystal structure was also observed. Together, our results provide a direct visualization and quantitative characterization of large-scale domain motions of NF-κB and shed light on the understanding of the role of protein dynamics in protein-protein interactions.