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

Area of Science:

• Molecular biology
• Biophysics
• Structural biology

Background:

• Nuclear factor kappa B (NFκB) is a key transcription factor regulating immune responses.
• IκBα acts as a negative regulator of NFκB, controlling its nuclear translocation.
• The mechanism by which IκBα facilitates NFκB release from DNA, termed molecular stripping, is not fully understood.

Purpose of the Study:

• To elucidate the allosteric mechanisms underlying IκBα-mediated molecular stripping of NFκB from DNA.
• To investigate the conformational changes in the NFκB (RelA-p50) heterodimer upon binding to DNA or IκBα.

Main Methods:

• Amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) was employed to probe protein dynamics.
• Coarse-grained molecular dynamics simulations were used to model the molecular stripping pathway.

Main Results:

• IκBα binding induces long-range allosteric changes in the NFκB heterodimer.
• DNA binding to NFκB increases amide exchange at the nuclear localization signal.
• IκBα binding globally stabilizes the DNA-binding domains of NFκB, reducing amide exchange.

Conclusions:

• Molecular stripping involves electrostatic repulsion by IκBα's PEST region and conformational twisting of NFκB.
• Allosteric communication between NFκB subdomains is crucial for regulating DNA binding and nuclear localization.
• HDX-MS data reveal distinct conformational states of NFκB upon binding to DNA versus IκBα.