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

Kristen M Ramsey1, Holly E Dembinski1, Wei Chen1

  • 1Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, USA.

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IκBα protein enhances nuclear factor kappa B (NFκB) release from DNA via molecular stripping. This involves electrostatic repulsion and conformational changes in NFκB, stabilizing its structure.

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IκB kinaseRel homology domainallosteryamide hydrogen/deuterium exchangetranscription regulation

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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.