FC0062
iκBα  -  NFκB

Biological function
IκBα binds and inhibits NFκB, an important transcription factor that regulates genes for cell growth, proliferation, apoptosis, and stress responses. IκBα exerts tight control over the activity of NFκB. IκB kinase,

Domain organization/sequence features
IκBα has six ARs (ankyrin repeat).

Structural evidence
In the absence of NFκB, ARs 5 and 6 of free IκBα have properties of an intrinsically disordered protein, while the rest of the protein (ARs 1 through 4) remains well folded. ARs 5 and 6 in free IκBα rapidly undergo amide hydrogen/deuterium (H/D) exchange, but amide exchange is markedly decreased when IκBα is bound to NFκB, providing strong evidence that the AR 5–6 region folds on binding. The ankyrin repeat (AR) 1–4 fluctuations were still present in the NFκB-bound state. The nuclear localization sequence of NFκB lies over the top of AR 1 in IκBα, and this interaction provides nearly 8 kcal/mol of binding affinity in the complex. On the other hand, the crystallographic B-factors for this part of the NFκB–IκBα complex are very high, implying disorder in this region. The H/D exchange in AR 1 only slightly decreases (1–2 amides fewer) upon binding to NFκB. smFRET data demonstrated that although the major conformation of free IκBα resembles that of the NFκB-bound one, free IκBα undergoes heterogeneous fluctuations to a more extended structure on the millisecond time scale. smFRET results revealed that ARs 1 and 6 undergo fluctuations at room temperature, suggesting that detachment/unfolding of the end repeats is a general property of AR domains. AR1 fluctuation enables ubiquitination and degradation of IκBα and release NFκB for its nuclear translocation.

Biochemical evidence
Deletion of the PEST sequence (residues 276-287) reduces the NfκB binding by ~5 kcal/mol. The PEST region does not become completely ordered upon binding to NfκB according to high resolution NMR spectroscopy data. The native state of the NfκB-IκBα complex thus retains regions with high dynamic character.

Mechanism category
flexibility modulation

Posttranslational modification
IKK phosphorylates IκBα, targeting it for ubiquitination and subsequent degradation. Phosphorylation do not significantly alter the binding affinity between NFκB and IκBα. The affinity of IκBα for NFκB is in the picomolar range, and in the absence of IKK, the intracellular half-life of the complex is many hours.

Significance
Fuzziness is important for the ability of IκBα to promote the dissociation of NFκB from DNA transcription sites, as well as for establishing the rapid degradation rate of free IκBα and maintaining low intracellular IκBα levels.

Further reading
22399319 19327364