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Suryajaya W, Biswas T, Shahabi S, Mealka M, Huxford T, Ghosh G. HDX-MS Analysis of Catalytic Activation of IKK2 in the IκB Kinase Complex. Biochemistry 2024. [PMID: 39185716 DOI: 10.1021/acs.biochem.4c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
The IκB Kinase (IKK) complex, containing catalytic IKK2 and noncatalytic NEMO subunits, plays essential roles in the induction of transcription factors of the NF-κB family. Catalytic activation of IKK2 via phosphorylation of its activation loop is promoted upon noncovalent association of linear or K63-linked polyubiquitin chains to NEMO within the IKK complex. The mechanisms of this activation remain speculative. To investigate interaction dynamics within the IKK complex during activation of IKK2, we conducted hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) on NEMO and IKK2 proteins in their free and complex-bound states. Altered proton exchange profiles were observed in both IKK2 and NEMO upon complex formation, and changes were consistent with the involvement of distinct regions throughout the entire length of both proteins, including previously uncharacterized segments, in direct or allosteric interactions. Association with linear tetraubiquitin (Ub4) affected multiple regions of the IKK2:NEMO complex, in addition to previously identified interaction sites on NEMO. Intriguingly, observed enhanced solvent accessibility of the IKK2 activation loop within the IKK2:NEMO:Ub4 complex, coupled with contrasting protection of surrounding segments of the catalytic subunit, suggests an allosteric role for NEMO:Ub4 in priming IKK2 for phosphorylation-dependent catalytic activation.
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Affiliation(s)
- William Suryajaya
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0357, United States
| | - Tapan Biswas
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0357, United States
| | - Shandy Shahabi
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0357, United States
| | - Matthew Mealka
- Structural Biochemistry Laboratory Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
| | - Tom Huxford
- Structural Biochemistry Laboratory Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0357, United States
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