Structure and dynamics of the kinase IKK-β – A key regulator of the NF-kappa B transcription factor

Abstract

The inhibitor κB kinase-β (IKK-β) phosphorylates the NF-κB inhibitor protein IκB leading to the translocation of the transcription factor NF-κB to the nucleus. The transcription factor NF-κB and consequently IKK-β are central to signal transduction pathways of mammalian cells. The purpose of this research was to develop a 3D structural model of the IKK-β kinase domain with its ATP cofactor and investigate its dynamics and ligand binding potential. Through a combination of comparative modelling and simulated heating/annealing molecular dynamics (SAMD) simulation in explicit water the model accuracy could be substantially improved compared to comparative modelling on its own as shown by model validation measures. The structure revealed the details of ATP/Mg(2+) binding indicating hydrophobic interactions with the adenine base and a significant contribution of Mg(2+) as a bridge between ATP phosphate groups and negatively charged side chains. The molecular dynamics trajectories of the ATP-bound and free enzyme showed two conformations in each case, which contributed to the majority of the trajectory. The ATP-free enzyme revealed a novel binding site distant from the ATP binding site that was not encountered in the ATP bound enzyme. Based on the overall structural flexibility, it is suggested that a truncated version of the kinase domain from Ala14 to Leu265 should be subjected to crystallisation trials. The 3D structure of this enzyme will enable rational design of new ligands and analysis of protein-protein interactions. Furthermore, our results may provide a new impetus for wet-lab based structural investigation focussing on a truncated kinase domain.

Binding of disordered proteins to a protein hub

“…Meanwhile, the binding site of IKKβ is predicted to be in a structured part of the protein (Supplementary Fig. 1), which is consistent with the homology model28 that illustrates that IKKβ is a well-folded protein (Supplementary Fig. 2).…”

“…2 and Supplementary Table 1). Notably, even though the structure of Kelch-IKKβ complex is currently not available, the free-state structure of IKKβ reveals that the Kelch domain binding region of this protein28 also forms a β-hairpin that has considerable resemblance (~0.5 Å Cα rmsd for 8 atom pairs) to the bound state structure of the NRF2 site 1 peptide (Supplementary Fig. 2).…”

Alpha-Tocopherol Alters Transcription Activities that Modulates Tumor Necrosis Factor Alpha (TNF-α) Induced Inflammatory Response in Bovine Cells1

“…The IKKs and IKK-related kinase are instrumental for activation of the host defense system 28. The data presented is consistent with the idea that the transcription factor NF-κB and consequently IKK are central to signal transduction pathways of mammalian cells29 in immune responses. This pathway is involved in the regulation of a wide spectrum of biological processes including cell proliferation, differentiation, apoptosis, lipid metabolism, and coagulation.…”

Binding Mode Analysis of Zerumbone to Key Signal Proteins in the Tumor Necrosis Factor Pathway

“…The nuclear factor κB (NF-κB) is a group of transcriptional proteins that is held inhibited in the cytoplasm by its inhibitor IκBα [ 28 , 29 , 30 , 31 , 32 ]. Binding of the TNF α to its receptor TNFR1 triggers a signal that leads to the ubiquitination of the IκBα followed by translocation of NF-κB to the nucleus where it leads to the transcription of cell proliferating genes.…”