Poly-ubiquitin drives the molecular interactions of NF-{kappa}B essential modulator by allosteric regulation [Protein Structure and Folding]

April 12th, 2015 by Catici, D. A. M., Horne, J. E., Cooper, G. E., Pudney, C. R.

NF-κB essential modulator (NEMO) is the master regulator of NF-κB signalling, controlling the immune and nervous system. NEMO affects the activity of a kinase, IKK-β, which relieves the inhibition of the NF-κB transcriptional regulation machinery. Despite major effort there is only a very sparse, phenomenological understanding of how NEMO regulates IKK-β; and shows specificity in its large range of molecular interactions. We explore NEMO's key molecular interactions using a molecular biophysics approach, incorporating rapid-mixing stopped flow, high-pressure and circular dichroism spectroscopy. Our study demonstrates that NEMO has a significant degree of native structural disorder and that molecular flexibility and ligand induced conformational change are at the heart of NEMO's molecular interactions. We find that long chain-length, unanchored, linear poly-ubiquitin drive NEMO activity, enhancing the affinity of NEMO for IKK-β and the kinase substrate, IκBα, as well as promoting membrane association. We present evidence that unanchored poly-ubiquitin achieves this regulation by inducing NEMO conformational change by an allosteric mechanism. We combine our quantitative findings to give a detailed molecular-mechanistic model for the activity of NEMO, providing insight into the molecular mechanism of NEMO activity as well as having broad implications for the biological role of free poly-ubiquitin.