Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach

The transcription factor nuclear factor kappa-B (NF kappa B) is a key regulator of pro-inflammatory and pro-proliferative processes. Accordingly, uncontrolled NF kappa B activity may contribute to the development of severe diseases when the regulatory system is impaired. Since NF kappa B can be triggered by a huge variety of inflammatory, pro-and anti-apoptotic stimuli, its activation underlies a complex and tightly regulated signaling network that also includes multi-layered negative feedback mechanisms. Detailed understanding of this complex signaling network is mandatory to identify sensitive parameters that may serve as targets for therapeutic interventions. While many details about canonical and non-canonical NF kappa B activation have been investigated, less is known about cellular I kappa B alpha pools that may tune the cellular NF kappa B levels. I kappa B alpha has so far exclusively been described to exist in two different forms within the cell: stably bound to NF kappa B or, very transiently, as unbound protein. We created a detailed mathematical model to quantitatively capture and analyze the time-resolved network behavior. By iterative refinement with numerous biological experiments, we yielded a highly identifiable model with superior predictive power which led to the hypothesis of an NF kappa B-lacking I kappa B alpha complex that contains stabilizing IKK subunits. We provide evidence that other but canonical pathways exist that may affect the cellular I kappa B alpha status. This additional I kappa B alpha:IKK gamma complex revealed may serve as storage for the inhibitor to antagonize undesired NF kappa B activation under physiological and pathophysiological conditions.