Title: Scaffolding, Multisite Phosphorylation and Other Mechanisms of Signal Transduction Regulation
Abstract: Protein activity is often regulated by ligand binding or by post-translational modifications such as phosphorylation. Moreover, proteins that are regulated in this way often contain multiple ligand binding sites or modification sites, which can operate to create an ultrasensitive dose response. Here, we consider the contribution of the individual modification/binding sites to the activation process, denoted as conformational free energy, and show how their individual values affect the ultrasensitive behavior of the overall system. We use a generalized Monod-Wyman-Changeux (MWC) model that allows for variable conformational free energy at distinct sites and associate a so-called activation parameter to each site. Our analysis shows that the ultrasensitivity generally decreases with increasing activation parameter values. We find that ultrasensitivity depends on the mean of the activation parameters and not on their variability. Experimentally, multisite transcription factor c-Jun from the JNK pathway has four distinct sites and its phosphorylation may have different effects on the protein’s activity. The experimental analysis shows that (1) c-Jun sites are phosphorylated at different rates, and the (2) docking site plays a role in c-Jun phosphorylation. These results provide insights into the performance objectives of multisite phosphorylation and thus gain a greater understanding of signaling and its role in diseases.