Systematic identification of phosphorylation-mediated protein interaction switches

Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions. We estimate that there are likely thousands of phosphorylation mediated switches yet to be uncovered, even among existing phosphorylation datasets. The results suggest that phosphorylation sites on globular, as distinct from disordered, parts of the proteome frequently function as switches, which might be one of the ancient roles for kinase phosphorylation.Author summary: Most biological processes occur by molecules connecting to other molecules, and the precise details of these connections can often be seen in their three-dimensional structures or inferred from those of similar molecules. The ways in which molecules fit together are often affected and regulated by small chemical modifications to the structures of the molecules. Thousands of these modifications have been found in large-scale experiments, without knowing what connections they might affect or how. Some make molecules fit together better and some make the fit worse. We have combined 3D structures with data for a particular type of modification known as 'phosphorylation' to predict these effects and have found more than a thousand phosphorylations that may strengthen or weaken molecular connections, thereby allowing us to explain how certain biological processes are regulated.