Systems biology at the molecular level is concerned with networks of interacting molecules, their structure, dynamic response to perturbations and their systems properties that determine measurable, macroscopic phenotypes. At any time, in any cell, multiple types of molecular networks are concurrently active. Substantial progress has been achieved in determining the basic -- in most cases, static -- structure of some of these networks, including transcriptional networks, protein:protein interaction networks, networks of synthetically interacting genes and networks of microRNA and their targets.

In the living cell, such networks are neither static nor are they independent. Perturbations of the cell induce coordinated changes in multiple networks and it is one of the predominant open questions in systems biology how this coordination is achieved, i.e. how cells processes information. Reversible protein phosphorylation catalyzed by protein kinases and phosphatases, respectively, is the most important known regulatory system in cells. Many of the multitude of signals received by the cell at any given time lead to the activation or deactivation of specific protein kinases/phosphatases which in turn propagate the signal via the phosphorylation/de-phosphorylation of specific cellular proteins and thus affect properties such as activity, interactions and cellular distribution.

While thousands of published research reports have studied the properties of specific kinases/phosphatases or phosphoproteins and their involvement in every imaginable process, there has been neither a conceptual framework nor a suitable technology to study this essential regulatory system as a whole. In fact, from the scientific literature it can be estimated that to date only about 10% of the whole human kinome has been studied in vivo, clearly demonstrating that we still know very little about kinase/phosphatase functions, their importance in basic cellular processes and the establishment of cellular phenotypes. In this project, for the first time, we will attempt to comprehensively study kinase-substrate networks in cells and thus to provide the basis to study the mechanisms by which cells process information. 

The research program of this project has three specific aims and builds on a number of recent technological and conceptual advances, achieved in large part by the groups involved in this project. First, we will map out the basic wiring diagram of phosphorylation mediated informational networks in cells. To achieve this goal, we will use protein:protein network analysis and high throughput phenotypic screens to connect the kinases/phosphatases to the sensors and signaling systems that provide their respective signal input. We will also use systematic silencing of the kinases/phosphatases and quantitative phosphoproteomics to identify substrates of each kinase/phosphatase, thus connecting these enzymes to specific effectors of cellular function.Second, we will use this basic wiring diagram to develop robust, sensitive and quantitatively accurate assays with sufficient throughput to measure phosphorylation dependent informational fluxes in different cells under a multitude of different conditions, a necessary requirement for the generation of mathematical models that simulate the dynamic behavior of biological processes. These assays and the reagents and informatics tools that support them will be freely disseminated.Third, we will apply these data and resources to four applied biological projects: cell cycle control, membrane trafficking, the response of cells to mechanical stress, and perturbed networks in cancer. These application projects will guide and drive the development efforts for technology and at the same time serve as its test bed, challenging the emerging technologies.