Living cells use protein-based signal transduction circuits to decide how to respond to environmental stimuli. In eukaryotic cells these signaling networks are organized in a hierarchical, component-based manner -- they are assembled from multiple interacting proteins, while individual proteins are assembled from combinations of a finite toolkit that includes catalytic domains (e.g. kinases, phosphates) and protein interaction domains. Current hypotheses suggests that complex cellular circuitry may have evolved through recombination of these protein domain components. The overall goal of this project is to exploit this framework to engineer novel protein-based sensors, circuits, and computational devices. The initial focus is on individual signaling proteins that function as input/output switches, analogous to the fundamental logic gates used to build complex electronic circuits. The proteins often have an output activity that is only triggered by a specific set of upstream inputs. Recent studies suggest that these regulatory properties result from a relatively simple mechanism in which the interplay of intra- and intermolecular domain interactions controls protein conformation and therefore activity. In this project domain recombination is being used to reprogram natural catalytic activities (e.g. acting nucleators, kinesis, phosphates) such that they are precisely controlled by a combination of selected molecular inputs (e.g. specific peptide ligands, phosphorylation/dephosphorylation). Targeted switch designs include AND, NAND, NOR, and XOR-type input/output relationships. If successful, this project will allow for engineering of complex cell-based sensors.
