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Cellular processes are largely controlled by the protein-DNA and protein-protein interactions that define them but only a small set of these interactions have been fully described. When one considers all the possible mutations that may influence these proteins and their potential binding partners, an inclusive screen of all possible interactions presents a seemingly insurmountable task. Alternatively we take a “holistic” synthetic approach to define the ligand-binding specificity of common protein domains in an attempt to go beyond the relatively limited set of interactions that have evolved naturally. Combined with structural modeling and in vivo confirmation of these binding behaviors and their functional consequences, we hope to provide a truly predictive understanding of protein function.
Protein-DNA interactions
C2H2 zinc fingers represent nearly 50% of the transcription factors in human and the great majority of these factors remain undefined. In fact, there are more human zinc fingers with unknown specificities than the collection of characterized human factors combined. We are taking a comprehensive, synthetic approach to understand this important domain that will hopefully lead to a predictive understanding of the rules that govern its DNA-binding specificity. From this approach we have also produced a code that allows for the simple design of zinc fingers! The size and immunogenic advantages of this domain are opening all kinds of doors for therapeutics.
Protein-protein interactions
Screens of common protein-protein mediating domains, such as PDZ and SH3 domains, have demonstrated that many of the important interactions in nature are low affinity. We are developing new approaches to recover the lower end of functional specificity with the goal of improving our predictive understanding of biologically important interactions. In addition, these domains are far more common in the microbiome than previously anticipated and they control signaling within these microbes. We hope to understand how these protein interactions help each microbe respond to its environment and their impact on the homeostasis of the microbiome. In addition, we hope to engineer these interactions for therapeutic applications.
Protein engineering
A benefit of the synthetic approaches we use is that we are also creating domains with novel functions. For example, we have modified our tools to engineer proteins that improve the precision of genome editing nucleases (ZFNs, TALENS, CRISPR, etc.) as well as artificial regulators. We are also engineering protein-protein interactions for artificial signaling pathways, artificial proteases, and hope to develop fine-tuned inhibitors of protein-protein interactions for therapeutic application.