Synthetic chemistry, protein engineering, and molecular evolution to create molecules that measure and control biological systems.
Research Interests:
The Dickinson Group at the University of Chicago is an interdisciplinary research team made up of synthetic chemists, biochemists, cell biologists, and synthetic biologists. The primary motivation behind my group’s work is that our ability as chemists to create new functional molecules will lead to biological discoveries and technologies. The functional molecules we are creating vary in terms of size (small molecules to proteins to engineered organisms) and discovery method (rational design to unbiased evolution). In all cases, our ultimate goal is to leverage new chemical and molecular technologies to better understand and treat human disease. Currently, we are pursuing three primary research areas:
Chemical approaches to interrogate cell signaling by dynamic protein lipidation
Hundreds of human proteins are modified by reversible palmitoylation of cysteine residues (S-palmitoylation).Proteome lipid signaling is regulated through the dynamic interplay between S-palmitoylation “erasers”, acyl-protein thioesterases (APTs), and “writers” (DHHCs). Therefore, to uncover the players and regulatory factors that control proteome-wide S-palmitoylation, we develop molecular imaging reagents and targeted inhibitors that allow us to study the roles of APTs and DHHCs in signaling. Our group has developed a series of molecular imaging reagents that report on APTs, protein lipidation “eraser” enzymes, in live human cells. We have used these molecules to discover that APT activities are not static, but respond dynamically to varied cellular input signals, such as growth factor signaling. Using targeted probes, we discovered that mitochondria house APTs, including a previously unrecognized role for APT1, the foundational member of this class of signaling enzymes. Finally, we discovered a new member of the APT family of regulatory proteins, which we characterized through biochemical, structural, and cell biological experimentation, and discovered this new APT regulates mitochondrial redox signaling through its S-depalmitoylation activity.
Development of biosensors to study, evolve, and control protein-protein interactions
Diverse areas of biotechnology, including directed evolution, synthetic biology, and bioengineering, are impeded by a lack of general methods to link chemical and biochemical processes to defined genetic outputs. Current approaches to engineer biosensors that produce RNA signals suffer from complex engineering requirements, low signal-to-noise ratios, incompatibility with diverse biological systems, and limitations in the scope of target activities that can be detected. Our group has developed proximity-dependent split RNA polymerase (RNAP)-based biosensors. We engineered previously-reported split RNAPs to be proximity dependent using rapid continuous evolution. The resultant evolved biosensors have a large dynamic range and can detect a multitude of input signals, including protein-protein interactions (PPIs), small molecules, and light. We have deployed the RNAP-based biosensors in mammalian synthetic biology applications including multidimensional PPI detection and CRISPR/Cas9 control. However, most importantly, our biosensors have opened up new opportunities for using powerful in vivo directed evolution systems, such as PACE, to solve problems in chemistry and biology. For example, we are developing new evolutionary tools to rapidly evolve protein interfaces, enzymes, and even peptide-based small molecule inhibitors.
Synthetic biology approaches to study and exploit the epitranscriptome
RNA transcribed from the genome in the nucleus bears little resemblance to the RNA polymer it will ultimately become in the cytoplasm where it is translated into protein. Well-known processes such as capping, splicing and polyadenylation, as well as the recently discovered and ever-expanding list of diverse chemical modifications and editing, significantly alter the properties and fates of a given RNA during the course of its lifetime. These alterations regulate critical aspects of RNA function such as stability, transport, protein binding, and translation, which are commonly mediated by interactions with RNA binding proteins. Especially in mammalian systems, these post-transcriptional gene expression regulatory processes are often a key determinant of genetic information flow. Our group has developed several new molecular technologies to study and exploit RNA modifications in mammalian cells. We developed a general method to evolve reverse-transcriptases (RT) to encodes RNA modifications in mutations for use in high-throughput sequencing analysis of the sites and abundances of RNA modifications, thus far focusing on m1A as an exemplar. We developed programmable RNA reader proteins by engineering RNA-targeting Cas systems with effector domains from RNA regulatory proteins in order to begin to study the role(s) of individual regulatory sites in the transcriptome. Finally, we developed an entirely human protein-based programmable RNA delivery systems, inspired by CRISPR/Cas9, which is smaller than the current RNA-targeting Cas systems, providing us with a powerful new approach to probe transcriptome regulation and also providing a path toward clinical applications of programmed epitranscriptome regulatory systems.
Selected References
