Current Projects
RNA Modifications and RNA/Protein Interactions
There are over 100 different nucleoside modifications found throughout RNA that are key determinants of RNA structure and function. Mutations in RNA modifying enzymes have been linked to a number of diseases including mitochondrial encephalomyopathy, heart disease, cancers, and delayed neurological development. As the study of post transcriptional modifications has exploded over the past decade with the discovery of modifications in mRNAs, many of the proteins that carry out post transcriptional modifications remain under studied. My lab studies three classes of RNA modifying enzymes: Pseudouridine Synthases, RNA methyltransferases, and demethylases. We use a combination of orthogonal approaches including x-ray crystallography, cryo-EM, and kinetics assays to characterize the structure, substrate selection and function of these proteins. We aim to translate this fundamental knowledge to important biological insights and the potential development of therapeutics or bio-applications.
Collaborators: Kristin Koutmou (UMich) and Dragony Fu (URochester)
Metalloenzymes
We are interested in discovering how biological catalysts accomplish “unusual” or “improbable” chemistries. One of our targets is vitamin B12 (cobalamin)-dependent methionine synthase (MS). MS is a multi-modular enzyme essential for folate one-carbon metabolism. The enzyme catalyzes the methyl transfer reaction from methyltetrahydrofolate to homocysteine to form methionine and tetrahydrofolate. The reaction is hard to accomplish at physiological pH because the methyl group binds the N5 position of folate, which is a tertiary amine, and homocysteine is thiol, making the reaction unlikely. MS accomplishes the reaction using two metals, Co (in cobalamin) and Zn. Our interest in MS stems not only from the chemically improbable methylation that it catalyzes but also from the unique capabilities of its cobalamin cofactor. The goal of our work is to uncover fundamental principles regarding how enzyme dynamics facilitate challenging chemistries. Furthermore, these principles could ultimately be used to reprogram MS (and/or cobalamin cofactor) to catalyze new reactions.
Collaborators: Alison Narayan (UMich) and Ruma Banerjee (UMich)
Mitochondrial RNA Biology and Processing
Ribonuclease P is the biological catalyst responsible for maturing the 5’ end of transfer RNAs (tRNAs), the essential molecules that carry amino acids to the ribosome. We use a combination of biochemistry (kinetic and binding assays), structural biology (x-ray crystallography, Cryo-EM), and in vivo studies to uncover the structure, mechanism, and physiological role of RNase Ps first discovered in human mitochondria (protein only RNase Ps (PRORPs)). PRORPs are essential to human health, and disruption of their action is directly linked to a number of mitochondrial diseases. Our studies provide the molecular-level understanding of PRORPs required to eventually develop treatments for diseases caused by disruptions in mitochondrial tRNA 5’ end processing.
Collaborators: Carol Fierke (Brandeis University)
RNA Crystallography and Dynamics
Riboswitches are genetic regulatory elements present in the 5’ UTRs many bacterial mRNAs. These structured elements bind small metabolites to control essential cellular metabolic processes. While riboswitches are essential for many pathogenic bacteria, they are not present in humans, making them a promising alternative target for drug design. We are working to develop high throughput methods to screen for small molecules that inhibit riboswitches using x-ray crystallography, ligand-RNA characterization and molecular dynamics simulations.
Collaborators: Aaron Frank (Arrakis Therapeutics) and Sarah Keane (UMich)
