OVERVIEW

We study what biological molecules do and how they do it, with the ultimate aim of better understanding their function in human health and disease contexts. We are interested in the formation and activation of protein molecular “machines” that perform reactions as required by the cell, notably proteases and nucleases that recycle proteins and nucleic acids respectively.

We use a suite of biophysical tools to understand how these molecular machines work with a high level of detail. These include isothermal titration calorimetry (ITC) and fluorescence for ligand binding and activity assays, conformational dynamics measurements via nuclear magnetic resonance (NMR) spectroscopy, hydrodynamics methodologies for characterizing molecular assembly, and computer modeling of the resultant data with mechanisms that explain biomolecular activity.

By working in the group, trainees will establish a well-rounded skillset featuring experimental and computational methods for biophysical research. This will facilitate employment in industry, academic, and government positions. Most importantly, students will develop a framework for thinking about and quantitatively modeling the behavior of biomolecules and the world around us.

(I) PROTEASES IN CELLULAR HOMEOSTASIS

The recycling of proteins within the cell is critical to health and development. To achieve this, cells deploy a host of oligomeric protease “machines”. These proteases capture and digest substrate proteins that are no longer required or are misfolded and pose a hazard if they aggregate. Their assembly into oligomers enables allosteric communication between subunits and multiple interfaces for effector protein binding, which provides layers of regulation in substrate consumption. Together, the self-assembly and activation mechanisms of these complexes enables stringent control of proteolysis reactions. The dysregulation of these molecular machines has been linked to the development of cancers and neurodegenerative disorders and, therefore, it is critically important to understand how they work as a first step in developing treatments for illnesses. We study how these oligomers form, how they interact with substrate molecules in their assembled state, and how their activity is modulated by disease mutations and post-translational modifications, toward illuminating the molecular basis for their function.

(II) NUCLEASES IN THE RNA LIFE CYCLE

We are interested in how the mRNA life cycle is regulated. The mRNA within eukaryotic cells is appended with a 3ʹ polyadenosine (polyA) tail that provides protection from non-specific degradation and promotes translation. When an mRNA is no longer required, the polyA tail must then be removed  in a process termed deadenylation, by enzymes known as deadenylases, so that the mRNA can be recycled. Deadenylation is the rate-limiting step in mRNA decay and consequently is a key determinant of the mRNA life cycle which, in turn, controls many other events in the cell. With its central role in cellular homeostasis, deadenylation must be tightly controlled to ensure mRNAs are appropriately modified. It has been suggested that the structural dynamics of deadenylases and substrate RNAs are critical to regulating deadenylation, though detailed insights into these conformational excursions and the role that they play in activity are lacking. We study the dynamics of these systems toward a better understanding of the mRNA homeostasis network.