The main focus of this lab is to examine how enzymes catalyze reactions for very specific functions in the cell. To this end, we employ an array of techniques to study macromolecular interactions in solution. To examine the energetics of the protein-nucleic acid, protein-protein, protein-peptide, and protein-nucleotide interactions we use fluorescence titrations, isothermal titration calorimetry, differential scanning calorimetry, analytical ultracentrifugation, and dynamic and static light scattering. Coupled with a knowledge of the energetics of these interactions we use pre-steady state rapid mixing kinetic techniques such as fluorescence stopped-flow and chemical quench flow to elucidate the kinetic mechanisms of binding and catalysis.

We are interested in understanding how motor proteins work to carry out their reactions in the cell. Specifically, we are interested in reactions catalyzed by a class of enzymes called motor proteins. Examples of well characterized motor proteins include enzymes such as helicases, polymerases, myosin, kinesin, and chaperones. Motor proteins couple the energy acquired from NTP binding and/or hydrolysis to translocate on a linear lattice. In addition to translocation, these enzymes typically perform other activities. For example, DNA helicases unwind duplex DNA, generating the ss DNA intermediates required for such activities as replication, recombination and repair. Likewise, polymerases must translocate along ss DNA while synthesizing a complementary strand of DNA or RNA. Chaperones, on the other hand, couple the energy of nucleotide binding and/or hydrolysis to conformation changes that aid in protein folding and others translocate along the polypeptide backbone to unfold proteins.

One project in the lab is focused on the Clp Chaperone/protease system. These macromolecular assemblies contain a hexameric chaperone component (e.g., ClpA, ClpB, ClpX, ClpY) which recognize specific protein targets in the cell and translocates along the polypeptide backbone while disrupting protein secondary structure. This newly unfolded protein is then released and allowed to refold. Alternatively, the newly unfolded protein can be spooled into the tetradecameric (ClpP) or dodecameric (ClpQ) subunit of the Clp protease where it is proteolytically degraded.

This activity, of removing proteins from the cell, is critically important to all organisms. For example, damaged proteins or partially synthesized proteins would build up and have a deleterious effect on the cell if there were no mechanism for removal. In the case of prion diseases, the misfolded protein that results in the disease somehow evades degradation. Also, and an often overlooked level of cell cycle regulation, is the removal of gene promoters and repressors. It is well known that genes are up regulated and down regulated through the expression of promoters and repressors, but at some point removal of these proteins is a critical component of the proteins life cycle and the health of the cell. Failure of these protein degradation pathways often results in cancer. Despite the clear biological importance of protein degradation and it’s role in a variety of human genetic diseases, little is known about the molecular details of how these enzymes catalyze these reactions.