Two main areas of research are outlined below.
1. Previous studies have demonstrated that proteins are highly cooperative with respect to folding and ligand binding. Furthermore, many enzymes display catalytic properties that are regulated allosterically. We are interested in understanding the physical mechanisms responsible for these cooperative and allosteric effects in proteins. Recent studies of PDZ (post-synaptic density-95/discs large/zonula occludens-1) domains using state-of-the-art solution nuclear magnetic resonance (NMR) dynamics experiments suggest that protein dynamics may be one possible mechanism used to propagate signals/energy within a protein molecule, a property known as intramolecular signaling (communication within a protein). (Figure 1. Propagation of dynamics to distal sites in hPTP1E PDZ2. Labeled residues have perturbed side-chain dynamics >7 ? from the peptide ligand. Fuentes et al., JMB (2004). This hypothesis will be further tested by characterizing the backbone and side-chain motions of various single-domain enzymes and signaling domains using NMR techniques coupled with detailed biochemical analysis. Future efforts will exploit intramolecular allostery to identify novel sites in proteins that modulate function, providing a molecular target for novel allosteric inhibitors.
2. Recent work has focused on a class of signaling molecules known as Rho GTPases, a sub-family of the well know Ras GTPases. Like Ras, Rho-family GTPases cycle between active GTP-bound and inactive GDP-bound states. In the active state, Rho GTPases interact with effector proteins that coordinate changes in gene expression and the actin cytoskeleton. Several regulatory molecules such as guanine exchange factors (GEFs) and GTPase activating proteins (GAPs) are critical for regulating the activity of Rho GTPases. The aberrant function of RhoGEFs has been associated with human diseases, including cancer, developmental anomalies, and mental retardation. In addition to the signature catalytic Dbl homology domain (DH domain), GEFs generally contain other signaling domains that contribute to function and/or signaling specificity. Studies in my laboratory will focus on the structural and biochemical features of these auxiliary domains that are critical for the cellular function and disease progression.
Figure 2. The regulatory cycle for Rho-family GTPases.