Research

Protocols

We use Nuclear Magnetic Resonance (NMR) spectroscopy as well as other biophysical and molecular biology techniques to study two classes of biomolecules: membrane proteins and DNA binding proteins.

Membrane Proteins

CNS Regeneration

Nogo is a membrane protein known to inhibit axonal growth within the central nervous system (CNS). Disabling Nogo following spinal cord injury or stroke may allow regrowth of damaged axons. One domain of Nogo, termed Nogo-66, is present extracellularly on the oligodentrocyte cells of the CNS. Nogo-66 achieves axonal growth inhibition by binding to the Nogo Receptor (NgR) on neuronal cells. We are interested in characterizing the structure of Nogo-66 and how it interacts with the Nogo Receptor. A detailed understanding of the interaction between Nogo-66 and NgR will prove useful for designing drugs that will interfere with the ligand-receptor interaction and provide recovery from CNS injury.

Natural Antibiotics

Defensins are family of antimicrobial peptides having activity against a range of microorganisms: gram-positive and gram-negative bacteria, fungi and some viruses. In addition to their antimicrobial activity, emerging evidence suggests that they can also assume fundamental roles in both innate and adaptive immunity.

More than 300 defensins have been identified to date and they are represented in a range of organisms including mammals, birds, invertebrates, plants and recently in the ebony-cup fungus. Our lab focuses on structural characterization of some of these defensins and their interactions with membranes to understand their mode of action.

DNA Binding Proteins

Tumor Suppressor

Mutations in the protein p53 are strongly correlated with the transformation of a healthy cell into a cancerous cell. Many cancers can be traced to a set of several individual point mutations in this protein that result in destabilization of the structure and thus inactivation of the protein. Several rescue mutations have been identified that when combined with the cancerous mutation restore stability and function in model systems. Our goal is to establish the mechanism through which these rescue mutations stabilize the structure through NMR dynamics measurements. Ultimately, we hope to use this knowledge for intelligent drug design of small molecules that can mimic the rescue mechanism. NMR also provides the avenue for testing promising compounds for their affect on protein dynamics to give support to drug design choices.

DNA Repair

Lesion bypass polymerases play an essential cellular role as they allow replication to proceed through damaged DNA. Mutation of a member of this class of polymerases, Pol eta, results in the condition xeroderma pigmentosum that can lead to cancer; thus Pol eta is a proven tumor supressor. Recently the structures of the bypass polymerases S. solfataricus DinB homologue (Dbh) and polymerase IV (Dpo4), and S. cerevisiae Pol eta were found to resemble the classic polymerase fold. The fidelity of the replicative polymerase is believed to rely on a protein conformational change from an open to closed state. The closed state has been proposed to be a crucial determinant of fidelity by restricting nucleotide incorporation to the base that fits correctly (induced fit mechanism). An unusual feature was noticed in the bypass polymerase structures: both Dbh and Pol eta are in a closed conformation even in the absence of substrate. This raises a question as to whether the bypass polymerase mechanism involves a protein conformational change similar to that of the replicative enzymes. Using NMR spectroscopy, we will probe the conformation of the protein in solution to determine if the closed state is the most populated or merely one of the existing conformations trapped by the crystallization process. To date, the polymerase mechanism has largely been studied from the substrate DNA perspective. These NMR studies will provide insight from the protein point of view; this will be the first characterization of polymerase motions with atomic level detail.

Gene Regulation

CytR is a bacterial transcription factor that represses production of the genes of the cytidine regulation pathway. While containing high sequence and functional homology to LacR, the lactose repressor, CytR has unique DNA sequence recognition ability in its dimeric form. While many DNA binding proteins form dimers to bind to palindromic sequences with a defined spacing, only CytR has been shown to have the ability to bind to half sites separated by a varying number of bases. Our NMR studies allow us to elucidate the structure and dynamics of the protein as it binds DNA. In collaboration with the Senear lab, we are working toward a greater understanding of the mechanism of gene recognition and expression regulation in general.