Structural biology of signaling and transport across biological membranes


My lab is broadly interested in the mechanisms of signaling and transport across cellular membranes. We use a variety of cell-based and in vitro biochemical assays, x-ray crystallography, cryogenic electron microscopy, and computational techniques (e.g., molecular dynamics simulations and bioinformatics analyses) to discover how these important proteins function in cells. Below are brief descriptions that illustrate our approaches and goals for specific projects.

Nramp transporters

Metals like iron and manganese are essential to physiological processes such as oxygen transport and energy metabolism. Nramps (Natural Resistance-Associated Macrophage Proteins) are transition metal transporters found in all kingdoms of life. They are the primary manganese importers in bacteria, and important metal uptake systems in plants, fungi, and animals. In humans, Nramp1 is part of the immune system’s metal withdrawal to counter microbial pathogens, while Nramp2 is responsible for dietary and cellular uptake of non-heme iron. Nramps are thus crucial for adequate supply of these metals while avoiding toxicity from over-accumulation. The goal of this project is to determine at atomic resolution the molecular mechanism of metal-ion transport by Nramps and distantly related Nramp-like transporters, including conformational change mechanisms, metal selectivity, and the role of protons and pH in regulating transport.

Non-classical cadherins

As the brain develops, neurons play a complex game of Twister to keep their neuronal processes from getting tangled up and improperly wired. For example, dendrites exhibit self-avoidance – avoid contact with other dendrites from the same neuron. In higher animals, the clustered protocadherins (cPCDHs) mediate this self-avoidance. Each cell has a random but unique set to distinguish it from neighboring cells. The cPCDHs create a biological ‘AND’ gate: a cell recognizes itself if and only if all expressed isoforms form homophilic interactions. Mutations in these proteins or their gene regulatory regions are linked to several neuropsychiatric diseases including bipolar disorder and schizophrenia.

We use structural, biochemical methods and cell-based assays to understand how cPCDHs form supramolecular inter-cellular signaling assemblies. We also use various sequence- and structure-based bioinformatics approaches to study cadherin diversity and evolution. We aim to understand how the diversity of sequences and structures in the cadherin superfamily contributes to their diverse signaling and adhesion functions mediated in the animal kingdom.

Insect Gustatory Receptors

We are interested in insect gustatory receptors as an example of a large and highly diversified family of sensory ion channels. Invertebrate Gustatory Receptors (GRs) are a large and evolutionarily diverse family of sensory receptors known to play important roles in invertebrate taste, smell and thermotransduction. Given the importance of these sensory modalities in host-seeking behavior in important human disease vectors like mosquitoes, GR family members serve as potentially powerful targets for vector control agents. We are using structural, biochemical, and biophysical tools to investigate key family members. We are also using bioinformatics, leveraging the large amount of sequence information, to understand the structure, function, and evolution of this family of ion channels.

Prodrug-Activating Peptidases

Both our microbiome and environmental microbes provide a rich source of bioactive small molecules useful as drugs or drug precursors, with penicillin as a classic example. Yet there remains a huge untapped potential to use and manipulate microbial biochemical activities to improve human health, which requires knowledge of the macromolecular structures and mechanisms of these biosynthetic pathways. We investigate on how an understudied family of peptidases activate important bacterial bioactive compounds. Our results will be useful in developing chemical tools to study our microbiome, and in future bioengineering efforts to produce new bioactive compounds from microbial sources.