Understanding the mechanistic details of how proteins recognize, manipulate and modify other molecules requires detailed knowledge of their structures. In my lab, x-ray crystallography is used as the primary tool to probe the molecular architecture of biological objects; the resulting detailed, three-dimensional models provide the context for interpreting established research findings and generating concrete functional hypothesis. These are then tested using further biochemical experiments to tease out the critical structure-function relationships.
At present, my lab is primarily focused on elucidating the structural organization of bacterial microcompartments, primarily the carboxysome. Carboxysomes are large (90 to 400 nm), polyhedral bodies found in the cytoplasm of cyanobacteria that catalyse the critical reaction that incorporates atmospheric CO2 into nascent sugars. Carboxysomes are made exclusively of protein, with a thin shell which is built from a handful of small proteins by tiling tens of thousands of copies into continuous triangular sheets. The interior core is comprised primarily with the CO2 fixing enzyme, RuBisCO, but also contains several other proteins that mediate a complex network of interactions necessary to structure and organize the body. The carboxysome appears to promote efficient carbon fixation by using its shell to confine CO2 near RuBisCO so that it is fixed, rather than escaping by diffusing through the cellular membranes. Most models of their functioning therefore imply that the shell traps CO2 but allows bicarbonate and other metabolites to pass – i.e. it effectively functions as a selectively permeable, but purely protein, membrane. Above and beyond this effect, the super-molecular organization of this complex possibly results in the emergence of new functional properties that further promote the efficiency of this critical biochemical process. For example, my lab recently showed that the key carbonic anhydrase in the carboxysome, CcmM, is indirectly activated by formation of the shell completion as this protects the enzyme from the reductive environment of the cytosol, allowing disulfide bonds to form. My laboratory is using crystallography to solve the structures of individual carboxysomal components, while in parallel using a variety of techniques to investigate their higher order organization. Ultimately we aim to understand how hundreds of thousands of individual protein chains can interact in a sufficiently controlled manner that an essentially identical object is produced each time.
In addition to this primary research theme, the lab generally has at least a few side projects underway not wholly related to the main research theme; examples include ClpP and its associated proteins (with researchers in Toronto and Cornell), aldolases (with the Seah lab), and proteins involved in LPS maturation and export (with the Whitfield and Lam labs).