My research is characterized primarily by the application of molecular dynamics simulations to problems fitting two major themes: (1) synthesis and maturation of proteins and (2) unique bacterial systems and structure.
Many proteins early in their development must be moved across, or into, a cellular membrane. Both functions are surprisingly accomplished by a single transmembrane protein-conducting channel, the SecY/Sec61 translocon. Conserved throughout all domains of life, the translocon interacts with various channel partners, e.g., the ribosome or the bacterial ATPase SecA, that bind and insert the nascent protein. My work has focused on how the channel gates both transversely and laterally to the membrane, how partners bind and interact with the channel, and how it discriminates between proteins bound for the periplasm or the membrane. More information can be found here.
Nearly all bacteria possess a cell wall, a semi-rigid, porous network that provides them with shape and stability. The structure of this network, composed of repeated units of a disaccharide/oligopeptide molecule termed peptidoglycan, is unknown, both for Gram-negative and Gram-positive organisms. In collaboration with cryo-electron tomographers, I aim to resolve the molecular organization of the cell wall. Additionally, I want to determine how multiple enzymes work in concert to synthesize it. Some of these enzymes are canonical antibacterial drug targets, while others have yet to be exploited, a critical deficiency given the emergence of drug-resistance mechanisms.
As structural biology moves to ever larger complexes of multiple, diverse molecules, there is an increasing need for novel methods to bridge the gap between the variety of experimental methods producing data at various resolutions and sizes. Molecular dynamics flexible fitting (MDFF) is one such method, in which high-resolution, but conformationally limited structures of individual components from, e.g., X-ray crystallography, are fitted into cryo-electron microscopy maps of large, physiological complexes. I have utilized MDFF to determine the structures of a number of biologically and industrially relevant complexes, including ribosomes bound to the translocon (see above) and spiral-forming nitrilases. In the process, I have developed additional refinements to the MDFF method, such as incorporating symmetry during fitting.
Another interesting problem is how Gram-negative bacteria (those possessing two membranes surrounding them) import large nutrients across the outer membrane. Since they cannot generate energy at the outer membrane, they utilize an inner membrane protein, TonB, that couples across the periplasm to an outer membrane transporter in order to import large and/or scarce nutrients, such as vitamin B12 or iron extracted from human transferrin. The mechanisms of this interaction and how it causes transport are still open questions in the field of microbiology.
Photosynthesis is an elemental process of nature and occurs not just in plants, but also in some bacteria as well. In these bacteria, membrane-bound pseudo-organelles known as chromatophores contain the proteins necessary to turn sunlight into chemical energy. These chromatophores come in different shapes depending on the organism but no one knows how they self-assemble into spheres or sheets. My previous work on chromatophores revealed the innate, species-depedent tendencies of some of the constituent proteins to curve the membrane in which they reside, and laid out hypotheses for how this local curvature causes formation of the large-scale structures observed. More information is provided here.