Protein-to-protein interactions are important to human health, but a large number of them remain uncharacterized. Some of this is due to a gap in imaging resolution between cell biology and structural biology. To bridge this gap, our lab is using crosslinking mass spectrometry (crosslinking MS) and other proteomics-based technologies combined with cryo-electron microscopy. These techniques allow us to visualize and describe how proteins are organized into molecular machines and are dynamically regulated. Our research goals are to functionally characterize newly discovered protein interactions and utilize disease models to understand their relevance to human health and cancer.

The topology of protein-to-protein interactions in situ in eukaryotic cells

The complexity and range of protein abundances in eukaryotic proteomes present a particular challenge for generating whole-cell interactomes by crosslinking MS and other technologies. The complexity of genetic tagging and difficult-to-purify protein complexes, such as those within membranes or phase-separated regions, requires studying interactions in situ. We pursue divide-and-conquer approaches to address this complexity and seek to generate a comprehensive 3D map of the proteome of an entire eukaryotic cell.

Discovery of novel protein complexes across human microbiome

The bacteria of the human gut have been implicated in many aspects of human health and disease. However, almost half of the protein-coding genes in the human gut microbiome do not yet have an annotated molecular function. This large proteomic 'dark matter' limits our interpretation of bulk genetic studies of the gut microbiome and of the roles of specific species. Crosslinking MS and other structural proteomics techniques allow us to generate whole-cell interactomes that enable us to design targeted experiments to characterize protein function.