Proximity proteomics

How do we use protein chemistry to capture complex organization and topography, and what is the best way to measure these context-sensitive chemistries from trace-level cellular extracts?  Our goal is to generate rich sets of restraint data that can be used to model both individual proteins and ultralarge protein complexes and networks. We explore novel strategies in protein crosslinking mass spectrometry (XL-MS) to produce precise distance restraints. We use fast-acting photolytic covalent labeling chemistries to probe surface topology (CL-MS) at high structural resolution. Our lab also pushes the boundaries in hydrogen-deuterium exchange mass spectrometry (HX-MS) for the detection of structure-function properties of large systems.

Computational methods

We actively develop software for analysis of mass spectrometry data.

Our latest project, Mass Spec Studio is a mass spectrometry analysis and applications development package that we use for higher-order structure analysis and integrative structural biology. It supports complete data analysis packages for HX-MS, CL-MS, XL-MS and a range of proteomics utilities.  Statistics algorithms and links to structural modelling are also available.

Visit to learn more or to try out  the software.  New versions coming soon!

Structure-function analysis of mitotic complexes

How does the microtubule lattice function as a regulator of mitosis, and to what extent do “feedback” mechanism exist between microtubules and their associated proteins? We are currently interested in microtubule depolymerizers such as MCAK and the role of +TIPs in establishing and regulating the enigmatic plus-end of the microtubule lattice. Our work has led to the discovery of a novel “fourth” druggable site on the microtubule lattice, which we are exploring as a link coupling microtubule dynamics to microtubule “signaling” events. We use HX-MS and XL-MS, along with modeling strategies, to generate new structural insights.

DNA Damage Repair

What proteins comprise the essential complexes for non-homologous end joining, and how are they coordinated to repair lesions in DNA induced by (among other things) ionizing radiation? Building an accurate structural model of this essential repair mechanism is key to understanding an essential biological process and should open up new anticancer therapeutic targets.  This is a collaborative project with the lab of Susan Lees-Miller in the Arie Charbonnneau Cancer Institute.

Host-Pathogen Interactions

How do bacterial transferrin-binding receptors recognize this host protein and remove iron, so important for the growth of many pathogenic bacteria? Understanding the nature and dynamics of the protein machinery for this process (at the atomic level) is essential for efficient development of vaccines targeting key bacteria involved in childhood infections (e.g. Neisseria meningitidis).  This is a collaborative project with the lab of Tony Schryvers in the Snyder Institute for Chronic Diseases.

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