Structural & Mechanistic Proteomics
At the Structural & Mechanistic Proteomics (STaMP) Lab, we use Hydrogen-Deuterium eXchange Mass Spectrometry (HDX-MS) to characterise the structure and conformational dynamics of biological systems, providing mechanistic insights into protein behaviour following interaction with binding partners such as small-molecule drugs, proteins, and biological membranes.
Structural proteomics for medicines discovery
Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a powerful biophysical tool which provides unique insights into how proteins are shaped and how they function. In a liquid environment such as water, proteins are not static structures, but instead, have structural plasticity; they wiggle and move about. It is the protein building blocks (amino acids), and more specifically, the hydrogens on these residues, which move, being in constant exchange with their surroundings. If a protein is placed in a “heavier” water containing deuterium in place of hydrogen (i.e., D2O), deuterium exchange leads to mass increases which can be easily measured by specialised techniques such as mass spectrometry (MS). The rate of deuterium exchange is dependent on a number of factors, including the location of the protein amino acids, and the presence of the very same structural elements that gives it its shape.
HDX-MS can be used to differentiate structured and unstructured protein regions, in a relatively quick fashion. This has great applicability in medicine and the screening of compound libraries for new drugs. The binding of a drug often triggers structure formation from an “intrinsically-disordered” state (or vice versa), serving as a molecular on/off button. This is notoriously difficult to measure using traditional biophysical tools. HDX-MS provides a solution. The unique selling point over analogous structural approaches such as crystallography and Cryo-EM, is that HDX-MS gives dynamic insights into protein interactions, rather than static snapshots. In other words, how proteins “dance”. The technique has proven to be an invaluable structural tool for the analysis of individual and multi-protein complexes, protein binding to small molecules such as drugs, and to monitor the folding of the protein into its correct shape. Accordingly, the technology has recently undergone rapid expansion in both the academic and pharmaceutical sector.
STaMP is fully-equipped to undertake cutting-edge structural proteomics experiments, housing a LEAP HDX Automation Robot (Trajan) and an Orbitrap Exploris 480 mass spectrometer with FAIMS (Thermo Scientific).
The lab is headed by Dr Darragh O'Brien. For collaboration enquiries, please contact darragh.obrien@ndm.ox.ac.uk