Hydrogen deuterium exchange: methods to probe protein dynamics at single residue resolution

The purpose of this work is to provide computational methods to fingerprint protein dynamics probed by hydrogen deuterium exchange mass spectroscopy (HDX-MS). Hydrogen deuterium exchange consists in the spontaneous exchange of amide hydrogens of amino acids with deuterium contained in solution. The consequent increase in mass of the protein can be monitored by mass spectroscopy. Moreover, the exchange rate (or protection factor) provides a parameter probing protein dynamics at single residue resolution. The ExPfact algorithm is a computational method implemented to extract fine-grained information out of coarse-grained HDX-MS experimental data. The method is validated through a comparison with protection factors estimated from HDX-NMR measurements probing the mouse prion protein. Also, a second application studying glycogen phosphorylase shows how structural changes between different states of the same protein can be detected at amino acidic resolution. Furthermore, fine-grained information extracted by ExPfact is coupled with a back-exchange correction to reproduce experimental spectra, suggesting that the information encoded in the centroids of the spectra is sufficient to characterize experimental data. Last but not least, an existing structural model connecting the structure of a protein to its protection factors is discusses and improved via the introduction of a dependence on the electrostatic potential of the protein.