An accurate understanding of the structure and dynamics of proteins is of paramount importance for understanding proper function, how disruptions lead to dysfunction, or to develop therapeutics. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a structural proteomics approach which is unique in its ability to simultaneously provide localized and time-resolved information on the structural dynamics of backbone amide groups. As such, HDX-MS has been successfully applied to probe the native state ensembles of proteins, macromolecular interactions, protein-small molecule interactions or protein folding and unfolding. However, the structural information reported by HDX-MS remains largely limited to peptide-level resolution. To address this, efforts in the Deredge lab have focused on leveraging HDX-MS with computational modeling and molecular dynamics simulations to bridge the gap between experimental observables and atomic-level structural detail. HDX ensemble reweighting (HDXer) is one such approach which uses a post hoc maximum entropy approach to adjust the weights of individual frames of a structural ensemble to conform to HDX-MS data. We have demonstrated the applicability of HDXer within various perspectives. For instance, we used HDXer to model the native ensemble of the putative therapeutic target PhuS, the cytoplasmic heme binding protein from P.aeruginosa, revealing cryptic drug binding sites. Additionally, we demonstrated the specific applicability of HDXer in leveraging lower resolution HDX-MS data to accurately model protein-small molecule interactions. Finally, we used HDXer to model the complex of Dengue virus Non-Structural 5 protein bound to the Stem Loop A (SLA) motif at the 5' end of the viral genome, a model we subsequently corroborated by cryoEM. In recent efforts to extend beyond post hoc ensemble reweighting, we are currently developing 1/ an HDX-MS-steered adaptive sampling workflow to guide enhanced sampling MD simulations, and 2/ a hybrid physics-based and machine-learning based models to model protein-ligand interaction from HDX-MS data.

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