Invité extérieur: Daniel Derege, University of Maryland School of Pharmacy in Baltimore, USA -« From protein ensembles to antiviral targets: integrative HDX-MS approaches to structure and function of dengue virus NS5 protein »

Résumé

A detailed understanding of protein structure and dynamics is central to elucidating
biological function and enabling therapeutic discovery, particularly for highly dynamic
systems. Research in the Deredge laboratory is centered on two complementary and
synergistic efforts: the development of integrative hydrogen–deuterium exchange mass
spectrometry (HDX-MS) frameworks to model protein native-state ensembles and
interactions, and the application of these approaches to uncover structure–function
relationships and therapeutic vulnerabilities in the Dengue virus non-structural 5 (NS5)
protein.
HDX-MS uniquely reports on protein conformational dynamics and interaction-induced
perturbations across multiple timescales, yet its structural interpretation is inherently
limited to its traditional peptide-level structural resolution. To bridge this gap, we
leverage HDX-MS data with various computational modeling and simulation approaches
to model ensemble-level, atomistic models that reconcile experimental observables with
physical structure. Using ensemble reweighting and related integrative strategies, we
have demonstrated how HDX-MS can be leveraged to model native conformational
landscapes, protein-small molecule interaction with high accuracy, and resolve large
protein–macromolecule complexes. Ongoing work extends these concepts toward HDX
guided sampling enhanced sampling molecular dynamics approaches and hybrid
computational frameworks that integrate physics-based modeling with emerging
machine-learning approaches.
These integrative methodologies are being applied to the Dengue virus NS5 protein, a
multifunctional and essential component of viral replication and a high-value antiviral
target. By combining HDX-MS, biophysical measurements, computational modeling, and
structural data, we are elucidating how NS5 conformational dynamics govern RNA
recognition and enzymatic function, providing a dynamic, ensemble-based view of NS5.
We further extended our characterization of NS5 to support ongoing structure-guided
therapeutic strategies.
Together, these efforts highlight how integrative structural mass spectrometry can move
beyond static representations to capture the dynamic principles underlying protein
function and druggability, with direct implications for antiviral discovery and broader
applications across complex biomolecular systems.