Year: 2026
Type: preprint
Abstract: Hydrogen-deuterium exchange mass spectrometry (HDX-MS) enables solution-phase characterization of protein interactions and conformational dynamics, but analysis of intact enveloped virions remains challenging because limited proteolytic accessibility restricts peptide recovery. Here, we developed an acoustic-assisted HDX-MS workflow integrating chemical denaturation with bath sonication during quenching and applied it to dengue virus serotype 2 (DENV2) strain D2Y98P. The workflow achieved sequence coverages of 96.0 ± 0.7%, 89.8 ± 0.8% and 87.1 ± 1.0% for the capsid (C), envelope (E) and membrane (M) proteins, respectively. Model peptide measurements showed comparable back-exchange between sonication and incubation at matched durations, although longer treatment increased deuterium loss. Improved E protein coverage enabled characterization of changes in deuterium uptake associated with binding of the neutralizing antibody 2D22. Protected regions overlapped spatially with the cryo-EM-defined quaternary interface, while additional protection occurred in regions remote from direct antibody contact. These findings are consistent with antibody-associated conformational stabilization extending beyond the binding interface. Acoustic-assisted HDX-MS therefore improves structural protein coverage and complements cryo-EM by revealing peptide-level changes in antibodyassociated protein dynamics in the intact virion context.
Source: ChemRxiv
Language: English
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7214953253