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PreprintCC BYChemRxiv

Acoustic-assisted HDX-MS for Intact Virion Analysis

  • Li Ching Pang1,2
  • Ying Deng1,2
  • Vinayak Gupta1,2
  • Wen Zheng Lo1,2
  • Shuangshuang Zhu1,2
  • Muen Shan3,4
  • Marrisa, Mei Zhang3,4
  • Xueming Dong1,2
4 affiliations
  1. 1School of Biological Sciences
  2. 2Nanyang Technological University
  3. 3School of Chinese Materia Medica & Key Laboratory of Chinese Internal Medicine
  4. 4Beijing University of Chinese Medicine
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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.

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Cite

BibTeXRIS
BibTeX
@misc{pang2026acousticassisted,
  title = {{Acoustic-assisted HDX-MS for Intact Virion Analysis}},
  author = {Li Ching Pang and Ying Deng and Vinayak Gupta and Wen Zheng Lo and Shuangshuang Zhu and Muen Shan and Marrisa, Mei Zhang and Xueming Dong},
  howpublished = {ChemRxiv},
  year = {2026},
  month = sep,
  doi = {10.26434/chemrxiv.15009664/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009664/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Acoustic-assisted HDX-MS for Intact Virion Analysis
AU  - Li Ching Pang
AU  - Ying Deng
AU  - Vinayak Gupta
AU  - Wen Zheng Lo
AU  - Shuangshuang Zhu
AU  - Muen Shan
AU  - Marrisa, Mei Zhang
AU  - Xueming Dong
PY  - 2026
DA  - 2026/09/29
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15009664/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009664/v1
AB  - 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.
ER  -