Skip to content
DraconiticResearch
Search Sources API
186,086 studies31 sourcesUpdated 24 min ago
PreprintCC BYChemRxiv

Studying Protein-Ligand Interactions with In-droplet Hydrogen-Deuterium Exchange Mass Spectrometry and Molecular Dynamics Simulations

  • Sohag Ahmed1,2
  • Mst Nigar Sultana1,2,3,4
  • Md Reaz Uddin5,6
  • Sultan Mahmud1,2
  • Mohammad A. Rahman1,2,7
  • Peng Li8
  • Stephen J. Valentine1,2,3,4
8 affiliations
  1. 1C. Eugene Bennett Department of Chemistry
  2. 2West Virginia University
  3. 3Department of Arts and Science
  4. 4University of Louisville
  5. 5Department of Molecular and Cellular Biology
  6. 6Kennesaw State University
  7. 7Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405
  8. 8Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, PA, 18015
Open at sourcePDFDOICite

Abstract

Native mass spectrometry (nMS) has been widely used for the characterization of biomolecules and their interactions with ligands under near-physiological conditions, yet connecting the change in conformational dynamics of proteins upon ligand binding remains challenging. In this work, the integration of capillary vibrating sharp-edge spray ionization based-nMS, in-droplet hydrogen deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations provides a platform to characterize ligand binding and ligand-induced conformational changes of bovine carbonic anhydrase II (BCAII) upon interaction with its inhibitor, acetazolamide (AZM). cVSSI-based-nMS preserves the protein native-like state and facilitates the direct identification and determination of the apparent binding affinity of the BCAII-AZM complex. In-droplet HDX-MS measurements show a reduction in deuterium incorporation upon AZM binding suggesting ligand-induced structural stabilization of the holo BCAII. MD simulations of the apo and holo protein revealed ligand-induced suppression in backbone fluctuations and enhanced structural rigidity. A new model that uses protection factors (PF) and HDX scoring derived from MD trajectories that is based on solvent accessible surface area (SASA) and hydrogen bonding propensity is further refined. The model reflects experimentally observed trends in deuterium incorporation and offers atomic-level insight into structural stabilization of BCAII upon AZM binding. The combination of the cVSSI-based nMS, in-droplet HDX-MS and MD simulations provides a framework for identification and quantification of protein-ligand interactions and elucidation of ligand-induced changes in conformational dynamics of the protein.

Related

  1. Mapping the TCR-Peptide-HLA Interface through Hydrogen-Deuterium Exchange Mass Spectrometry.
    Thomas Powell, Alice Colyer, Gemma Wildsmith +5
    Analytical chemistryPeer-reviewedCC BYFull textPhysical chemistryEurope PMC
  2. Online Soil Column Chromatography Coupled with Mass Spectrometry for Studying Sorption of Per- and Polyfluoroalkyl Substances and Other Organic Contaminants
    Anh T. Ngoc Do, Nobuhide Fujitake, Satoshi Endo
    ChemRxivPreprintCC BY-NC-NDFull textEnvironmental chemistryChemRxiv
  3. Molecular Mapping of Atherosclerotic Plaques with MALDI Mass Spectrometry Imaging
    Dawid Leksa, Dorota Bartusik-Aebisher, Daniel Roshan Justin Raj +6
    International Journal of Molecular SciencesPeer-reviewedCC BY 4.0Full textPhysical chemistryCrossrefEurope PMC
  4. NEVPT2 Multiple Spawning Molecular Dynamics Simulations for Uracil
    Yoshio Nishimoto
    ChemRxivPreprintLicence not statedGeneral chemistryChemRxiv
  5. A simple time coarse graining method for molecular dynamics simulations of liquids
    Maxime Martin, Levi Pereon, Quoc Tuan Truong +1
    Chemical PhysicsPeer-reviewedLicence not statedFull textPhysical chemistryHAL

Cite

BibTeXRIS
BibTeX
@misc{ahmed2026studying,
  title = {{Studying Protein-Ligand Interactions with In-droplet Hydrogen-Deuterium Exchange Mass Spectrometry and Molecular Dynamics Simulations}},
  author = {Sohag Ahmed and Mst Nigar Sultana and Md Reaz Uddin and Sultan Mahmud and Mohammad A. Rahman and Peng Li and Stephen J. Valentine},
  howpublished = {ChemRxiv},
  year = {2026},
  month = aug,
  doi = {10.26434/chemrxiv.15008038/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008038/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Studying Protein-Ligand Interactions with In-droplet Hydrogen-Deuterium Exchange Mass Spectrometry and Molecular Dynamics Simulations
AU  - Sohag Ahmed
AU  - Mst Nigar Sultana
AU  - Md Reaz Uddin
AU  - Sultan Mahmud
AU  - Mohammad A. Rahman
AU  - Peng Li
AU  - Stephen J. Valentine
PY  - 2026
DA  - 2026/08/30
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15008038/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008038/v1
AB  - Native mass spectrometry (nMS) has been widely used for the characterization of biomolecules and their interactions with ligands under near-physiological conditions, yet connecting the change in conformational dynamics of proteins upon ligand binding remains challenging. In this work, the integration of capillary vibrating sharp-edge spray ionization based-nMS, in-droplet hydrogen deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations provides a platform to characterize ligand binding and ligand-induced conformational changes of bovine carbonic anhydrase II (BCAII) upon interaction with its inhibitor, acetazolamide (AZM). cVSSI-based-nMS preserves the protein native-like state and facilitates the direct identification and determination of the apparent binding affinity of the BCAII-AZM complex. In-droplet HDX-MS measurements show a reduction in deuterium incorporation upon AZM binding suggesting ligand-induced structural stabilization of the holo BCAII. MD simulations of the apo and holo protein revealed ligand-induced suppression in backbone fluctuations and enhanced structural rigidity. A new model that uses protection factors (PF) and HDX scoring derived from MD trajectories that is based on solvent accessible surface area (SASA) and hydrogen bonding propensity is further refined. The model reflects experimentally observed trends in deuterium incorporation and offers atomic-level insight into structural stabilization of BCAII upon AZM binding. The combination of the cVSSI-based nMS, in-droplet HDX-MS and MD simulations provides a framework for identification and quantification of protein-ligand interactions and elucidation of ligand-induced changes in conformational dynamics of the protein.
ER  -