Probing Universal Protein Dynamics Using Hydrogen–Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy

Hydrogen–deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to monitor protein intrinsic dynamics. The technique provides high-resolution information on how protein intrinsic dynamics are altered in response to biological signals, such as ligand binding, oligomerization, or allost...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2021-09, Vol.93 (38), p.12840-12847
Main Authors: Smit, Jochem H, Krishnamurthy, Srinath, Srinivasu, Bindu Y, Parakra, Rinky, Karamanou, Spyridoula, Economou, Anastassios
Format: Article
Language:English
Subjects:
Allosteric properties
Analytical chemistry
Chemistry
Data points
Datasets
Deuterium
Free energy
Gibbs free energy
Homology
Hydrogen-based energy
Hydrogen-deuterium exchange
Mass spectrometry
Mass spectroscopy
Oligomerization
Peptides
Proteins
Residues
Scientific imaging
Spectroscopy
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Summary:Hydrogen–deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to monitor protein intrinsic dynamics. The technique provides high-resolution information on how protein intrinsic dynamics are altered in response to biological signals, such as ligand binding, oligomerization, or allosteric networks. However, identification, interpretation, and visualization of such events from HDX-MS data sets is challenging as these data sets consist of many individual data points collected across peptides, time points, and experimental conditions. Here, we present PyHDX, an open-source Python package and webserver, that allows the user to batch extract the universal quantity Gibbs free energy at residue levels over multiple protein conditions and homologues. The output is directly visualized on a linear map or 3D structures or is exported as .csv files or PyMOL scripts.
ISSN:0003-2700
1520-6882
DOI:10.1021/acs.analchem.1c02155