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PyHDX: Derivation and visualization of protection factors from Hydrogen-Deuterium Exchange Mass Spectrometry at near residue resolution

View ORCID ProfileJochem H. Smit, View ORCID ProfileSrinath Krishnamurthy, View ORCID ProfileBindu Y. Srinivasu, View ORCID ProfileSpyridoula Karamanou, View ORCID ProfileAnastassios Economou
doi: https://doi.org/10.1101/2020.09.30.320887
Jochem H. Smit
KU Leuven, Department of Microbiology and Immunology, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
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  • ORCID record for Jochem H. Smit
Srinath Krishnamurthy
KU Leuven, Department of Microbiology and Immunology, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
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Bindu Y. Srinivasu
KU Leuven, Department of Microbiology and Immunology, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
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Spyridoula Karamanou
KU Leuven, Department of Microbiology and Immunology, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
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Anastassios Economou
KU Leuven, Department of Microbiology and Immunology, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
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  • For correspondence: tassos.economou@kuleuven.be
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Abstract

Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS) is a powerful technique to monitor the intrinsic and conformational dynamics of proteins. Most HDX-MS experiments compare protein states (e.g. apoprotein vs liganded) and provide detailed information on differential dynamics between them obtained from multiple overlapping peptides. However, differential dynamics are difficult to compare across protein derivatives, oligomeric assemblies, homologues and samples treated under different buffer and protease conditions. A main reason is that peptide-based D-uptake differences do not inform on absolute intrinsic dynamics at the level of single aminoacyl residues. Such information is offered by protection factors, i.e. the position of the local equilibrium between the D-exchange-competent ‘open’ state and the non-exchanging ‘closed’ state. We present PyHDX, a software tool to calculate protection factors and Gibbs free energies typically within minutes from HDX-MS-derived peptide lists. PyHDX provides intrinsic information on the thermodynamics of protein dynamics at single-residue level. An interactive web interface further streamlines the process of transforming peptide lists to either coloured linear sequence maps or 3D structures of Gibbs free energies/protection factors.

Availability PyHDX source code is released under the MIT license and can be accessed at the project’s GitHub page.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/Jhsmit/PyHDX

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 02, 2020.
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PyHDX: Derivation and visualization of protection factors from Hydrogen-Deuterium Exchange Mass Spectrometry at near residue resolution
Jochem H. Smit, Srinath Krishnamurthy, Bindu Y. Srinivasu, Spyridoula Karamanou, Anastassios Economou
bioRxiv 2020.09.30.320887; doi: https://doi.org/10.1101/2020.09.30.320887
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PyHDX: Derivation and visualization of protection factors from Hydrogen-Deuterium Exchange Mass Spectrometry at near residue resolution
Jochem H. Smit, Srinath Krishnamurthy, Bindu Y. Srinivasu, Spyridoula Karamanou, Anastassios Economou
bioRxiv 2020.09.30.320887; doi: https://doi.org/10.1101/2020.09.30.320887

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