scholarly journals Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry

2018 ◽  
Author(s):  
Andy M. C. Lau ◽  
Zainab Ahdash ◽  
Chloe Martens ◽  
Argyris Politis
Keyword(s):  
Mass Spectrometry ◽  
Conformational Dynamics ◽  
Rapid Analysis ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Visualization Of Data ◽  
Hdx Ms

AbstractSummaryHydrogen deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful technique for interrogating the conformational dynamics of proteins and their complexes. Currently, analysis of HDX-MS data remains a laborious procedure, mainly due to the lack of streamlined software to process the large datasets. We present Deuteros which is a standalone software designed to be coupled with Waters DynamX HDX data analysis software, allowing the rapid analysis and visualization of data from differential HDX-MS.AvailabilityDeuteros is open-source and can be downloaded from https://github.com/andymlau/Deuteros, under the Apache 2.0 license.Implementationwritten in MATLAB and supported on both Windows and MacOS. Requires the MATLAB runtime [email protected]

scholarly journals Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry

2019 ◽  
Vol 35 (17) ◽  
pp. 3171-3173 ◽  
Author(s):  
Andy M C Lau ◽  
Zainab Ahdash ◽  
Chloe Martens ◽  
Argyris Politis
Keyword(s):  
Mass Spectrometry ◽  
Conformational Dynamics ◽  
Rapid Analysis ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Visualization Of Data ◽  
Hdx Ms

Abstract Summary Hydrogen deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful technique for interrogating the conformational dynamics of proteins and their complexes. Currently, analysis of HDX-MS data remains a laborious procedure, mainly due to the lack of streamlined software to process the large datasets. We present Deuteros which is a standalone software designed to be coupled with Waters DynamX HDX data analysis software, allowing the rapid analysis and visualization of data from differential HDX-MS. Availability and implementation Deuteros is open-source and can be downloaded from https://github.com/andymlau/Deuteros, under the Apache 2.0 license. Written in MATLAB and supported on both Windows and MacOS. Requires the MATLAB runtime library. According to the Wellcome Trust and UK research councils' Common Principles on Data Policy on data, software and materials management and sharing, all data supporting this study will be openly available from the software repository.

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

2020 ◽  
Author(s):  
Jochem H. Smit ◽  
Srinath Krishnamurthy ◽  
Bindu Y. Srinivasu ◽  
Spyridoula Karamanou ◽  
Anastassios Economou
Keyword(s):  
Mass Spectrometry ◽  
Local Equilibrium ◽  
Conformational Dynamics ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Free Energies ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Hdx Ms

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

scholarly journals Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 286
Author(s):  
Oliver Ozohanics ◽  
Attila Ambrus
Keyword(s):  
Mass Spectrometry ◽  
Membrane Proteins ◽  
Structural Biology ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Ligand Interaction ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Hdx Ms

Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a rapidly evolving technique for analyzing structural features and dynamic properties of proteins. It may stand alone or serve as a complementary method to cryo-electron-microscopy (EM) or other structural biology approaches. HDX-MS is capable of providing information on individual proteins as well as large protein complexes. Owing to recent methodological advancements and improving availability of instrumentation, HDX-MS is becoming a routine technique for some applications. When dealing with samples of low to medium complexity and sizes of less than 150 kDa, conformation and ligand interaction analyses by HDX-MS are already almost routine applications. This is also well supported by the rapid evolution of the computational (software) background that facilitates the analysis of the obtained experimental data. HDX-MS can cope at times with analytes that are difficult to tackle by any other approach. Large complexes like viral capsids as well as disordered proteins can also be analyzed by this method. HDX-MS has recently become an established tool in the drug discovery process and biopharmaceutical development, as it is now also capable of dissecting post-translational modifications and membrane proteins. This mini review provides the reader with an introduction to the technique and a brief overview of the most common applications. Furthermore, the most challenging likely applications, the analyses of glycosylated and membrane proteins, are also highlighted.

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