Hydrogen-Deuterium Exchange Mass Spectrometry to Study Protein Complexes

  • Brent A. Kochert
  • Roxana E. Iacob
  • Thomas E. Wales
  • Alexandros Makriyannis
  • John R. Engen
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)


Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) can provide valuable information about binding, allostery, and other conformational effects of interaction in protein complexes. For protein-ligand complexes, where the ligand may be a small molecule, peptide, nucleotide, or another protein(s), a typical experiment measures HDX in the protein alone and then compares that with HDX for the protein when part of the complex. Multiple factors are critical in the design and implementation of such experiments, including thoughtful consideration of the percent protein bound, the effects of the labeling protocol on the protein complex, and the dynamic range of the analysis method. With careful planning and techniques, HDX MS analysis of protein complexes can be very informative.

Key words

Dissociation constant Binding Deuteration Percent bound LC-MS Interactions Ligand 



Support from the NIH (R01 GM101135, J.R.E.) and a research collaboration with the Waters Corporation are gratefully acknowledged.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Brent A. Kochert
    • 1
    • 2
  • Roxana E. Iacob
    • 1
  • Thomas E. Wales
    • 1
  • Alexandros Makriyannis
    • 1
    • 2
  • John R. Engen
    • 1
  1. 1.Department of Chemistry and Chemical BiologyNortheastern UniversityBostonUSA
  2. 2.Center for Drug DiscoveryNortheastern UniversityBostonUSA

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