Top-down hydrogen/deuterium exchange and ECD-stitched FTICR-MS for probing structural dynamics of a 29-kDa enzyme

Jingxi Pan, Jun Han, Christoph H. Borchers

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


Top-down hydrogen/deuterium exchange mass spectrometry (HDX-MS) is becoming a powerful tool for structural biology. Using gas-phase sequencing methods such as electron capture dissociation (ECD), "H/D scrambling free" top-down HDX measurements on proteins can be made with high resolution and full sequence coverage. Although it has clear advantages over traditional proteolysis- and liquid chromatography-based HDX-MS, its application has thus far been limited to small (<18 kDa) proteins. The current study has extended the top-down approach to structural dynamics characterization of a nearly 30 kDa protein, carbonic anhydrase II (CAII). Employing a novel "ECD- stitching" method, which combines two different ECD settings optimized for the observation of small and large fragments respectively, a total of 120 fragment ions were obtained with sufficient signal/noise for top-down HDX-MS analysis. These ions cover the whole sequence of the protein and provide an average resolution of 2 residues. The results have shown that the most protected region in CAII is the β-sheet motif located in the center of the enzyme, while α-helices located at the outer surface exhibit much less protection. A high degree of protection was also found in loops where solvent access is restricted. These observations are compatible with the structural features of CAII as provided by X-ray crystallographic studies. In addition, the drug-induced conformational transitions of CAII were also characterized. The ECD-stitching top-down approach should be readily applicable to other large proteins and protein complexes, and may give better insights into conformational changes and other solution-phase processes than can be obtained via crystallographic techniques.

Original languageEnglish
Pages (from-to)130-138
Number of pages9
JournalInternational Journal of Mass Spectrometry
Publication statusPublished - 1 Jul 2012
Externally publishedYes


  • Conformational change
  • Drug binding
  • ECD
  • Electron capture dissociation
  • HDX
  • Hydrogen/deuterium exchange
  • Structural dynamics
  • Top-down


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