Localizing carbohydrate binding sites in proteins using hydrogen/deuterium exchange mass spectrometry

• Author(s) / Creator(s)

  • Kitova, Elena N.
  • Klassen, John S.
  • Eugenio, Luiz
  • Li, Jun
  • Ng, Kenneth
  • Zhang, Jingjing

• The application of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to localize ligand binding sites in carbohydrate-binding proteins is described. Proteins from three bacterial toxins, the B subunit homopentamers of Cholera toxin and Shiga toxin type 1 and a fragment of Clostridium difficile toxin A, and their interactions with native carbohydrate receptors, GM1 pentasaccharides (β-Gal-(1→3)-β-GalNAc-(1→4)[α-Neu5Ac-(2→3)]-β-Gal-(1→4)-Glc), Pk trisaccharide (α-Gal-(1→4)-β-Gal-(1→4)-Glc) and CD-grease (α-Gal-(1→3)-β-Gal-(1→4)-β-GlcNAcO(CH2)8CO2CH3), respectively, served as model systems for this study. Comparison of the differences in deuterium uptake for peptic peptides produced in the absence and presence of ligand revealed regions of the proteins that are protected against deuterium exchange upon ligand binding. Notably, protected regions generally coincide with the carbohydrate binding sites identified by X-ray crystallography. However, ligand binding can also result in increased deuterium exchange in other parts of the protein, presumably through allosteric effects. Overall, the results of this study suggest that HDX-MS can serve as a useful tool for localizing the ligand binding sites in carbohydrate-binding proteins. However, a detailed interpretation of the changes in deuterium exchange upon ligand binding can be challenging because of the presence of ligand-induced changes in protein structure and dynamics.

• Date created

  2016

• Subjects / Keywords

  • Hydrogen/deuterium exchange mass spectrometry
  • Protein–carbohydrate complexes
  • Hydrogen bonds

• Type of Item

  Article (Published)

• DOI

  https://doi.org/10.7939/R31G0J78M

• License

  © 2016 Zhang, J., Kitova, E. N., Li, J., Eugenio, L., Ng, K., & Klassen, J. S. This version of this article is open access and can be downloaded and shared. The original author(s) and source must be cited.