Usage
  • 13 views
  • 5 downloads

Mapping protein-ligand interactions in the gas phase using a functional group replacement strategy: Comparison of CID and BIRD activation methods

  • Author(s) / Creator(s)
  • Intermolecular interactions in the gaseous ions of two protein–ligand complexes, a single chain antibody (scFv) and its trisaccharide ligand (α-D-Galp-(1→2)-[α-D-Abep-(1→3)]-α-Manp-OCH3, L1) and streptavidin homotetramer (S4) and biotin (B), were investigated using a collision-induced dissociation (CID)-functional group replacement (FGR) strategy. CID was performed on protonated ions of a series of structurally related complexes based on the (scFv + L1) and (S4 + 4B) complexes, at the +10 and +13 charge states, respectively. Intermolecular interactions were identified from decreases in the collision energy required to dissociate 50 % of the reactant ion (Ec50) upon modification of protein residues or ligand functional groups. For the (scFv + L1)10+ ion, it was found that deoxygenation of L1 (at Gal C3 and C6 and Man C4 and C6) or mutation of His101 (to Ala) resulted in a decrease in Ec50 values. These results suggest that the four hydroxyl groups and His101 participate in intermolecular H-bonds. These findings agree with those obtained using the blackbody infrared radiative dissociation (BIRD)-FGR method. However, the CID-FGR method failed to reveal the relative strengths of the intermolecular interactions or establish Man C4 OH and His101 as an H-bond donor/acceptor pair. The CID-FGR method correctly identified Tyr43, but not Ser27, Trp79, and Trp120, as a stabilizing contact in the (S4 + 4B)13+ ion. In fact, mutation of Trp79 and Trp120 led to an increase in the Ec50 value. Taken together, these results suggest that the CID-FGR method, as implemented here, does not represent a reliable approach for identifying interactions in the gaseous protein–ligand complexes.

  • Date created
    2013
  • Subjects / Keywords
  • Type of Item
    Article (Published)
  • DOI
    https://doi.org/10.7939/R30K26R2S
  • License
    © 2013 Deng, L., Kitova, E. N., & 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.
  • Language
  • Citation for previous publication
    • Deng, L., Kitova, E. N., & Klassen, J. S. (2013). Mapping protein-ligand interactions in the gas phase using a functional group replacement strategy: Comparison of CID and BIRD activation methods. Journal of the American Society for Mass Spectrometry, 24(7), 988-996. http://doi.org/10.1007/s13361-013-0651-8
  • Link to related item
    http://doi.org/10.1007/s13361-013-0651-8