Mapping Protein–Ligand Interactions in the Gas Phase Using a Functional Group Replacement Strategy. Comparison of CID and BIRD Activation Methods

Research Article

Abstract

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.

Key words

Protein–ligand complexes Collision-induced dissociation Intermolecular interactions Dissociation kinetics 

Notes

Acknowledgment

The authors are grateful for financial support provided by the Natural Sciences and Engineering Research Council of Canada and the Alberta Glycomics Centre.

Supplementary material

13361_2013_651_MOESM1_ESM.doc (1.2 mb)
ESM 1(DOC 1274 kb)

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Copyright information

© American Society for Mass Spectrometry 2013

Authors and Affiliations

  1. 1.Department of Chemistry and Alberta Glycomics CentreUniversity of AlbertaEdmontonCanada

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