Stabilization of Compact Protein Structures by Macrocyclic Hosts Cucurbit[n]urils in the Gas Phase

: Characterization of intact protein structures in the gas phase using electrospray ionization combined with ion mobility mass spectrometry has become an important tool of research. However, the biophysical properties that govern the structures of protein ions in the gas phase remain to be understood. Here, we investigated the impact of host-guest complexation of ubiquitin (Ubq) with macrocyclic host molecules, cucurbit[ n ]urils (CB[ n ]s, n = 6, 7), on its structure in the gas phase. We found that CB[ n ] complexation induces the formation of compact Ubq ions. Both CB[6] and CB[7] exhibited similar effects despite differences in their binding properties in solution. In addition, CB[ n ] attachment prevented Ubq from unfolding by collisional activation. Based on the experimental results, we suggest that CB[ n ]s prevent unfolding of Ubq during transfer to the gas phase to promote the formation of compact protein ions. Furthermore, interaction with positively charged residues per se is suggested to be the most important factor for the host-guest complexation effect.