Probing conformational changes of ubiquitin by host-guest chemistry using electrospray ionization mass spectrometry

Jong Wha Lee, Sung Woo Heo, Shin Jung C. Lee, Jae Yoon Ko, Hyungjun Kim, Hugh I. Kim

Research output: Contribution to journalArticlepeer-review

28 Citations (Scopus)


We report mechanistic studies of structural changes of ubiquitin (Ub) by host-guest chemistry with cucurbit[6]uril (CB[6]) using electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism spectroscopy and molecular dynamics (MD) simulation. CB[6] binds selectively to lysine (Lys) residues of proteins. Low energy collision-induced dissociation (CID) of the protein-CB[6] complex reveals CB[6] binding sites. We previously reported (Anal. Chem. 2011, 83, 7916-7923) shifts in major charge states along with Ub-CB[6] complexes in the ESI-MS spectrum with addition of CB[6] to Ub from water. We also reported that CB[6] is present only at Lys6 or Lys11 in high charge state (+13) complex. In this study, we provide additional information to explain unique conformational change mechanisms of Ub by host-guest chemistry with CB[6] compared with solvent-driven conformational change of Ub. Additional CID study reveals that CB[6] is bound only to Lys 48 and Lys63 in low charge state (+7) complex. MD simulation studies reveal that the high charge state complexes are attributed to the CB[6] bound to Lys11. The complexation prohibits salt bridge formation between Lys11 and Glu34 and induces conformational change of Ub. This results in formation of high charge state complexes in the gas phase. Then, by utilizing stronger host-guest chemistry of CB[6] with pentamethylenediamine, refolding of Ub via detaching CB[6] from the protein is performed. Overall, this study gives an insight into the mechanism of denatured Ub ion formation via host-guest interactions with CB[6]. Furthermore, this provides a direction for designing function-controllable supramolecular system comprising proteins and synthetic host molecules.

Original languageEnglish
Pages (from-to)21-29
Number of pages9
JournalJournal of the American Society for Mass Spectrometry
Issue number1
Publication statusPublished - 2013 Jan
Externally publishedYes


  • Collision-induced dissociation
  • Conformational change
  • Cucurbit[6]uril
  • Electrospray ionization
  • Host-guest chemistry
  • Supramolecular chemistry
  • Ubiquitin

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy


Dive into the research topics of 'Probing conformational changes of ubiquitin by host-guest chemistry using electrospray ionization mass spectrometry'. Together they form a unique fingerprint.

Cite this