ArticleJournal of the American Society for Mass Spectrometry2013
Probing conformational changes of ubiquitin by host-guest chemistry using electrospray ionization mass spectrometry.
Article in Journal of the American Society for Mass Spectrometry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 30 citations in OpenAlex.
- Macrocyclic Compounds for Drug and Gene Delivery in Immune-Modulating Therapy.International journal of molecular sciences · 2019Review
- Supramolecular Chemistry Targeting Proteins.Journal of the American Chemical Society · 2017Article
- HDAC7 Ubiquitination by the E3 Ligase CBX4 Is Involved in Contextual Fear Conditioning Memory Formation.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2017Article
- Supramolecular Adducts of Cucurbit[7]uril and Amino Acids in the Gas Phase.Journal of the American Society for Mass Spectrometry · 2016Article
- Molecular simulation-based structural prediction of protein complexes in mass spectrometry: the human insulin dimer.PLoS computational biology · 2014Article
- Host-guest chemistry in the gas phase: complex formation of cucurbit[6]uril with proton-bound water dimer.Journal of the American Society for Mass Spectrometry · 2014Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 Lys(6) or Lys(11) 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 Lys(63) in low charge state (+7) complex. MD simulation studies reveal that the high charge state complexes are attributed to the CB[6] bound to Lys(11). The complexation prohibits salt bridge formation between Lys(11) and Glu(34) 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.
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