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.

The gas-phase helix propensities of alanine-based polypeptides are studied with different locations of a Lys residue and host-guest interactions with 18-Crown-6 (18C6). A series of model peptides Ac-Ala(9-n)-LysH(+)-Ala(n) (n = 0, 1, 3, 5, 7, and 9) is examined alone and with 18C6 using traveling wave ion mobility mass spectrometry combined with molecular dynamics (MD) simulations. The gas-phase helices are observed from the peptides whose Lys residue is located close to the C-terminus so that the Lys exerts its capping effect on the C-terminal carbonyl groups. The peptides, which interact with 18C6 in the gas phase, show enhanced helical propensities. The enhanced helicity of the peptide in the complex is attributed by isolation of the Lys butylammonium group from the helix backbone and the interaction of methylene groups of 18C6, which possess localized positive partial charges, with C-terminal carbonyl groups serving as a cap to stabilize the helix.

Noncovalent interactions of cucurbit [6]uril (CB[6]) with haloacetate and halide anions are investigated in the gas phase using electrospray ionization ion mobility mass spectrometry. Strong noncovalent interactions of monoiodoacetate, monobromoacetate, monochloroacetate, dichloroacetate, and trichloroacetate on the exterior surface of CB [6] are observed in the negative mode electrospray ionization mass spectra. The strong binding energy of the complex allows intramolecular S N 2 reaction of haloacetate, which yields externally bound CB[6]-halide complex, by collisional activation. Utilizing ion mobility technique, structures of exteriorly bound CB[6] complexes of haloacetate and halide anions are confirmed. Theoretically determined low energy structures using density functional theory (DFT) further support results from ion mobility studies. The DFT calculation reveals that the binding energy and conformation of haloacetate on the CB[6] surface affect the efficiency of the intramolecular S N 2 reaction of haloacetate, which correlate well with the experimental observation.

Field-induced droplet ionization (FIDI) is a recently developed ionization technique that can transferions from the surface of microliter droplets to the gas phase intact. The air-liquid interfacial reactions of cholesterol sulfate (CholSO 4 ) in a 1-palmitoyl-2-oleoyl-sn-phosphatidylglycerol (POPG) surfactant layer with ozone (O 3 ) are investigated using field-induced droplet ionization mass spectrometry (FIDI-MS). Time-resolved studies of interfacial ozonolysis of CholSO 4 reveal that water plays an important role in forming oxygenated products. An epoxide derivative is observed as a major product of CholSO 4 oxidation in the FIDI-MS spectrum after exposure of the droplet to O 3 for 5 s. The abundance of the epoxide product then decreases with continued O 3 exposure as the finite number of water molecules at the air-liquid interface becomes exhausted. Competitive oxidation of CholSO 4 and POPG is observed when they are present together in a lipid surfactant layer at the air-liquid interface. Competitive reactions of CholSO 4 and POPG with O 3 suggest that CholSO 4 is present with POPG as a well-mixed interfacial layer. Compared with CholSO 4 and POPG alone, the overall ozonolysis rates of both CholSO 4 and POPG are reduced in a mixed layer, suggesting the double bonds of both molecules are shielded by additional hydrocarbons from one another. Molecular dynamics simulations of a monolayer comprising POPG and CholSO 4 correlate well with experimental observations and provide a detailed picture of the interactions between CholSO 4 , lipids, and water molecules in the interfacial region.