Ion mobility-tandem mass spectrometry of bulky tert-butyl thiol ligated gold nanoparticles.

Gold nanoparticles (AuNPs) synthesized in the 1-3 nm range have a specific number of gold core atoms and outer protecting ligands. They have become one of the "hot topics" in recent decades because of their interesting physical and chemical properties. The characterization of their structures is usually achieved by crystal X-ray diffraction although the structures of some AuNPs remain unknown because they have not been successfully crystallized. An alternative method for studying the structure of AuNPs is electrospray ionization-ion mobility-tandem mass spectrometry (ESI-IM-MSMS). This research evaluated how effectively ESI-IM-MSMS using the commercially available Waters Synapt XS instrument yielded useful structural information from two AuNPs; Au23 (S-tBu)16 and Au30 (S-tBu)18 . The study used the maximum range of available collision energies along with ion mobility separation to measure the energy-dependence of the product ions and their drift times which is a measure of their spatial size. For Au23 (S-tBu)16 , the dissociation gave the masses of the outer protecting monomeric [RS-Au-SR] and trimeric [SR-Au-SR-Au-SR-Au-SR] staples where R = tBu, and complete dissociation of the outer layer Au and tBu groups to reveal the Au15 S8 core. For Au30 (S-tBu)18 , the dissociation products was primarily through the loss of the partial ligands S-tBu and tBu from the outer protecting layer and the loss of single Au4 (S-tBu)4 unit. These results showed the that ESI-IM-MSMS analysis of the smaller Au23 (S-tBu)16 gave information on all it major structural components whereas for Au30 (S-tBu)18 , the overall structural information was limited to the ligands of the outer layer.

Thermochemical Studies of Ni(II) and Zn(II) Ternary Complexes using Ion Mobility-Mass Spectrometry.

This article describes an experimental protocol using electrospray-ion mobility-mass spectrometry (ES-IM-MS) and energy-resolved threshold collision-induced dissociation (TCID) to measure the thermochemistry of the dissociation of negatively-charged [amb+M(II)+NTA]- ternary complexes into two product channels: [amb+M(II)] + NTA or [NTA+M(II)]- + amb, where M = Zn or Ni and NTA is nitrilotriacetic acid. The complexes contain one of the alternative metal binding (amb) heptapeptides with the primary structures acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 or acetyl-Asp1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7, where the amino acids' Aa1,2,6,7 positions are the potential metal-binding sites. Geometry-optimized stationary states of the ternary complexes and their products were selected from quantum chemistry calculations (presently the PM6 semi-empirical Hamiltonian) by comparing their electronic energies and their collision cross-sections (CCS) to those measured by ES-IM-MS. From the PM6 frequency calculations, the molecular parameters of the ternary complex and its products model the energy-dependent intensities of the two product channels using a competitive TCID method to determine the threshold energies of the reactions that relate to the 0 K enthalpies of dissociation (ΔH0). Statistical mechanics thermal and entropy corrections using the PM6 rotational and vibrational frequencies provide the 298 K enthalpies of dissociation (ΔH298). These methods describe an EI-IM-MS routine that can determine thermochemistry and equilibrium constants for a range of ternary metal ion complexes.

Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide.

Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analogue methanobactin peptide-5, amb5) and in particular to explore the role of zinc binding in reactivity. Fragmentation pathways, their mechanisms, and collision energy transfer are discussed. The probability distributions of the pathways are compared with the results of the experimental IM-MS, MS/MS spectrum and previous thermal simulations. Collisional activation gives both statistical and non-statistical fragmentation pathways with non-statistical shattering mechanisms accounting for a relevant percentage of reactive trajectories, becoming dominant at higher energies. The tetra-coordination of zinc changes qualitative and quantitative fragmentation, in particular the shattering. The collision energy threshold for the shattering mechanism was found to be 118.9 kcal mol-1 which is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal mol-1 identified previously during thermal simulations. This difference can be attributed to the tetra-coordinated zinc complex that hinders the availability of the sidechains to undergo direct collision with the Ar projectile.

Comparison of the pH-dependent formation of His and Cys heptapeptide complexes of nickel(II), copper(II), and zinc(II) as determined by ion mobility-mass spectrometry.

The analog methanobactin (amb) peptide with the sequence ac-His1 -Cys2 -Gly3 -Pro4 -Tyr5 -His6 -Cys7 (amb5A ) will bind the metal ions of zinc, nickel, and copper. To further understand how amb5A binds these metals, we have undertaken a series of studies of structurally related heptapeptides where one or two of the potential His or Cys binding sites have been replaced by Gly, or the C-terminus has been blocked by amidation. The studies were designed to compare how these metals bind to these sequences in different pH solutions of pH 4.2 to 10 and utilized native electrospray ionization (ESI) with ion mobility-mass spectrometry (IM-MS) which allows for the quantitative analysis of the charged species produced during the reactions. The native ESI conditions were chosen to conserve as much of the solution-phase behavior of the amb peptides as possible and an analysis of how the IM-MS results compare with the expected solution-phase behavior is discussed. The oligopeptides studied here have applications for tag-based protein purification methods, as therapeutics for diseases caused by elevated metal ion levels or as inhibitors for metal-protein enzymes such as matrix metalloproteinases.

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides.

Electrospray ionization (ESI) can transfer an aqueous-phase peptide or peptide complex to the gas-phase while conserving its mass, overall charge, metal-binding interactions, and conformational shape. Coupling ESI with ion mobility-mass spectrometry (IM-MS) provides an instrumental technique that allows for simultaneous measurement of a peptide's mass-to-charge (m/z) and collision cross section (CCS) that relate to its stoichiometry, protonation state, and conformational shape. The overall charge of a peptide complex is controlled by the protonation of 1) the peptide's acidic and basic sites and 2) the oxidation state of the metal ion(s). Therefore, the overall charge state of a complex is a function of the pH of the solution that affects the peptides metal ion binding affinity. For ESI-IM-MS analyses, peptide and metal ions solutions are prepared from aqueous-only solutions, with the pH adjusted with dilute aqueous acetic acid or ammonium hydroxide. This allows for pH dependence and metal ion selectivity to be determined for a specific peptide. Furthermore, the m/z and CCS of a peptide complex can be used with B3LYP/LanL2DZ molecular modeling to discern binding sites of the metal ion coordination and tertiary structure of the complex. The results show how ESI-IM-MS can characterize the selective chelating performance of a set of alternative methanobactin peptides and compare them to the copper-binding peptide methanobactin.

Direct Dynamics Simulations of Fragmentation of a Zn(II)-2Cys-2His Oligopeptide. Comparison with Mass Spectrometry Collision-Induced Dissociation.

Abnormalities in zinc metabolism have been linked to many diseases, including different kinds of cancers and neurological diseases. The present study investigates the fragmentation pathways of a zinc chaperon using a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analog methanobactin peptide-5, amb5). DFT/M05-2X and B3LYP geometry optimizations of [amb5-3H+Zn(II)]- predicted three lowest energy conformers with different chelating motifs. Direct dynamics simulations, using the PM7 semiempirical electronic structure method, were performed for these conformers, labeled a, b, and c, to obtain their fragmentation pathways at different temperatures in the range 1600-2250 K. The simulation results were compared with negative ion mode mass spectrometry experiments. For conformer a, the number of primary dissociation pathways are 11, 14, 24, 70, and 71 at 1600, 1750, 1875, 2000, and 2250 K, respectively. However, there are only 6, 10, 13, 14, and 19 pathways corresponding to these temperatures that have a probability of 2% or more. For conformer b, there are 67 pathways at 2000 K and 71 pathways at 2250 K. For conformer c, 17 pathways were observed at 2000 K. For conformer a, for two of the most common pathways involving C-C bond dissociation, Arrhenius parameters were calculated. The frequency factors and activation energies are smaller than those for C-C homolytic dissociation in alkanes due to increased stability of the product ions as a result of hydrogen bonding. The activation energies agree with the PM7 barriers for the C-C dissociations. Comparison of the simulation and experimental fragmentation ion yields shows the simulations predict double or triple cleavages of the backbone with Zn(II) retaining its binding sites, whereas the experiment exhibits single cleavages of the backbone accompanied by cleavage of two of the Zn(II) binding sites, resulting in b- and y-type ions.

Weak Acid-Base Interactions of Histidine and Cysteine Affect the Charge States, Tertiary Structure, and Zn(II)-Binding of Heptapeptides.

Zinc fingers are proteins that are characterized by the coordination of zinc ions by an amino acid sequence that commonly contains two histidines and two cysteines (2His-2Cys motif). Investigations of oligopeptides that contain the 2His-2Cys motif, e.g., acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7, have discovered they exhibit pH-dependent Zn(II) chelation and have redox activities with Cu(I/II), forming a variety of metal complexes. To further understand how these 2His-2Cys oligopeptides bind these metal ions, we have undertaken a series of ion mobility-mass spectrometry and B3LYP/LanL2DZ computational studies of structurally related heptapeptides. Starting with the sequence above, we have modified the potential His, Cys, or C-terminus binding sites and report how these changes in primary structure affect the oligopeptides positive and negative charge states, conformational structure, collision-induced breakdown energies, and how effectively Zn(II) binds to these sequences. The results show evidence that the weak acid-base properties of Cys-His are intrinsically linked and can result in an intramolecular salt-bridged network that affects the oligopeptide properties.

Binding Selectivity of Methanobactin from Methylosinus trichosporium OB3b for Copper(I), Silver(I), Zinc(II), Nickel(II), Cobalt(II), Manganese(II), Lead(II), and Iron(II).

Methanobactin (Mb) from Methylosinus trichosporium OB3b is a member of a class of metal binding peptides identified in methanotrophic bacteria. Mb will selectively bind and reduce Cu(II) to Cu(I), and is thought to mediate the acquisition of the copper cofactor for the enzyme methane monooxygenase. These copper chelating properties of Mb make it potentially useful as a chelating agent for treatment of diseases where copper plays a role including Wilson's disease, cancers, and neurodegenerative diseases. Utilizing traveling wave ion mobility-mass spectrometry (TWIMS), the competition for the Mb copper binding site from Ag(I), Pb(II), Co(II), Fe(II), Mn(II), Ni(II), and Zn(II) has been determined by a series of metal ion titrations, pH titrations, and metal ion displacement titrations. The TWIMS analyses allowed for the explicit identification and quantification of all the individual Mb species present during the titrations and measured their collision cross-sections and collision-induced dissociation patterns. The results showed Ag(I) and Ni(II) could irreversibly bind to Mb and not be effectively displaced by Cu(I), whereas Ag(I) could also partially displace Cu(I) from the Mb complex. At pH ≈ 6.5, the Mb binding selectivity follows the order Ag(I)≈Cu(I)>Ni(II)≈Zn(II)>Co(II)>>Mn(II)≈Pb(II)>Fe(II), and at pH 7.5 to 10.4 the order is Ag(I)>Cu(I)>Ni(II)>Co(II)>Zn(II)>Mn(II)≈Pb(II)>Fe(II). Breakdown curves of the disulfide reduced Cu(I) and Ag(I) complexes showed a correlation existed between their relative stability and their compact folded structure indicated by their CCS. Fluorescence spectroscopy, which allowed the determination of the binding constant, compared well with the TWIMS analyses, with the exception of the Ni(II) complex. Graphical abstract ᅟ.

Applying Ion Mobility-Mass Spectrometry Techniques for Explicitly Identifying the Products of Cu(II) Reactions of 2His-2Cys Motif Peptides.

The Cu(II) and pH titrations of four structurally similar 2His-2Cys motif peptides were investigated by electrospray ionization-ion mobility-mass spectrometry. The results provided insight into the pH dependent redox processes that took place in solution and identified the number of inter- or intramolecular disulfide bridges, the number of Cu(I) or Cu(II) ions, the deprotonation sites, and likely Cu(I/II) coordination of the various products. Competitive Cu(II) titrations of binary peptide mixtures at pH 5 indicated which species would preferably bind Cu(I) ions over forming the intramolecular disulfide bridge. Moreover, these reactions were pH dependent and included the formation of various multimers and multiple Cu(I/II) binding. For example, for the mildly acidic solution (pH ∼ 3-6) each monomer (whether it was free or in a multimer) primarily bound up to 3 Cu(I) ions, whereas at pH ∼ 8-11 the fully oxidized monomer or multimer (where all Cys formed a disulfide bond) primarily bound up to 2 Cu(II) ions. This behavior was indicative of linear bridging of Cu(I) by Cys thiolate and His imidazole groups, whereas the coordination of Cu(II) involved His and the nitrogens of deprotonated backbone amide groups, resulting in either distorted T-shaped or square planar geometries.

The multiple conformational charge states of zinc(II) coordination by 2His-2Cys oligopeptide investigated by ion mobility-mass spectrometry, density functional theory and theoretical collision cross sections.

Whether traveling wave ion mobility-mass spectrometry (IM-MS), B3LYP/LanL2DZ density functional theory, and ion size scaled Lennard-Jones (LJ) collision cross sections (CCS) from the B3LYP optimized structures could be used to determine the type of Zn(II) coordination by the oligopeptide acetyl-His1 -Cys2 -Gly3 -Pro4 -Tyr5 -His6 -Cys7 (amb5 ) was investigated. The IM-MS analyses of a pH titration of molar equivalents of Zn(II):amb5 showed that both negatively and positively charged complexes formed and coordination of Zn(II) increased as the His and Cys deprotonated near their pKa values. The B3LYP method was used to generate a series of alternative coordination structures to compare with the experimental results. The method predicted that the single negatively charged complex coordinated Zn(II) in a distorted tetrahedral geometry via the 2His-2Cys substituent groups, whereas, the double negatively charged and positively charged complexes coordinated Zn(II) via His, carbonyl oxygens and the C-terminus. The CCS of the B3LYP complexes were calculated using the LJ method and compared with those measured by IM-MS for the various charge state complexes. The LJ method provided CCS that agreed with five of the alternative distorted tetrahedral and trigonal bipyramidal coordinations for the doubly charged complexes, but provided CCS that were 15 to 31 Å2 larger than those measured by IM-MS for the singly charged complexes. Collision-induced dissociation of the Zn(II) complexes and a further pH titration study of amb5B , which included amidation of the C-terminus, suggested that the 2His-2Cys coordination was more significant than coordinations that included the C-terminus. Copyright © 2016 John Wiley & Sons, Ltd.

Redox activity and multiple copper(I) coordination of 2His-2Cys oligopeptide.

Copper binding motifs with their molecular mechanisms of selective copper(I) recognition are essential molecules for acquiring copper ions, trafficking copper to specific locations and controlling the potentially damaging redox activities of copper in biochemical processes. The redox activity and multiple Cu(I) binding of an analog methanobactin peptide-2 (amb2) with the sequence acetyl-His1-Cys2-Tyr3-Pro4-His5-Cys6 was investigated using ion mobility-mass spectrometry (IM-MS) and UV-Vis spectrophotometry analyses. The Cu(II) titration of amb2 showed oxidation of amb2 via the formation of intra- and intermolecular Cys-Cys disulfide bridges and the multiple Cu(I) coordination by unoxidized amb2 or the partially oxidized dimer and trimer of amb2. The principal product of these reactions was [amb2 + 3Cu(I)](+) which probably coordinates the three Cu(I) ions via two bridging thiolate groups of Cys2 and Cys6 and the δN6 of the imidazole groups of His6, as determined by geometry optimized structures at the B3LYP/LanL2DZ level of theory. The products observed by IM-MS showed direct correlation to spectral changes associated with disulfide bond formation in the UV-Vis spectrophotometric study. The results show that IM-MS analysis is a powerful technique for unambiguously determining the major ion species produced during the redox and metal binding chemistry of oligopeptides.

Probing the stability of insulin oligomers using electrospray ionization ion mobility mass spectrometry.

The peptide hormone insulin is central to regulating carbohydrate and fat metabolism in the body by controlling blood sugar levels. Insulin's most active form is the monomer and the extent of insulin oligomerization is related to insulin's activity of controlling blood sugar levels. Electrospray ionization (ESI) of human insulin produced a series of oligomers from the monomer to the undecamer identified using quadrupole ion mobility time-of-flight mass spectrometry. Previous research suggested that only the monomer, dimer and hexamer are native forms of insulin in solution and the range of oligomers observed in the gas-phase are ESI artifacts. Here the properties of three distinct oligomer bands I, II and III, where both the charge state and number of insulin units of the oligomer increase incrementally, were investigated. When Zn(ii) was added to the insulin sample the same oligomers were observed but with 0-6 Zn(ii) ions bound to each of the oligomers. The oligomers of bands I, II and III were characterized by comparing their drift times, collision cross- sections, relative intensities, collision-induced dissociation (CID) patterns and relative breakdown energies. Insulin oligomers of band I dissociated primarily by releasing either the 2+ or 3+ monomer accompanied by an oligomer that conserved the mass, charge and Zn(ii) of the precursor. Insulin oligomers of bands II and III dissociated primarily by releasing the 2+ monomer accompanied by an oligomer which conserved the mass, charge and Zn(ii) of the precursor. Comparison of CID patterns and breakdown energies showed all the oligomers in band II required higher collision energies to dissociate than the oligomers in band I, and the oligomers of band III required higher energies to dissociate than oligomers of band II. These results show that the amount of excess charge on the oligomer in respect to the number of insulin monomers in the oligomer affects their stability.

The pH dependent Cu(II) and Zn(II) binding behavior of an analog methanobactin peptide.

The pH dependent reactivity of an analog methanobactin peptide (amb) with the sequence acetyl-His1-Cys2-Gly3-Pro4-His5-Cys6 (Mw = 694.79 Da) was investigated for its binding ability for a series of biologically active metal ions using ion mobility-mass spectrometry. Cu(II), Zn(II) and, to a lesser extent, Ni(II) were observed to form complexes with amb from 1 : 1 molar equivalent amb:metal(II) solutions at pH > 6, indicating the deprotonation of the imidazole N of His (pKa = 6.0) must occur to allow the initial anchoring of the metal(II) ion. The amb-metal(II) complexes were observed as both positive and negative ions, although the Zn(II) complexes preferred forming an overall negative ion complex which is consistent with the two thiolate groups of Cys2 and Cys6 being involved in Zn(II) coordination. The Cu(II) addition, however, always resulted in a Cys-Cys disulfide bridge in both Cu-free amb and Cu-bound amb, which excluded thiolate coordination to Cu(II). Collision cross- section measurements showed the Zn(II) and Cu(II) negative ion complexes were smaller than the positive ion complexes, suggesting Zn(II) binds most compactly via the imidazole N of His and the thiolate groups of Cys, whereas Cu(II) binds most compactly via the imidazole N of His and two deprotonated N of two amide groups on the peptide backbone. The lowest energy structures from the B3LYP/LanL2DZ level of theory showed the functional groups of His5, Cys2 and Cys6 coordinated to Zn(II), whereas the His1 and the amide nitrogens of Cys2 and Gly3 coordinated to Cu(II), producing an overall negative charged complex. The positive ion complexes of Zn(II) and Cu(II) were both shown to coordinate via the two imidazole nitrogens of His1 and His5 and either the oxygen of the backbone carbonyl of Cys6 or the oxygen of the C-terminal, respectively.

Analysis of methanobactin from Methylosinus trichosporium OB3b via ion mobility mass spectrometry.

Methanobactins (mbs) are Low molecular mass copper binding chromopeptides analogous to pyoverdin class iron-binding siderophores. Mb produced by Methylosinus trichosporium OB3b (mb-oB3b) has been used as a model molecuLe for methanobactin although the amino acid sequence of mb-OB3b differs significantly from other characterized mbs. In particular, there is the presence of a pair of cystine residues which are absent in other characterized mbs. The role of the Cys3-Cys6 in copper binding, Cu(ll) reduction and its role on the mb-OB3b structure remains in debate. Here, we use a single-step dithiothreitol treatment as an effective method in reducing the disulfide bond allowing in-depth ion mobility-mass spectrometry (IM-MS) analysis. The IM-MS results show mb-oB3b exists in the gas-phase as three different negatively-charged states and exists in multiple conformational states, when introduced via electrospray ionization from aqueous solution near physiological pH. The disulfide bond serves a structural role and is not involved in the Cu(I/ll) binding capability of mb-OB3b, with the binding of a second Cu(I/ll) related to a further deprotonation of mb-OB3b. Overall, these findings are in good correlation with expected solution-phase behavior of mb-OB3b. The results suggest IM-MS is an effective tool for better understanding the complex nature of this intriguing peptide.

Study of metal ion labeling of the conformational and charge states of lysozyme by ion mobility mass spectrometry.

The efficiency of Zn(2+), Cu(2+), Ni(2+), Co(2+), Fe(2+) or Mn(2+) labeling of the conformational and charge states of lysozyme was studied in H(2)O solvent at pH 2.5-6.8. Labeling of lysozyme was conducted with 50 M, 100 M and 500 M excess of the metal ion, resulting in the number of metal ions attached to lysozyme increasing two-fold over this range. At pH 6.2-6.8, Zn(2+), Cu(2+), Ni(2+), Co(2+) and Mn(2+) labeled the highly folded 7+ conformer and the 8+ and 9+ partially unfolded conformers of lysozyme with the same number of metal ion tags, with only Fe(2+) exhibiting no labeling. Lysozyme conserved its charge after metal ion labeling which shows at each charge state the divalent metal ion is replacing two protons. As the pH is lowered to 4.7-5.0 and 2.5-2.9, the labeling of lysozyme by Zn(2+), Cu(2+), Ni(2+), Co(2+) or Mn(2+) decreased in efficiency due to increased competition from protons for the aspartate and glutamate binding sites. The metal ions preferentially labeled the highly folded 7+ and partially unfolded 8+ conformers, but labeling decreased as the charge of lysozyme increased. In contrast to the other metal ions, Fe(2+) exhibited labeling of lysozyme only at the lowest pH of 2.8. At higher pH, the oxidation of Fe(2+) and formation of hydroxy-bridged complexes probably make the Fe(2+) unreactive towards lysozyme.

Metal complexes as artificial proteases in proteomics: a palladium(II) complex cleaves various proteins in solutions containing detergents.

Most popular agents for site-specific protein cleavage are proteolytic enzymes. Because they become denatured and inactivated by detergents, enzymes are inconvenient for proteomic analysis of hydrophobic proteins which require detergents as solubilizing agents. We used cis-[Pd(en)(H(2)O)(2)](2+) (in which en represents ethylenediamine) as an artificial protease to effect cleavage of three bovine proteins, namely ubiquitin, ß-casein, and serum albumin, in separate experiments. Cleavage took place in aqueous solutions containing 1.0%wt./vol. of either 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) or Zwittergent 3-14 at 2.5

Ion mobility-mass spectrometry study of folded ubiquitin conformers induced by treatment with cis-[Pd(en)(H2O2]2+.

Ion mobility-mass spectrometry is used to study the new conformers of bovine ubiquitin (Ub) and the palladium(II) binding sites after the incubation with cis-[Pd(en)(H(2)O)(2)](2+) where en = ethylenediamine. Palladium(II) complexes are potentially useful proteomic reagents because they selectively bind to the side groups of methionine and histidine and hydrolytically cleave the peptide bond. Incubating 1.0 mM solution of Ub with 10.0 molar excess of cis-[Pd(en)(H(2)O)(2)](2+) results with one to four Pd(2+) or Pd(en)(2+) being attached to intact Ub and two conformer families at each of the 4+ to 11+ charge states. The 4+ and 5+ species exhibit a compact form, which is also observed in untreated Ub, and a new highly folded conformer. The 6+ to 10+ exhibit an elongated form, also observed in Ub, and a new partially folded conformer. The new conformers are shown to be more stable if they contain at least one Pd(2+), rather than all Pd(en)(2+). IM-MS/MS of [UbPd(2)en+5H](9+) shows that both the partially folded and elongated conformers first lose the en ligand, followed by dissociating into product ions that indicate that Met1, Glu51/Asp52, His68, and Glu16 are binding sites for Pd(2+). These results suggest that Pd(2+) is simultaneously binding to multiple side groups across different regions of Ub. This type of sequestering of Pd(2+) probably reduces the efficiency of Pd(2+) ions to selectively cleave Ub because it prevents Pd(2+) anchoring to only Met or His and to an adjacent backbone amide nitrogen and forming the "activated complex" necessary for specific peptide bond cleavage.

Effects of transition metal ion identity and π-cation interactions in metal-bis(peptide) complexes containing phenylalanine.

Electrospray ionization-tandem mass spectrometry was used to study the effects of the metal ion identity and π-cation interactions on the dissociation pathways of metal-bis(peptide) complexes, where the metal is either Mn(2+), Co(2+), Ni(2+), Cu(2+), or Zn(2+); and the peptide is either FGGF, GGGG, GF, or GG, where G is glycine and F is phenylalanine. The [(FGGF)(FGGF-H) + M(2+)](+) and [(GGGG)(GGGG-H) + M(2+)](+) complexes dissociated by losing one FGGF or GGGG, respectively. Relative binding affinities were measured using the crossover points, where the parent and product ions were equal in ion abundance and a normalized-collision energy scale. The results indicate the relative binding affinities for FGGF and GGGG follow the same order with respect to the transition metal ion identity: Cu(2+) < Ni(2+) < Mn(2+) ≈ Zn(2+) < Co(2+), and the π-cation interactions in the FGGF complex have a measureable stabilizing effect. In contrast, the main fragmentation channels of [(GF)(GF-H) + M(2+)]+ and [(GG)(GG-H) + M(2+)](+) are loss of CO(2) and 2CO(2) with the [(GF)(GF-H) + M(2+)](+) complex also exhibiting cinnamic acid ,GF, residual glycine, cinnamate and styrene loss.

Ion mobility mass spectrometry of Au25(SCH2CH2Ph)18 nanoclusters.

Ion mobility mass spectrometry (IM-MS) can separate ions based on their size, shape, and charge as well as mass-to-charge ratios. Here, we report experimental IM-MS and IM-MS/MS data of the Au(25)(SCH(2)CH(2)Ph)(18)(-) nanocluster. The IM-MS of Au(25)(SCH(2)CH(2)Ph)(18)(-) exhibits a narrow, symmetric drift time distribution that indicates the presence of only one structure. The IM-MS/MS readily distinguishes between the fragmentation of the outer protecting layer, made from six [-SR-Au-SR-Au-SR-] "staples' where R = CH(2)CH(2)Ph, and the Au(13) core. The fragmentation of the staples is characterized by the predominant loss of Au(4)(SR)(4) from the cluster and the formation of eight distinct bands. The consecutive eight bands contain an increasing variety of Au(l)S(m)R(n)(-) product ions due to the incremental fragmentation of the outer layer of Au(21)X(14)(-), where X = S or SCH(2)CH(2)Ph. The mobility of species in each individual band shows that the lower mass species exhibit greater collision cross sections, facilitating the identification of the Au(l)S(m)R(n)(-) products. Below the bands, in the region 1200-2800 m/z, product ions relating to the fragmentation of the Au(13) core can be observed. In the low mass 50-1200 m/z region, fragment ions such as Au(SR)(2)(-), Au(2)(SR)(3)(-), Au(3)(SR)(4)(-), and Au(4)(SR)(5)(-) are also observed, corresponding to the large fragments Au(25-x)(SR)(18-(x+1)). The study shows that most of the dominant large fragments are of the general type Au(21)X(14)(-/+), and Au(17)X(10)(-/+) with electron counts of 8 and 6 in negative and positive mode, respectively. This suggests that geometric factors may outweigh electronic factors in the selection of Au(25)(SR)(18) structure.

Threshold collision-induced dissociation of hydrogen-bonded dimers of carboxylic acids.

Energy-resolved competitive collision-induced dissociation is used to investigate the proton-bound heterodimer anions of a series of carboxylic acids (formic, acetic, and benzoic acid) and nitrous acid with their conjugate bases. The dissociation reactions of the complexes [CH3COO.H.OOCH]-, [CH3COO.H.ONO]-, [HCOO.H. ONO]-, [C6H5COO.H.OOCH]-, and [C6H5COO.H.ONO]- are investigated using a guided ion beam tandem mass spectrometer. Cross sections of the two dissociation channels are measured as a function of the collision energy between the complex ions and xenon target gas. Apparent relative gas-phase acidities are found by modeling the cross sections near the dissociation thresholds using statistical rate theory. Internal inconsistencies are found in the resulting relative acidities. These deviations apparently result from the formation of higher-energy conformers of the acids within the complex ions induced by double hydrogen bonding, which impedes the kinetics of dissociation to ground-state product acid conformations.