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This dissertation presents extensive structural studies of gas-phase peptide fragment ions, with a specific focus on b₂⁺ ions. Fragment ion structures can provide important insights into peptide fragmentation mechanisms. Based on the structures formed, information about the preference of competing b ion formation pathways can be obtained. b₂⁺ ion structures are of interest because of their large relative abundances in MS/MS spectra, which are difficult to predict. Prior to this work, only a few b₂⁺ ion structures were determined; these systems featured only aliphatic residues and all formed oxazolones. The work presented herein examines the influence of basic, acidic, and backbone-attached sidechains on peptide fragmentation mechanisms, as revealed by the resulting b₂⁺ fragment ion structure(s) formed. Specifically, the structures of several histidine, aspartic acid, and proline-containing b₂⁺ ions are determined by using action IRMPD spectroscopy, fragment ion HDX, and DFT calculations. The structures of a series of histidine analogue-containing b₂⁺ ions reveal that the location and availability of the pi-nitrogen is essential for diketopiperazine formation. The histidine sidechain bulk or strain interferes with the complete trans-cis isomerization required for diketopiperazine formation, so the oxazolone structure is also present. Xxx- Pro b₂⁺ ions favor oxazolone formation with aliphatic N-terminal residues. HP favors the diketopiperazine, combining the histidine effect and the proline cis conformation propensity. For Xxx-Asp b₂⁺ ions, aspartic acid significantly influences b₂⁺ ion structure only with an N-terminal histidine or lysine; both HD and KD form a mixture of oxazolone, anhydride, and diketopiperazine structures, presenting the first spectroscopic evidence for the anhydride b₂⁺ion structure. The HA and AH b₂⁺ ions feature the same structures, but HP and PH do not, showing that residue position matters. Additionally, while relative intensities and HDX rates featured some fluctuation, peptide precursor composition differences did not alter the mixture of b₂⁺ ion structures formed for a given b₂⁺ ion. To complement existing gas-phase structural methods, the utility of a new technique, QCID-HDX-IRMPD, was applied to m/z 552.28 from YAGFL-OH. Both the standard b₅⁺ fragment ion and an isobaric non-C-terminal water loss ion are present. Without separation of these isomers, MS/MS spectral interpretation would be complicated.

Actin's ability to engage in a wide range of physiological functions requires that it be subject to complex spatial and temporal regulation. This regulation is achieved internally through monomer-monomer contacts and externally through interactions with actin binding proteins. The first part of my thesis focused on better understanding the role of inter-monomeric ionic interactions proposed between subdomains 2 and 3 of opposing monomers in F-actin stabilization. I studied several yeast actin mutants: A167R to disrupt a proposed ionic attraction with R39, A167E to mimic a proposed ionic attraction in muscle actin, and D275R to disrupt a proposed ionic attraction with R39. I investigated the effects of mutations in vivo, effects on filament polymerization characteristics and appearance in vitro, as well as interaction of the mutants with the filament severing protein cofilin. While both in vivo and in vitro data demonstrated the importance of the R39-D275 interaction for yeast actin and the interaction of the filament with cofilin, disruption of this interaction alone did not cause filament fragmentation. Conversely, results with A167 do demonstrate the in vivo and in vitro importance of another potential R39 ionic interaction for filament stabilization. In the second part of my work I used amide proton hydrogen/deuterium (HD) exchange detected by mass spectrometry as a tool to gain structural insight into yeast and muscle actin and profilin isoform differences and the actin-profilin interaction. The yeast and muscle actin HD analysis showed greater exchange for yeast G-actin compared to muscle actin in the barbed end pivot region and areas in subdomains 1 and 2, and for F-actin in monomer-monomer contact areas. These results suggest greater flexibility of the yeast actin monomer and filament compared to muscle actin. For yeast-muscle hybrid G-actins, the muscle-like and yeast-like parts of the molecule generally showed exchange characteristics resembling their parent actins. There were a few exceptions to this rule, however: a peptide on top of subdomain 2 and the pivot region between subdomains 1 and 3. These exhibited muscle actin-like exchange characteristics even though the areas were yeast-like, suggesting that there is crosstalk between subdomains 1 and 2 and the large and small domains. Hybrid F-actin data showing greater exchange compared to both yeast and muscle actins are consistent with mismatched yeast-muscle actin interfaces resulting in decreased stability of the hybrid filament contacts. Actin-profilin HD exchange results demonstrated a possible differential interaction of specific profilin isoforms with specific actin isoforms. While profilin binding mostly caused a decreased exchange for yeast actin peptides, it caused an increase in exchange for muscle actin peptides. Many of the changes observed were in peptides that line or contact the nucleotide cleft, consistent with profilin's ability to alter the kinetics of nucleotide exchange.

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Presented in this dissertation are FT-ICR H/D exchange and fragmentation studies of protonated peptides for the purpose of better understanding gas phase conformation and protonation motifs, and their affect on fragmentation patterns. In addition, a new ion activation method is developed to enhance the abundance of higher energy fragmentation pathways, thereby providing additional structural and/or mechanistic information.Studies to probe the relay mechanism of H/D exchange in small, model peptides found that residue position, proline configuration, and availability of the termini have a measurable effect on the H/D exchange behavior reflective of different conformation / protonation motifs.Charge remote cleavage C-terminal to aspartic acid was studied with the fixed charge derivative tris(2,4,6-trimethoxyphenyl) phosphonium (tTMP-P+). Ab initio calculations demonstrate that tTMP-P+ cannot activate the proposed aspartic acid nucleophile, the acidic side chain hydrogen initiates cleavage. Despite the absence of an ionizing proton, the derivatized peptide P+LDIFSDF (where P+ = tTMP-P+) exchanges three acidic hydrogens for deuterium. This supports the proposed aspartic acid cleavage mechanism that occurs without the direct involvement of an ionizing proton because acidic protons are able to participate in H/D exchange in the absence of an added proton. In addition, H/D exchange of P+LDIFSDF analogues provides insight into the sites and mechanisms of H/D exchange.H/D exchange to separate distinct peptide populations with differing rates and their subsequent fragmentation demonstrate that conformation / protonation motif affects the fragmentation spectrum observed. Studies of [P+LDIFSDF + H]2+, [RPPGFSPFR + 2H]2+ (bradykinin), and [RVYIFPF + 2H]2+ show that at least two distinct structures exist with different rates of H/D exchange and different fragmentation patterns. The overall MS/MS spectrum is a linear combination of all conformations and protonation motifs. In addition, fragmentation of labeled populations suggests that complementary bn+ / ym-n+ ion pairs are being formed from doubly-charged precursor by the same mechanism.SORI-RE CID is a new FT-ICR ion activation method based on the combination of sustained off-resonance irradiation (SORI) and on-resonant excitation (RE) with the purpose of enhancing higher energy fragmentation while maintaining low energy processes. The experiments presented serve to illustrate the usefulness of SORI-RE in diverse cases.

No description available.

Previous research has established that the majority of nominally anhydrous minerals (NAMs) in Earth’s mantle can incorporate water in the form of structurally bound hydrogen and, correspondingly, the mantle is thought to contain a substantial volume of water. Water has been shown to play a key role in the geodynamics of the Earth’s interior and quantifying the amount, and distribution, of water in the mantle is an important step in understanding many deep-Earth processes. One of the parameters highly sensitive to the incorporation of water in the mantle is electrical conductivity, as hydrogen is highly mobile and acts as the dominant charge-carrying species. In theory, this relationship can be used in conjunction with geophysical techniques that measure mantle-scale electrical conductivity to ‘map-out’ the deep Earth’s water content – but accurate interpretation of such data requires full understanding of hydrogen mobility in NAMs under extreme conditions, which remains poorly constrained. The aim of this project is to contribute to the reconciliation of geophysical observations with laboratory measurements of electrical conductivity, by considering hydrogen-deuterium exchange in single crystals. In a novel experimental design, hydrogen in crystals synthesised under mantle conditions (such that the hydrogen defects present correspond to the conditions being studied) exchanges with deuterium from a liquid source under controlled (mantle) pressure and temperature conditions for a specified time period. This results in hydrogen-deuterium exchange profiles that can be characterised by SIMS and subsequently fitted to Fick’s law to calculate hydrogen diffusion coefficients – which in turn can be related to electrical conductivity through the Nernst-Einstein equation. Analysis of the experimental results underlines the complexity of the influence of hydrogen on electrical conductivity in NAMs, and emphasises the need for careful consideration when interpreting and applying the results of diffusion studies. Ultimately, the data obtained in this study provides a useful contribution to understanding hydrogen diffusion in mantle minerals, but the non-trivial nature of both the experimental and analytical aspects mean that the method cannot easily be applied to other mantle phases.

By using two electrospray emitters containing different solutions (“dual-spray”) we have recently conducted in-source hydrogen/deuterium exchange (HDX) reactions and synthesized organometallic species. For dual-spray HDX reactions, peptide and protein solutions were electrosprayed through one emitter and the deuterating agent D2O through the secondary electrospray emitter. Clear shifts in isotope distributions indicated hydrogen-deuterium exchange occurring within the ion source. By ion mobility, simultaneous deuterium exchange for two isobaric species, the oxytocin monomer and dimer, was observed. Lysozyme has a linear relation between the charge state and the average number of exchanges, indicating that lysozyme becomes increasingly unfolded as the charge state increases. Based on deuterium uptake data and the lack of a temperature dependence, the dual-spray HDX reaction is thought to occur mostly in the gas phase. Tris(2,2’-bipyridine)ruthenium(II) and similar complexes containing the 1,10-phenanthroline ligand were formed by spraying a ligand solution and the ruthenium trichloride solution through two independent ESI emitters. This was confirmed by comparing ion mobility drift time, mass spectra, and CID fragmentation with the reference standard compounds. Tris(2,2’-bipyridine)iron(II), tris(1,10-phenantroline)iron(II) and mixed ligand complexes of iron(II) formed by dual-spray showed two additional hydrogens bonded to the complex. By CID, these unique gas phase complexes showed similar initial ligand loss to the reference standards however the secondary ligand loss showed dissimilar dissociation channels and energetics. Using DFT calculations, geometry optimizations for the [Fe(phen)3 + 2H]2+ complex and its fragment ions were done. After the initial ligand loss, the additional hydrogens are believed to transfer to the central iron atom. The relative energy of the dissociation channels showed good agreement with experimental breakdown curves.

This work focuses on the effects of formulation and manufacturing as it effects protein structure and physical stability. Using common physical characterization techniques, X-ray photoelectron spectroscopy, and solid-state hydrogen/deuterium exchange with mass spectrometry, correlations are identified between these results and accelerated stability studies.

No description available.