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Defining the mechanics and consequences of protein adduction is crucial to understanding the toxicity of reactive electrophiles. Application of tandem mass spectrometry and data analysis algorithms enables detection and mapping of chemical adducts at the level of amino acid sequence. Nevertheless, detection of adducts does not indicate relative reactivity of different sites. In this dissertation I describe a method to measure the kinetics of competing adduction reactions at different sites on the same protein using quantitative mass spectrometry. Adducts are formed by electrophiles at Cys-14 and Cys-47 on the metabolic enzyme glutathione-S-transferase P1-1 and accompanied by a loss of enzymatic activity. Relative quantitation of protein adducts was done by tagging N-termini of peptide digests with isotopically labeled phenyl isocyanate and tracking the ratio of light-tagged peptide adducts to heavy-tagged reference samples. This method was used to measure rate constants for adduction at both positions with two different model electrophiles, IAB and BMCC. The results indicate that Cys-47 was approximately 2-3-fold more reactive toward both electrophiles than was Cys-14. This result was consistent with the relative reactivity of these electrophiles in a complex proteome system. Quantitative analyses of protein modifications provide a means of determining the reactivity and selectivity of damaging protein modifications in chemical toxicity.Another area of study explored in this dissertation is looking at the effects of protein alkylation on activating cellular signaling pathways, specifically the JNK signaling pathway. Protein adduction has been shown to be selective between different alkylating agents. It would then be reasonable to think this selectivity of adduction translates to selectivity of downstream consequences or cellular events directly tied to specific adductions. My work will show how treatment of HEK293 cells with either IAB or BMCC leads to differences in activation of JNK signaling. In addition, I've been able to show a difference in selectivity of a number of adducted targets by each alkylating agent, which are directly involved in regulation of the JNK signaling pathway. These studies illustrate not only the significance of protein adduction, but the importance for continual research to better understand their behavior in living systems.

Yes / It has long been known that Tissue Factor (TF) plays a role in blood coagulation and has a direct thrombotic action that is closely related to cardiovascular risk, but it is becoming increasingly clear that it has a much wider range of biological functions that range from inflammation to immunity. It is also involved in maintaining heart haemostasis and structure, and the observation that it is down-regulated in the myocardium of patients with dilated cardiomyopathy suggests that it influences cell-to-cell contact stability and contractility, and thus contributes to cardiac dysfunction. However, the molecular mechanisms underlying these coagulation-independent functions have not yet been fully elucidated. In order to analyse the influence of TF on the cardiomyocitic proteome, we used functional biochemical approaches incorporating label-free quantitative proteomics and gene silencing, and found that this provided a powerful means of identifying a new role for TF in regulating splicing machinery together with the expression of several proteins of the spliceosome, and mRNA metabolism with a considerable impact on cell viability.

Condensed phase membrane introduction mass spectrometry (CP-MIMS) is a direct, in situ analysis technique that is well suited to persistent organic pollutants, pesticides, and other small molecules. In CP-MIMS, neutral analytes permeate a hollow fibre membrane, typically polydimethylsiloxane (PDMS), driven by a concentration gradient. Analytes are subsequently dissolved by a liquid (condensed) solvent acceptor phase that is continuously flowed through the membrane lumen, which finally entrains the analytes to a mass spectrometer for detection. The membrane rejects charged and particulate matrix components, therefore eliminating sample cleanup that is otherwise necessary for conventional (i.e., chromatographic) techniques. However, larger analytes may suffer from relatively lengthy response times and lower sensitivity. A heptane cosolvent was therefore doped into the PDMS membrane, resulting in a polymer inclusion membrane (PIM). Through a system coupling CP-MIMS to electrospray ionization (ESI), the use of a PIM for model compounds resulted in faster response (~3×) and improved sensitivity (~3.5×, parts per trillion level detection limits). While effective for the demonstration of the PIM, pairing ESI with CP-MIMS represents an inherent incongruity: ESI is effective for polar, hydrophilic analytes, whereas CP-MIMS (i.e., PDMS membranes) is effective for hydrophobic analytes. CP-MIMS was therefore coupled with liquid electron ionization (LEI) as a more suitable ionization strategy. In LEI, the post-membrane solvent flow is entrained at nanolitre per minute flowrates to a LEI source, where the liquid is sequentially nebulized, vaporized, and ionized. The CP-MIMS-LEI coupling was optimized for the measurements of polycyclic aromatic hydrocarbon (PAH) isomer classes from aqueous samples, demonstrating low ng/L detection limits and response times (≤1.6 min). CP-MIMS-LEI was also applied to PAH isomer classes from soil samples, demonstrating rapid sample throughput (15 samples/hr) and low μg/kg detection limits, and additionally was quantitatively comparable to conventional techniques. A similar CP-MIMS-LEI system was applied to online monitoring of catalytic oxidation and alkylation reactions, demonstrating quantitative, real-time results for harsh, complex organic reaction mixtures. A significant analytical improvement was conducted by intentionally exploiting the already present liquid acceptor phase as an in situ means of providing liquid chemical ionization (CI) reagents for improved analyte sensitivity and selectivity (i.e., CP-MIMS-LEI/CI). Acetonitrile and diethyl ether were used as a combination acceptor phase/CI reagent system (i.e., proton transfer reagents) for the direct analysis of bis(2-ethylhexyl)phthalate from house dust (6 mg/kg detection limit). CP-MIMS-LEI/CI was then applied to PAHs from soils. Using methanol and dichloromethane combination acceptor phase/CI reagents, CP-MIMS-LEI/CI was shown to quantify and resolve PAH isomers from direct soil analyses via diagnostic PAH adduct ions: [M+CH2Cl+CH3OH-HCl]+ or [M+CHCl2-HCl]+. Using these selective ions, CP-MIMS-LEI/CI was again shown to be rapid (15 soils/hr), sensitive (ng/g detection limits) and quantitatively comparable to gas chromatography-MS for PAH measurements (average percent difference of -9% across 9 PAHs in 8 soil samples). The results across this thesis present a compelling argument for direct, quantitative screening from complex samples using CP-MIMS-LEI/CI, particularly given the simple workflow and short analytical duty cycle. / Graduate

Der erste Teil dieser Arbeit beschreibt die Durchführung eines quantitativen Ansatzes zur Detektion von Protein-Protein-Interaktionen (PPI) mit einem Schwerpunkt für Proteine, die in vier häufigen neurodegenerativen Krankheiten eine Rolle spielen: die Alzheimer-, Parkinson- und Huntington-Krankheit, sowie die spinozerebelläre Ataxie Typ 1 (SCA1). Die Interaktionsstudie kombiniert die stabile Isotopen-Markierung von Aminosäuren in der Zellkultur mit der Affinitätsaufreinigung von Proteinen und hochauflösender Massenspektrometrie. Dieser Ansatz zielt darauf ab, systematisch die Interaktionspartner von gesunden und krankheitsassoziierten Proteinvarianten zu identifizieren und zu quantifizieren. Darüber hinaus wurde das quantitative Interaktionsverfahren genutzt, um zu prüfen ob PPI durch krankheitsassoziierte Mutationen beeinträchtigt werden. Neben der Validierung möglicher Nebeneffekte, sowie dem Vergleich mit Informationen über PPI aus der Literatur, wurde ein Teil der identifizierten Interaktoren durch zusätzliche Koimmunopräzipitations-Experimente in zwei verschiedenen Zelllinien bestätigt. Mit Hilfe von Drosophila SCA1-Krankheitsmodellen und in Kombination mit RNAi-basierter Stummschaltung identifizierter Interaktoren wurde festgestellt, dass ein großer Teil der Kandidaten Neurodegeneration in vivo beeinflusst. Zusätzlich wurden die Alzheimer-spezifischen PPI-Daten auf genomweite Assoziationsstudien übertragen. Bemerkenswerterweise waren Polymorphismen in einzelnen Nukleotiden in den Genen zugehöriger Interaktoren wahrscheinlicher mit solchen Genen assoziiert, die eine Prädisposition für die Alzheimer-Krankheit haben, als mit zufällig ausgewählten Genen. Schlussendlich konnten Folgeexperimente für zwei ausgewählte Interaktionspartner den Nachweis für eine bislang unbekannte Rolle der N-Glykosylierung und einen neuen Zusammenhang zwischen dem RNA-bindenden Protein LRPPRC und mitochondrialer Dysfunktion in der Alzheimer-Krankheit vorlegen. / The first part of the present thesis describes the establishment of a quantitative protein-protein interaction (PPI) screen with a focus on proteins involved in four common neurodegenerative diseases (NDDs): Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD) and spinocerebellar ataxia type 1 (SCA1). The interaction screen combines stable-isotope labeling by amino acids in cell culture (SILAC) with protein affinity purification and high-resolution mass spectrometry. This approach aims to systematically identify and quantify interaction partners of normal and known disease-associated variants of proteins involved in NDDs. Moreover, the quantitative interaction screen was employed to study how PPIs are affected by disease-associated mutations. Along with validation of possible off-target effects and comparison of the data with literature-reported PPIs, a subset of identified interactors was validated by additional co-immunoprecipitation experiments in two different cell lines. Utilizing Drosophila models for SCA1 in combination with RNAi-mediated silencing of identified interactors, a large fraction of candidates was observed to also affect neurodegeneration in vivo. In addition, AD-specific PPI data was mapped to patient cohort data obtained from genome-wide associations studies. Notably, single-nucleotide polymorphisms in the genes of interactors of the disease-associated protein variants were more likely associated with susceptibility to AD than randomly selected genes. Finally, functional follow-ups for two selected interaction partners provided evidence for a yet unreported role of N-linked glycosylation in AD, and a novel link to mitochondrial dysfunction in AD by means of the RNA-binding protein LRPPRC.