Thesis advisor: Eranthie Weerapana / Disulfide-bonding cysteine residues perform critical roles in the structural stabilization and redox regulation of protein function. Secreted proteins are often enriched for structural disulfide bonds conferring conformational stability in the oxidizing extracellular environment. The controlled formation of disulfide bonds in secreted proteins is regulated in the endoplasmic reticulum (ER) by the protein disulfide isomerase (PDI) family. To investigate disulfide-bond formation in the ER, quantitative chemical-proteomic methods were coupled to subcellular-fractionation-based ER enrichment. Cysteine reactivity studies identified highly reactive post-translationally modified cysteine residues including disulfide-bonding cysteines. Upon discovering a highly reactive population of traditionally oxidized cysteines, the percentage of oxidation for cysteines localizing to the ER was determined. Next, ER function was chemically perturbed to evaluate changes to cysteine oxidation following upregulation of the unfolded protein response (UPR). Disulfide bond formation was specifically disrupted in the ER by CRISPR-Cas9-mediated PDIA1 and PDIA4 knockout. The effects of PDI knockout on cancer cell phenotype and changes to cysteine oxidation states were evaluated. Finally, in vitro studies were performed to evaluate PDIA4 oxidase activity and identify potential PDIA4-selective inhibitors. In the future, the platforms developed within may be applied to profiling changes to cysteine oxidation in other biological systems such as other organelles and disease states. / Thesis (PhD) — Boston College, 2019. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Structural properties of phosphoglucose isomerases isolated from a variety of species have been compared by peptide fingerprinting, predicted amino acid sequence homologies and by denaturation and renaturation studies. The enzymes are more readily denatured in guanidinium chloride than in urea, and the isomerase isolated from yeast is more stable toward acid pH than the rabbit muscle enzyme. The rates of guanidinium chloride-induced denaturation are markedly increased by ionic strength and decreased by substrates, competitive inhibitors or glycerol. The enzyme can be renatured, but only in the presence of glycerol. The renaturation process is dependent on protein concentration and temperature and provides a method for the formation of mixed species heterodimers.

Cholera toxin (CT) is a classic A-B type protein toxin that has an A subunit (A1 + A2) and a pentameric B subunit. The catalytic A1 domain is linked to the A2 domain via a disulfide linkage. CTA1 must be dissociated from the rest of the toxin to cause a cytopathic effect. Protein disulfide isomerase (PDI) can reduce the CTA1/CTA2 disulfide bond, but disassembly of the reduced toxin requires the partial unfolding of PDI that occurs when it binds to CTA1. This unfolding event allows PDI to push CTA1 away from the rest of the toxin. My research question is whether the efficiency of PDI in disassembling CT would be affected by molecular crowding, where a dense internal cell environment is recreated in vitro by the use of chemical agents such as Ficoll. This will give insight on how CT behaves inside a cell. Our hypothesis was that molecular crowding would make CTA1 disassembly more efficient by recreating the tight packing of macromolecules in cells, which provides an extra nudge to enhance toxin disassembly. We then used enzyme-linked immunosorbent assays (ELISAs), a pull-down assay and a biochemical assay to determine how molecular crowders affect the binding, reduction, and disassembly of CT by PDI. Our results will bring about a deeper understanding of the cellular events that may affect the course of a cholera infection. From the preliminary results, molecular crowders increased PDI's ability to bind to CTA1 and did not prevent PDI from cleaving the CTA1/CTA2 disulfide bond. Based off the disassembly results, molecular crowders reduced PDI's ability to displace CTA1 from the rest of the toxin. This contradicts our original hypothesis. Our new hypothesis is that crowders block PDI unfolding, which is required for CT disassembly. Biophysical experiments using Fourier Transform Infrared Spectroscopy will test this prediction in future work.

Cholera, caused by the secretion of cholera toxin (CT) by Vibrio cholerae within the intestinal lumen, triggers massive secretory diarrhea which may lead to life-threatening dehydration. CT is an AB5-type protein toxin that is comprised of an enzymatically active A1 chain, an A2 linker, and a cell-binding B pentamer. Once secreted, the CT holotoxin moves from the cell surface to the endoplasmic reticulum (ER) of a host target cell. To cause intoxication, CTA1 must be displaced from CTA2/CTB5 in the ER and is then transferred to the cytosol where it induces a diarrheal response by stimulating the efflux of chloride ions into the intestinal lumen. Protein disulfide isomerase (PDI), a resident ER oxidoreductase and chaperone, is involved in detaching CTA1 from the holotoxin. The PDI domain(s) that binds to CTA1 and precisely how this interaction is involved in CTA1 dissociation from the holotoxin are unknown. The goal of this project is to identify which domain(s) of PDI is responsible for binding to and dislodging CTA1 from the CT holotoxin. Through incorporation of ELISA, surface plasmon resonance (SPR), and Fourier transform infrared (FTIR) spectroscopy techniques in conjunction with a panel of purified PDI deletion constructs, this project aims to provide important molecular insight into a crucial interaction of the CT intoxication process.

No description available.

No description available.

Em condições inflamatórias do sistema vascular, altas concentrações de mieloperoxidase somada à presença do ácido úrico, sugerem a formação local do oxidante hidroperóxido de urato. A ação desse peróxido já foi demonstrada sobre glutationa e peroxirredoxinas, tornando plausível a possibilidade de que outras proteínas tiólicas também pudessem ser alvo de oxidação. A proteína dissulfeto isomerase é uma ditiol-dissulfeto oxidoredutase e chaperona, localizada principalmente no retículo endoplasmático, onde participa do enovelamento de proteínas nascentes. Além disso, um pool dessas enzimas foi identificado na superfície da célula e no meio extracelular (secretada) e parece ser especialmente importante em eventos vasculares como ativação e agregação de plaquetas, trombose e remodelamento vascular. Primeiramente, foi investigado se o hidroperóxido de urato era capaz de oxidar a PDI. Pelo ensaio do DTNB foi verificado que os tióis livres da proteína eram consumidos após reação com o peróxido e, em seguida, por nLC-MS/MS os resíduos de cisteínas dos sítios catalíticos foram identificados como os principais alvos de oxidação. Embora não tenham sido verificadas outras modificações além de dissulfetos, foi observado que o tratamento com hidroperóxido promoveu agregação e inativação da proteína. Os estudos subsequentes envolveram uma linhagem de células endoteliais (HUVECs). Análises preliminares de citotoxicidade (detecção da atividade da enzima lactato desidrogenase no sobrenadante e incorporação de sondas fluorescentes ao DNA) mostraram que tratamentos com concentrações de até 400 µM de hidroperóxido de urato não são letais às células em cultura. Usando alquilantes impermeáveis à membrana celular foi mostrado que o hidroperóxido de urato oxida não só a proteína dissulfeto isomerase, mas também proteínas tiólicas totais expressas na superfície das HUVECs. Experimentos de wound healing foram feitos para avaliação da capacidade de migração das células mediante o tratamento com hidroperóxido de urato, mas nenhuma diferença foi observada. Contudo, a incubação das células com os agentes oxidantes hidroperóxido de urato e diamida, inibidores de PDI e integrina e um alquilante de tiol, resultaram, pelo menos nos trinta primeiros minutos, em menor capacidade de adesão das células à fibronectina. Além disso, as células tratadas com hidroperóxido de urato se tornaram mais sensíveis ao destacamento da placa de cultura e apresentaram alteração na morfologia. O tratamento com o peróxido também afetou a homeostase redox das HUVECs, observado pela diminuição da razão GSH/GSSG. Finalmente foram apresentadas evidênciasindiretas de que o ácido úrico é substrato da peroxidasina, uma heme peroxidase abundantemente expressa no sistema vascular. Primeiro, pelo ensaio do Amplex Red foi observado que a presença de ácido úrico na mistura reacional resultou em menor taxa de oxidação do reagente. Depois, por LC-MS/MS, também em amostra na qual o ácido úrico estava presente, foi identificado o hidroxiisourato, álcool resultante da decomposição do hidroperóxido de urato. Todo o conjunto de dados deverá contribuir para o maior entendimento da participação do hidroperóxido de urato em processos oxidativos vasculares − especialmente a oxidação de proteínas − que pode ser um dos mecanismos responsáveis pela alteração da função endotelial e da homeostase vascular. / During vascular inflammatory conditions, high amounts of myeloperoxidase added to the presence of uric acid, suggest the local formation of urate hydroperoxide. Its oxidative action has already been demonstrated on glutathione and peroxiredoxins, making plausible the possibility that other thiol proteins could also be a target for oxidation. The protein disulfide isomerase is a dithiol-disulfide oxidoreductase and chaperone, located mainly in the endoplasmic reticulum, where it is involved in the correct folding of nascent proteins. Also, a pool of these enzymes has been identified in cell surface and the extracellular (secreted) milieu and appears to be important in vascular events, such as platelet activation and aggregation, thrombosis and vascular remodeling. First, it was investigated whether urate hydroperoxide was capable of oxidizing PDI. By the DTNB assay, it was found that the free thiols of the protein were consumed after reaction with the peroxide and then, by nLC-MS / MS, the active redox cysteine residues were identified as the main oxidation targets. Although no modifications other than disulfides have been found, hydroperoxide treatment has been shown to promote protein aggregation and inactivation. Subsequent studies involved an endothelial cell line (HUVECs). Preliminary cytotoxicity analyzes (detection of lactate dehydrogenase enzyme activity in the supernatant and incorporation of fluorescent probes into DNA) have shown that treatments with concentrations up to 400 µM are not lethal to cells in culture. Then, using alkylating agents impermeable to the cell membrane, urate hydroperoxide was shown to oxidize not only PDI but also total thiol proteins expressed on HUVECs surface. Wound healing experiments were performed to evaluate cell migration after treatment with urate hydroperoxide, but no difference was observed. However, incubation of the cells with the oxidizing agents urate hydroperoxide and diamide, inhibitors of both PDI and integrin and a thiol alkylator, resulted, at least for the first thirty minutes, in reduced cell adhesion to fibronectin. In addition, cells treated with urate hydroperoxide became more sensitive to detachment from the culture dish and exhibited alterations in morphology. Treatment with the peroxide also affected the redox homeostasis of the HUVECs, observed by a decrease in the GSH / GSSG ratio. Finally, indirect evidence was presented that uric acid is a substrate of peroxidasin, a heme peroxidase abundantly expressed in the vascular system. First, with the Amplex Red assay it was observed that the presence of uric acid in the reaction mixture resulted in lower oxidation rates of the reagent. Then, by LC-MS / MS, hydroxyisourate, which is the alcohol derived from urate hydroperoxide decomposition, was also identified in samples containing uric acid. Taken together, the data presented should contribute to a better understanding of the involvement of urate hydroperoxide in vascular oxidative processes − especially protein oxidation − that may be one mechanism associated to disturbances in endothelial function and vascular homeostasis.

Processos celulares que governam as NADPH oxidases vasculares em condições patológicas não estão claros ainda. Como os processos redox são parte intrínseca da resposta da célula ao estresse, temos investigado se o estresse oxidativo pode convergir com outros tipos de estresse via Nox(es). No presente estudo, focamos na inibição do proteasoma como uma condição relevante de estresse. A incubação de células musculares lisas com concentrações não apoptóticas de inibidores do proteasoma, MG132 e lactacistina, promoveu aumento na produção basal de superóxido e na atividade da NADPH oxidase, diminuição da atividade da SOD e da razão GSH/GSSG. Por outro lado, a inibição do proteasoma diminui a atividade da Nox após estímulo com Angiotensina II ou Tunicamicina, conhecido estressor do retículo endoplasmático. Em condições basais, MG132 induz a expressão de mRNA da Nox1, entretanto o aumento de Nox1 induzido por Angiotensina II foi diminuído na presença de MG132. O mesmo efeito ocorre com a indução de Nox4 pela Tunicamicina, que nesse caso foi drasticamente reduzida na presença de MG132. Além disso, tanto Angiotensina II quanto Tunicamicina induziram a atividade lítica do proteasoma 20S. A seguir, investigamos as conseqüências fisiológicas do MG132 na sinalização do estresse do RE, uma conhecida resposta mediada por Nox4. Células vasculares incubadas com MG132 induzem a expressão de marcadores do estresse do RE, GRP78 e XBP1, e também os marcadores mais tardios ATF4 e o próapoptótico CHOP/GADD153. Resultados similares ocorrem também com a Tunicamicina. Entretanto, a co-incubação de Tunicamicina e MG132 diminui e a sinalização do estresse do RE. AKT e p38 MAPK foram ativados por MG132, possivelmente como resposta ao estresse induzido pela inibição do proteasoma. Assim, a inibição do proteasoma bloqueia a NADPH oxidase, com aumento da atividade basal e expressão da Nox1 versus forte inibição da ativação e expressão da Nox4 frente ao estímulo. A inibição da Nox4 associa-se e pode contribuir para a inibição pelo MG132 da sinalização do estresse do RE. Portanto, o proteasoma parece exercer papel na integração de estresses celulares envolvendo a NADPH oxidase. A inibição do proteasoma pode ter papel na terapia de doenças associadas a estresse do RE. / Cellular processes governing vascular Nox family NADPH oxidases in disease conditions are unclear. Since redox processes are intrinsic to cell stress response, we asked whether oxidative stress merges with other types of stress via Nox(es). We focused on proteasome inhibition as a relevant stress condition. Vascular smooth muscle cells (VSMC) incubation with non-apoptotic concentrations of proteasome inhibitors MG132 or lactacystin promoted increased baseline superoxide generation (HPLC/DHE products) and NADPH oxidase activity, decreased SOD activity and GSH/GSSG ratio. Conversely, proteasome inhibitors decreased by Nox response to Angiotensin II (AngII) and abrogated Nox response to endoplasmic reticulum (ER) stressor tunicamycin. With MG132, basal Nox1 mRNA levels were increased, while Nox1 response to AngII was blunted. Moreover, MG132 abolished Nox4 mRNA levels TN-induced. Both AngII and TN (at 2 and 4 hs) promoted increased 20S proteasome lytic activity. We next assessed physiological consequences of MG132 in ER stress signaling, a known Nox4- mediated response. VSMC incubation with MG132 alone enhanced expression of the ER stress markers Grp78 and XBP1 and late markers such as ATF4 and proapoptotic CHOP/GADD153. Similar results occurred with the known ER stressor TN. However, co-incubation of TN and MG132 decreased Grp78, Grp94 and CHOP/GADD153, indicating that proteasome inhibition interrupts ER stress. AKT and p38 are activated by MG132 as response to stress and recover to survival. Thus, proteasome inhibition disrupts NADPH oxidase, with increased baseline activity and Nox1 expression vs. strong inhibition of stimulated Nox1 and Nox4 activation/expression. The later effect may underlie MG132-mediated inhibition of ER stress signaling. (Support: FAPESP, CNPq Milênio Redoxoma)

Proteína dissulfeto isomerase (PDI) é uma ditiol-dissulfeto óxido redutase ubíqua que é responsável por uma série de funções celulares, inclusive na sinalização celular e nas respostas a eventos que causam dano celular. Entretanto, a PDI pode se tornar disfuncional através das modificações pós-traducionais, incluindo as promovidas por oxidantes biológicos. Estes oxidantes são provavelmente os responsáveis pelas modificações oxidativas pós-traducionais da PDI que foram detectadas em várias condições associadas ao estresse oxidativo, levando à disfunção da proteína. Devido a falta de estudos cinéticos com a PDI nativa e a falta de caracterização dos produtos dessas reações, investigamos se a diminuição da fluorescência da PDI nativa pode ser empregada para estudos da cinética de oxidação com peróxido de hidrogênio. Posteriormente, investigamos a cinética e os produtos da reação entre PDI e peroxinitrito. Nossos experimentos mostraram que a oxidação por excesso de peróxido de hidrogênio levava a uma diminuição da fluorescência de forma dependente do tempo e da concentração do oxidante, permitindo a determinação da constante de velocidade de segunda ordem (k = (17,3±1,3) M-1 s-1, pH 7,4, 25 ºC). Relevantemente, mostramos que o processo era totalmente revertido por DDT, mostrando que o peróxido de hidrogênio oxida quase que exclusivamente os grupos ditióis da PDI (Cys53 e Cys56 e Cys397 e Cys400). Utilizando a mesma abordagem para estudar a oxidação da PDI por peroxinitrito, notamos que o decréscimo da fluorescência intrínseca da PDI nativa e a velocidade só era proporcional à concentrações sub-estequiométricas ou estequiométricas do oxidante em relação aos tióis reativos da PDI. Somente nessas condições o processo se mostrava reversível por DDT, indicando que os ditióis da PDI eram o alvo preferencial do peroxinitrito mas que a oxidação de outros resíduos também ocorria. A reação dos tióis reativos da PDI com peroxinitrito foi considerada relativamente rápida (6,9 ± 0,6 × 104 M-1 s-1, pH 7,4, 25 °C), e os resíduos de Cys reativos dos domínios a e a\' aparentam reagir com constantes de velocidade similares. Experimentos de proteólise limitada, simulações cinética e análises de MS e MS/MS confirmaram que o peroxinitrito oxida preferencialmente os tióis redox ativos da PDI para os ácidos sulfênicos correspondentes, que, subsequentemente, reagem com os tióis vizinhos, produzindo dissulfetos (Cys53- Cys56 e Cys397- Cys400). Entretanto, uma fração de peroxinitrito decai para radicais levando à hidroxilação e nitração de outros resíduos próximos ao sítio redox ativo (Trp52 Trp396 e Tyr393). Assim, investigamos também a oxidação da PDI por excesso de peroxinitrito em relação aos grupos tióis reativos por diferentes metodologias. Experimentos de SDS-PAGE, western-blot e atividade redutase mostraram que o peroxinitrito promove inativação, nitração e agregação da PDI de forma dependente da concentração de peroxinitrito. Análises de MS e MS/MS mostraram que, em excesso, o peroxinitrito promove nitração (Tyr43, Tyr49, Tyr196, Tyr393, Trp52, Trp396) e hidroxilação (Trp52, Trp396) da PDI. Em síntese, nossos estudos contribuem para melhor compreensão da oxidação da PDI por peroxinitrito e de suas possíveis consequências biológicas. / Protein disulfide isomerase (PDI) is a ubiquitous dithiol-disulfide oxidoreductase that performs an array of cellular functions, including in cellular signaling and responses to cell-damaging events. Nevertheless, PDI can become dysfunctional by post-translational modifications, including those promoted by biological oxidants. These oxidants are likely responsible for the oxidative post-translational modifications of PDI, which have detected under various conditions associated with oxidative stress, leading to protein dysfunction. However, the kinetics of the reactions of PDI with biological oxidants received limited studies and the products of these reactions were not characterized. Here, we examined whether the decrease in PDI fluorescence can be employed to follow the kinetics of the reaction of the full-length protein with biological oxidants. Also, we investigated the kinetics and products of the reaction between PDI and peroxynitrite. Our experiments showed that oxidation by excess hydrogen peroxide led to a decrease of PDI intrinsic fluorescence in a time- and concentration-dependent manner , permitting the determination of the second-order rate constant of the reaction (k = (17.3 ± 1.3 ) M1 s-1, pH 7.4, 25 ° C). The oxidation was reversed by DDT, indicating that hydrogen peroxide oxidizes mainly PDI dithiols (Cys53 and Cys56 and Cys397 and Cys400). Using the same approach to study PDI oxidation by peroxynitrite we noted that the decrease of the native PDI fluorescence was proportional to sub-stoichiometric or stoichiometric concentrations of the oxidant relative to that of PDI reactive thiols. Only under these conditions, PDI oxidation was reversed by DDT, indicating that PDI dithiols were the preferred target of peroxynitrite but that oxidation of other residues also occurred. The reaction of the active redox thiols of the PDI with peroxynitrite can be considered relatively fast (6.9 ± 0.6 × 104 M-1 s-1, pH 7.4, 25 ° C), and the reactive Cys residues of domains a and a\' were kinetically indistinguishable. Limited proteolysis experiments, kinetic simulations, and MS and MS/MS analyses confirmed that peroxynitrite preferentially oxidizes the redox-active Cys residues of PDI to the corresponding sulfenic acids, which subsequently react with the resolving thiols to produce disulfides (Cys53-Cys56 and Cys397-Cys400). However, a fraction of peroxynitrite decays to radicals leading to hydroxylation and nitration to other residues located close to the active site (Trp52 Trp396 and Tyr393). SDS-PAGE, western blotting and inhibition of the reductase activity experiments confirmed that excess peroxynitrite promotes further PDI oxidation, nitration, inactivation and aggregation in a concentration-dependent manner. MS and MS/MS analyzes showed that peroxynitrite in a ten times excess relative to PDI reactive thiols promote PDI nitration (Tyr43, Tyr49, Tyr196, Tyr393, Trp52, Trp396) and hydroxylation (Trp52, Trp396). In conclusion, our studies contribute to a better understanding of PDI oxidation by peroxynitrite and its possible biological consequences

Xu, Meng. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 112-129). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.