Introdução: As proteinases tem um papel importante no desenvolvimento, na destruição tecidual e na produção de muco causada pela DPOC. O inibidor de proteinase de origem vegetal Enterolobium contortisiliquum Tripsin Inhibitor (EcTI) inibe tanto as proteinases da classe serina quanto da classe cisteína. Objetivos: Avaliar os efeitos do tratamento com EcTI nas alterações pulmonares induzidas pela elastase em camundongos. Métodos: Camundongos C57Bl6 receberam elastase via intratraqueal (50 uL/animal, grupo ELA) ou salina (grupo SAL). Os camundongos foram tratados com EcTI (2mg/kg) nos dias 1, 15 e 21 após a instilação de elastase (grupo ELA-EcTI) ou salina (grupo SAL-EcTI). No dia 28 do protocolo, os animais foram anestesiados, a mecânica pulmonar foi medida e o óxido nítrico exalado coletado. Posteriormente, foi realizado o lavado broncoalveolar e os pulmões foram removidos para a preparação de lâminas de histoquímica e imunohistoquímica. Por meio de morfometria analisamos o número de células positivas para neutrófilos, TNF-alfa, MMP-9, MMP-12, TIMP-1, iNOS, eNOS assim como a fração de volume de 8-iso-PGF2alfa, fibras colágenas e elásticas, nos septos alveolares e nas vias aéreas. Também foram avaliados o número de células positivas para macrófagos nos septos alveolares e MUC5ac nas vias aéreas. Resultados: O inibidor de proteinase EcTI reduziu as alterações de mecânica pulmonar (Ers, Htis e Raw), destruição do septo alveolar (Lm) e o número de células no lavado broncoalveolar (células totais, macrófagos, neutrófilos, linfócitos e eosinógilos) induzidos pela elastase. Em relação a resposta inflamatória, o EcTI reduziu o número de neutrófilos e de células TNFalfa positivas no septo alveolar e nas vias aéreas além de reduzir o número de macrófagos no septo alveolar. Considerando o remodelamento de matriz extracelular, o inibidor de proteinase atenuou a fração de volume de fibras colágenas e o número de células MMP-9 e MMP-12 positivas nos septos alveolares e nas vias aéreas. Além disso, nas vias aéreas ocorreu uma atenuação da fração de volume de fibras elásticas, e nos septos alveolares uma atenuação da quantidade de células que expressam TIMP-1. Em relação a resposta de estresse oxidativo, o EcTI reduziu a fração de volume de isoprostano e o número de células iNOS e eNOS positivas tanto nos septos alveolares quanto nas vias aéreas. O EcTI também reduziu o número de células MUC5ac positivas nas vias aéreas. Conclusões: O tratamento como inibidor EcTI modulou a mecânica pulmonar e reduziu as alterações inflamatórias, de remodelamento e de estresse oxidativo induzidas pela elastase intratraqueal. Embora sejam necessários mais estudos para elucidar os mecanismos envolvidos neste processo, o inibidor de proteinase EcTI pode ser considerado como um potencial instrumento terapêutico para o tratamento da DPOC / Background: Proteinases play a key role on emphysema development, tissue destruction and mucus production. Enterolobium contortisiliquum Tripsin Inhibitor (EcTI) is a proteinase inhibitor from plant that neutralizes serine and cysteine proteinases. Aims: To evaluated the effects of the EcTI treatment in pulmonary alterations induced by elastase in mice. Methods: C57Bl6 mice received elastase intratracheally (50 uL/animal, ELA group) or saline (SAL group). Afterwards, mice were treated with EcTI (2 mg/kg) at days 1, 15 and 21 after elastase instillation (ELA-EcTI group). Control group received saline and EcTI using the same protocol (SAL-EcTI group). At day 28, mice were anesthetized, respiratory mechanics were collected, and exhaled nitric oxide were analyzed. Afterwards, broncoalveolar lavage fluid was obtained and lungs were removed to perform histochemistry and immunohistochemistry stains. By morphometry, the number of neutrophils, TNF-alfa, MMP-9, MMP-12, TIMP-1, iNOS, eNOS positive cells as well as the volume proportion of 8-iso-PGF2alfa, collagen and elastic fibers content in alveolar septum and airways walls were performed. In airways walls, we also analyzed the number of MUC-5 positive cells and the number of macrophages. Results: The proteinase inhibitor EcTI was able to reduce the pulmonary mechanical alterations (Ers, Htis and Raw), alveolar septum disruption (Lm) and the BAL cell count (total cells, macrophages, neutrophils, lymphocytes and eosinophils) induced by elastase. Regarding the inflammatory response, EcTI also reduced the number of neutrophils and TNFalfa positive cells in both alveolar septum and airway walls, and also reduced the number of macrophages in alveolar septum. Considering the extracellular matrix remodeling, the proteinase inhibitor attenuated the volume fraction of collagen fibers, MMP-9 and MMP-12 positive cells in both alveolar septum and airway walls. Besides, in airway there were attenuation in the volume fraction of elastic fibers, and in the alveolar septa a decrease of the amount of the cells expressing TIMP-1. Regarding the oxidative stress response, EcTI reduced the volume fraction of isoprostane and the number of iNOS and eNOS positive cells in both airways walls and alveolar septa, Finally, EcTI reduced the number of MUC5ac positive cells in airway walls. Conclusions: The treatment with EcTI modulated lung mechanics and reduced inflammatory, remodeling and oxidative stress alterations induced by elastase. Although more studies need to be performed to elucidate the mechanisms involved in this process, we may considerate EcTI as a potential therapeutic tool for COPD management

LIMA, Glauber Pacelli Gomes de. Purificação, caracterização bioquímica e atividade biológica in vitro contra insetos praga de um novo inibidor de tripsina isolado de sementes de Sapindus saponaria L. (Sapindaceae). 119 f. : Dissertação (Mestrado) - Universidade Federal do Ceará, Centro de Ciências, Departamento de Bioquímica e Biologia Molecular, Programa de Pós-Graduação em Bioquímica. Fortaleza-CE, 2012. / Submitted by Eric Santiago (erichhcl@gmail.com) on 2016-05-20T13:23:01Z No. of bitstreams: 1 2012_dis_gpglima.pdf: 2370771 bytes, checksum: 509ae0531057d53f967b325467f88d5c (MD5) / Approved for entry into archive by demia Maia (demiamlm@gmail.com) on 2016-05-23T11:59:24Z (GMT) No. of bitstreams: 1 2012_dis_gpglima.pdf: 2370771 bytes, checksum: 509ae0531057d53f967b325467f88d5c (MD5) / Made available in DSpace on 2016-05-23T11:59:24Z (GMT). No. of bitstreams: 1 2012_dis_gpglima.pdf: 2370771 bytes, checksum: 509ae0531057d53f967b325467f88d5c (MD5) Previous issue date: 2012 / Environmental toxicity, low biodegradability and increased resistance in agricultural pest insects and in insect vectors of diseases to insecticides traditionally used for their control have encouraged the development of chemical alternatives with greater specificity and biodegradability especially from plants. In this way, the present study aimed the purification, characterization and evaluation of activity towards pest insect digestive enzymes of a new trypsin inhibitor obtained from Sapindus saponaria seeds. This new trypsin inhibitor obtained from S. saponaria seeds (SSTI2) belongs to Potato I inhibitor family and was purified by protein precipitation with trichloroacetic acid, affinity chromatography and reverse phase chromatography using UFLC system. The native inhibitor and its fragments generated by enzymatic treatment with trypsin and pepsin were analyzed and sequenced by MALDI-TOF and ESI-TOF mass spectrometry, determining its accurate molecular mass (MM = 7571, 976 Da) and primary structure (64 of 69 amino acids). The SSTI2 showed an IC50 of 8.3 x 10-2 μmol.L-1 against bovine trypsin, and a much lower inhibitory activity on the enzymes chymotrypsin (13.24 ± 0.28%) and papain (5.28 ± 0 , 42%), but was unable to inhibit proteolysis promoted by bromelain. In spite to show moderate inhibition of total digestive enzymes (4.74 ± 0.45% to 56.06 ± 1.41%), the inhibitor was very effective upon trypsin-like enzymes present in Aedes aegypti (92.44 ± 0.99%), Anthonomus grandis (77.93 ± 0.12%), Anticarsia gemmatalis ( 32.21 ± 0.57%) and Spodoptera frugiperda (71.44 ± 1.23%) guts. This strong inhibitory effect of SSTI2 on the catalytic activity of trypsin-like peptidases of insect’s midguts suggests a possible suppressive effect on development and survival of insects fed with diets containing the inhibitor. Thus, future in vivo assays and evaluation of other biochemical properties will be important to establish the potential biotechnological application of SSTI2, especially for the combat of Ae. aegypti, A. grandis and An. gemmatalis. Furthermore, the sequence of SSTI2 elucidated in this study allows the chemical synthesis, cloning of coding gene sequence and heterologous expression of this potential new biotechnological tool. / A toxicidade ao meio ambiente, a baixa biodegrabilidade e a crescente resistência de insetos praga da agricultura e de insetos vetores de doenças aos inseticidas tradicionalmente utilizados tem estimulado o desenvolvimento de alternativas com maior biodegradabilidade e especificidade, especialmente de origem vegetal. Nesse sentido, o presente estudo consistiu na purificação, caracterização e avaliação do efeito biológico in vitro de um novo inibidor de tripsina obtido das sementes de Sapindus saponaria sobre as enzimas digestivas de insetos. Através de precipitação com ácido tricloroacético (TCA), cromatografia de afinidade à tripsina e cromatografia de fase reversa em sistema UFLC, foi purificado um novo inibidor de tripsina (SSTI2) pertencente ao grupo de inibidores do tipo Batata I, uma categoria de inibidores de peptidases serínicas com reconhecido efeito tóxico sobre insetos. O inibidor nativo e fragmentos desse gerados por tratamento enzimático com tripsina e pepsina foram analisados e sequenciados por espectrometria de massa do tipo MALDI-TOF e ESI-TOF, determinando assim a sua massa molecular acurada (MM = 7571, 976 Da) e elucidando a sua estrutura primária (64/69 aminoácidos). O inibidor apresentou uma IC50 de 8,3 x 10-2 μmol.L-1 contra a tripsina bovina, mas apresentou baixa atividade inibitória sobre as enzimas quimotripsina (13,24 ± 0,28%) e papaína (5,28 ± 0,42%), e não foi capaz de inibir a proteólise promovida pela bromelaína. O SSTI2 inibiu moderadamente a atividade catalítica das enzimas digestivas totais dos insetos, com percentual de inibição variando entre 4,74 ± 0,45% a 56,06 ± 1,41%. No entanto, o inibidor foi eficaz em atuar sobre as enzimas digestivas do tipo tripsina presentes nos intestinos dos insetos Aedes aegypti (92,44 ± 0,99%), Anthonomus grandis (77,93 ± 0,12%), Anticarsia gemmatalis (32,21 ± 0,57%) e Spodoptera frugiperda (71,44 ± 1,23%). Esse expressivo efeito inibitório do SSTI2 sobre a atividade catalítica das peptidases do tipo tripsina provenientes do intestino médio dos insetos sugere um possível efeito supressor no desenvolvimento e sobrevivência de insetos alimentados com dietas contendo o inibidor. Assim, futuros estudos in vivo e avaliações de outras propriedades bioquímicas do inibidor serão importantes para determinar a potencial aplicação biotecnológica do SSTI2, especialmente para o combate de A. aegypti, A. grandis e A. gemmatalis. Além disso, a sequência do SSTI2 elucidada nesse estudo possibilita a síntese, clonagem do gene codificante e expressão heteróloga dessa potencial ferramenta biotecnológica.

O presente trabalho avaliou a efetividade do tratamento com tripsina (TT) na eliminação do BoHV-1 Colorado, causador da Rinotraqueíte Infecciosa Bovina (IBR). Camundongos fêmeas Swiss, com idade entre 6 e 8 semanas, foram superovuladas com 0,2mL a 5UI de hormônio eCG e, após 48h com hCG e acasaladas com machos inteiros da mesma linhagem e idade. Após 18 horas, as fêmeas foram eutanasiadas e, através de abertura no peritônio, os zigotos foram coletados. Foram separados zigotos para cinco ensaios que forneceram os seguintes dados: o BoHV-1 Colorado altera a taxa de clivagem e a morfologia do embrião; a tripsina, seguindo recomendações da IETS, não danifica o embrião; os embriões expostos aos vírus e submetidos ao TT não alteram sua morfologia e taxa de clivagem; foram detectados (nested-PCR+) vírus viáveis (MDBK+) após o TT. Estes resultados demonstram que o TT não foi efetivo para eliminar o BoHV-1 Colorado, porém em alguns ensaios o TT demonstrou eficiência na inativação do vírus o que torna-o um importante método de controle in vitro. / This study evaluated the effectiveness of treatment with trypsin (TT) in the elimination of BoHV-1 Colorado, which causes infectious bovine rhinotracheitis (IBR) Swiss female mice, aged 6 and 8 weeks, were superovulated with 0.2 mL 5UI hormone eCG and 48h after hCG and mated with males of the same lineage and age. After 18 hours, females were euthanized, and through na opening in the peritoneum, the zygotes were collected. Zygotes were separated for five trials that provided the following data: the Colorado BoHV-1 alters the cleavage rate and embryo morphology; trypsin, following recommendations of the IETS, does not damage the embryo; the embryos exposed to the virus and subjected to TT does not change their morphology and cleavage rate; were detected (nested-PCR +) viable virus (MDBK +) after the TT. These results demonstrate that TT was not effective to eliminate the BoHV-1 Colorado, but in some tests showed the TT efficiency in inactivating the virus makes it na important method of control in vitro.

Golgi apparatus protein 1 (GLG1) est une protéine transmembranaire de 160 kDa qui interagit avec l’apolipoprotéine B100 (apoB100), le récepteur des lipoprotéines de basse densité (LDLR) et la proprotein convertase subtilisin/kexin type 9 (PCSK9). Cependant, son mécanisme d’action et sa régulation post-traductionnelle sont inconnus. Des études ont montré que GLG1 subit deux clivages résultant en fragments solubles secrétés de 150 kDa et 55 kDa. Dans cette étude, notre premier objectif est d’identifier les enzymes responsables de la protéolyse de GLG1 ainsi que l’effet du clivage sur sa fonction dans le métabolisme des lipides. De plus, les résultats de nos collaborateurs montrent que les souris adultes déficientes en GLG1 ont un plus grand nombre d’adipocytes mais de taille plus petite que les souris de type sauvage. Notre deuxième objectif est de mesurer la variation de l’expression ainsi qu’identifier l’effet de GLG1 lors de la différentiation des fibroblastes en adipocytes. Pour le premier objectif, les cellules HEK293T surexprimant GLG1 ont été soit transfectées avec des convertases de proprotéines (PCSK) soit incubées avec différents inhibiteurs d’enzymes. Les milieux et les lysats cellulaires ont été analysés par immunobuvardage à la Western. Il n’y a pas eu de nouveaux fragments générés en présence des PCSK. Cependant, en présence d’inhibiteurs des sérines protéases apparentées à la trypsine soit AEBSF et Gabexate mesylate, il y a eu une réduction de la formation du fragment de 55 kDa. Pour identifier la métalloprotéase responsable du clivage de l’ectodomaine générant le fragment de 150 kDa, GLG1 a été transfectée avec les Tissue Inhibitor of Metalloproteinase (TIMP 1-4). Nos résultats ont montré que TIMP3 empêche la relâche de l’ectodomaine de GLG1 dans le milieu de culture. Finalement, nos analyses de plasma de souris par immunobuvardage à la Western ont montré la présence des fragments de 150 kDa et 55 kDa de GLG1 in vivo. Pour le deuxième objectif de l’étude, les fibroblastes préadipocytaires de souris 3T3-L1 ont été différenciés en adipocytes. Des lysats cellulaires et l’isolation d’ARN ont été effectués aux jours 0, 2, 4, 6, 8 et 10 de la différenciation. Des immunobuvardages à la Western ainsi que des RT-qPCR ont été réalisés pour analyser l’expression de GLG1 au cours de la différenciation. Nos résultats ont montré que l’expression de GLG1 augmente durant la différenciation. Bref, nos résultats démontrent que des enzymes trypsin-like clivent GLG1 et génèrent le fragment de 55 kDa. L’inhibition du clivage de l’ectodomaine de GLG1 par TIMP3 suggère que les ADAMs sont impliquées dans la relâche du fragment de 150 kDa. De plus, nous avons montré que l’expression de GLG1 augmente au cours de la différenciation adipocytaire. / Golgi apparatus protein 1 (GLG1) is a 160 kDa transmembrane protein interacting with apolipoprotein B100 (apoB100), low-density lipoprotein receptor (LDLR) and proprotein convertase subtilisin/kexin type 9 (PCSK9). However, the protein’s posttranslational regulation and mechanism of action are poorly understood. Previous studies showed that GLG1 is cleaved resulting in two fragments of 150 kDa and 55 kDa secreted at the cell surface and in the extracellular matrix. The first objective of this study is to identify enzymes responsible for GLG1 proteolysis and the effect of cleavage on its function in lipid metabolism. Furthermore, our collaborators showed that mice with GLG1 knockout have a higher number of adipocytes, but those cells are smaller in size compared to those in wild type mice. Therefore, the second objective of the study is to measure the variation of GLG1 expression during adipocytes differentiation and to identify the effects of GLG1 knockout on adipocytes differentiation. For the first objective, HEK293T cells overexpressing GLG1 were either transfected with basic amino acid-specific proprotein convertases (PCSK) or treated with enzyme inhibitors. Media and cell lysates were analyzed by Western blot. No new fragments were detected in media of PCSK-transfected cells. Cell treatment with trypsin-like serine proteases inhibitors, AEBSF and Gabexate mesylate, reduced the secretion of the 55 kDa fragment. To identify the metalloproteinase responsible for GLG1 shedding, GLG1 was co-transfected with Tissue Inhibitors of Metalloproteinase (TIMP1-4). Our results showed that TIMP3 inhibits shedding of the 150 kDa fragment. Finally, wild-type mouse plasma was analyzed by Western blot and showed the presence of both fragments in vivo. For the second objective of the study, fibroblasts 3T3-L1 cells were differentiated into adipocytes and GLG1 mRNA and protein expression were measured at day 0, 2, 4, 6, 8 and 10 by qPCR and Western Blot. Our results showed that GLG1 expression increased during differentiation and a peak was observed at day 4. To conclude, in the first objective of our study, our results showed that trypsin-like enzymes cleave GLG1 and produce a 55 kDa fragment. Shedding of GLG1 is inhibited by TIMP3, which suggests that ADAM10 or ADAM17 are involved in the release of the 150 kDa fragment. In addition, both 55 kDa and 150 kDa fragments were found in normal mouse plasma supporting the relevance of our findings in vivo. In the second objective of our study, GLG1 expression increased during adipocyte differentiation suggesting a role in adipose tissue development and/or morphology. In conclusion, our study will help elucidate how proteolysis of GLG1 impacts its role in the regulation of apoB and PCSK9 secretion and lipid metabolism and how can GLG1 expression affect adipocytes differentiation.

The theoretical part of work is focused on the issue of biomass which can be used for energy purposes, inparticular agricultural waste, as well as can serve as a substrate for biogas station. It also deals with proteomics, its goals and approaches, separation methods. The aim of this work was to measure each sample of enzyme activity of biomass, which are used as a raw materials for biogas plants and their proteomic identification.

Medical devices, such as catheters and heart valves, are an important part of patient care. However, blood-contacting devices can activate the blood coagulation cascade to produce factor (f) Xa, the clotting enzyme that induces thrombin generation. By activating platelets and converting soluble fibrinogen to fibrin, thrombin leads to blood clot formation. Blood clots that form on medical devices create problems because they may foul the device and/or serve as a nidus for infection. In addition, clots can break off from the device, travel through the circulation and lodge in distant organs; a process known as embolization. This is particularly problematic with central venous catheters because clots that form on them can break off and lodge in pulmonary arteries, thereby producing a pulmonary embolism. Similarly, clots that form on heart valves can break off and lodge in cerebral arteries, thereby producing a stroke. Therefore, anticoagulants, blood thinning drugs, are frequently used to prevent clotting on medical devices. Conventional anticoagulants, such as heparin and warfarin, target multiple clotting factors. Heparin binds to antithrombin in plasma and accelerates the rate at which it inhibits fXa, thrombin and many other clotting enzymes. Warfarin, which is a vitamin K antagonist, attenuates thrombin generation by interfering with the synthesis of the vitamin K-dependent clotting factors, which include fX and prothrombin, the precursor of thrombin. In contrast to heparin and warfarin, more recent anticoagulants inhibit only a single clotting enzyme. For example, fondaparinux, a synthetic heparin fragment, only inhibits fXa and dabigatran, an oral thrombin inhibitor, only targets thrombin. Although effective for many indications, fondaparinux was less effective than heparin for preventing clotting on catheters in patients undergoing heart interventions and dabigatran was less effective than warfarin for preventing strokes in patients with mechanical heart valves. The failure of these new anticoagulants highlights the need for a better understanding into the drivers of clotting on medical devices. Therefore, the overall purpose of this thesis is to gain this understanding so that more rational approaches to its prevention can be identified. In the classical model of blood coagulation, clotting is triggered via two distinct pathways; the tissue factor (TF) pathway or extrinsic pathway and the contact pathway or intrinsic pathway; pathways which are initiated by fVIIa and fXIIa, respectively. The mechanism by which medical devices initiate clotting is uncertain. Platelet and complement activation and microparticle formation have been implicated, which would drive clotting via the TF pathway. Alternatively, medical devices can bind and activate fXII, thereby initiating the contact pathway. We hypothesized that medical devices trigger clotting via the contact pathway and induce the local generation of fXa and thrombin in concentrations that exceed the capacity of fondaparinux and dabigatran to inhibit them. To test this hypothesis, we used catheters as a prototypical medical device and we used a combination of in vitro and rabbit models. Several lines of evidence indicate that catheters initiate clotting via the contact pathway. First, catheter segments shortened the clotting time of human plasma, and this activity was attenuated in fXII- or fXI-deficient plasma, which are key components of the contact pathway, but not in fVII-deficient plasma, which is the critical component of the extrinsic pathway. Second, corn trypsin inhibitor (CTI), a potent and specific inhibitor of fXIIa, attenuates catheter thrombosis. Third, selective knockdown of fXII or fXI with antisense oligonucleotides attenuated catheter-induced thrombosis in rabbits, whereas knockdown of fVII had no effect. Therefore, these results revealed the importance of the contact pathway in device-associated thrombosis, and identified CTI or fXII or fXI knockdown as novel strategies for preventing this problem. Focusing on fXIIa as the root cause of medical device associated clotting, we coated catheters with CTI using a polyethylene glycol (PEG) spacer. In addition to unmodified catheters, other controls included catheters coated with albumin via a PEG spacer or catheters coated with PEG alone. Compared with unmodified catheters or with the other controls, CTI-coated catheters attenuated clotting in buffer or plasma systems and were resistant to occlusion in rabbits. These findings support the concept that catheter-induced clotting is driven via the contact pathway and identify CTI coating as a viable strategy for its prevention. We next set out to test the hypothesis that fondaparinux and dabigatran, which inhibit fXa and thrombin, respectively, are less effective than heparin, which inhibits multiple clotting enzymes. Fondaparinux and dabigatran were less effective than heparin at preventing catheter induced clotting and thrombin generation, respectively. Likewise, in a rabbit model of catheter thrombosis, fondaparinux was less effective than heparin and dabigatran was only effective when administered at doses that yielded plasma dabigatran levels similar to those found at peak in human given the drug; at trough levels, dabigatran was no better than placebo. Finally, we also showed synergy between heparin and either fondaparinux or dabigatran. Thus, when co-administered to rabbits in doses that on their own had no effect, the combination of fondaparinux or dabigatran plus heparin extended the time to catheter thrombosis. These findings support the hypothesis that when catheters trigger clotting via the contact pathway, fXa and thrombin are generated in concentrations that overwhelm the capacity of fondaparinux or dabigatran to inhibit them. Furthermore, the synergy between heparin and fondaparinux or dabigatran has clinical implications because it explains why supplemental heparin attenuated the risk of catheter thrombosis in patients treated with fondaparinux who underwent cardiac procedures and it identifies the potential role of supplemental heparin in dabigatran-treated patients who require such interventions. In summary, we have shown that catheters trigger clotting via the contact pathway and have identified CTI coating or fXII or fXI knockdown as viable strategies for prevention of this problem. In addition, for prevention of catheter thrombosis, we also have shown that heparin, which inhibits multiple coagulation enzymes, is more effective than fondaparinux or dabigatran, which only inhibit fXa or thrombin, respectively; findings consistent with the clinical observations. Moreover, the synergy that we observed between fondaparinux or dabigatran and heparin identifies supplemental heparin as strategy for preventing catheter thrombosis in patients receiving these drugs. Taken together, these studies provide insight into the mechanisms of catheter thrombosis and potential strategies for its prevention. / Thesis / Doctor of Philosophy (PhD)

Proteins and their intricate network of interactions are fundamental to many molecular processes that govern life. Mass spectrometry-based structural proteomics represents a powerful set of techniques for characterizing protein structures and interactions. The last decade has witnessed a large-scale adoption in the application of these techniques toward solving a variety of biological questions. Addressing these questions has often been coincident with the further development of these techniques. Insight into the structures of individual proteins and their interactions with other proteins in a proteome-wide context has been made possible by recent developments in the relatively new field of chemical crosslinking combined with mass spectrometry. In these experiments crosslinking reagents are used to capture protein-protein interactions by forming covalent linkages between proximal amino acid residues. The crosslinked proteins are then enzymatically digested into peptides, and the covalently-coupled crosslinked peptides are identified by mass spectrometry. These identified crosslinked peptides thus provide evidence of interacting regions within or between proteins. In this dissertation the development of tools and methods that facilitate this powerful technique are described. The primary arc of this work follows the development and application of mass spectrometry-based approaches for the identification of protein crosslinks ranging from those which exist endogenously to those which are introduced synthetically. Firstly, the development of a novel strategy for comprehensive determination of naturally occurring protein crosslinks in the form of disulfide bonds is described. Secondly, the application of crosslinking reagents to create synthetic crosslinks in proteins coupled with molecular dynamics simulations is explored in order to structurally characterize the intrinsically disordered tau protein. Thirdly, improvements to a crosslinking-mass spectrometry method for defining a protein-protein interactome in a complex sample is developed. Altogether, these described approaches represent a toolset to allow researchers to access information about protein structure and interactions. / Graduate