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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
41

Significance of PTEN Phosphorylation and its Nuclear Function in Lung Cancer

Malaney, Prerna 16 November 2016 (has links)
Phosphorylation mediated inactivation of PTEN leads to multiple malignancies with increased severity. However, the consequence of such inactivation on downstream functions of PTEN are poorly understood. Therefore, the objective of my thesis is to ascertain the molecular mechanisms by which PTEN phosphorylation drives lung cancer. PTEN phosphorylation at the C-terminal serine/threonine cluster abrogates its tumor suppressor function. Despite the critical role of the PTEN C-tail in regulating its function, the crystal structure of the C-tail remains unknown. Using bioinformatics and structural analysis, I determined that the PTEN C-tail is an intrinsically disordered region and is a hot spot for post-translational modifications (particularly phosphorylation) and protein-protein interactions. Evolutionary analysis of PTEN and its interacting proteins revealed that the PTEN C-tail has only recently evolved to acquire the ability to engage in a myriad of protein-protein interactions, resulting in its versatile functions. Replacement of the PTEN C-tail serine/threonine residues with alanines generated an artificial mutant, PTEN-4A, which remained “phospho-deficient” and therefore constitutively active. Interestingly, PTEN-4A suppressed cell proliferation and migration to a greater extent than PTEN-WT. PTEN-4A preferentially localized to the nucleus where it suppressed E2F-mediated transcription of cell cycle genes. PTEN physically interacted with the E2F1 protein and at E2F1-binding sites on chromatin, a likely mechanism for its transcriptional function. Further, deletion analysis on various PTEN domains revealed that the C2 domain of PTEN is indispensable for suppression of E2F-related genes. Systematic transcriptional promoter-reporter assays identified disease-associated C2 domain mutations that lose their ability to suppress E2F-mediated transcription, supporting the concept that these mutations are oncogenic in patients. Consistent with my findings, I observed increased level of PTEN phosphorylation and reduced nuclear PTEN levels in lung cancer patient samples. Further, to determine whether the enhanced growth-suppressive properties of PTEN-4A may be due to differential protein-protein interactions, I performed a comparative proteomic profiling of PTEN-WT and PTEN-4A interactomes using the SILAC methodology. Galectin-1 was identified as a candidate protein that binds preferentially to PTEN-WT and inhibits its tumor suppressive function. Taken together, the various tumor suppressive mechanisms of PTEN-4A may be harnessed therapeutically as adjunctive cancer therapy. Use of small molecule inhibitors that hinder PTEN C-tail phosphorylation is a plausible approach to activate PTEN function to reduce tumor burden.
42

Compact-disc microfluidic methods for characterization of therapeutic antibodies : Analysis of post-translational modifications

Tran, Thi Thuy January 2012 (has links)
Characterization of post-translational modifications (PTMs) of therapeutic proteins is very important during the bioprocess development to maintain desired product quality and during the submission process to regulatory authorities for product approval. Monitoring glycosylation in pharmacokinetic studies can be useful to evaluate the dependence of clearance rates on different glycoforms. The cost and efficiency of characterization affect the speed to market of biopharmaceutical proteins. A reduction in the number of manual processing steps, cost of reagents and consumption of sample, as well as the time required for chemical analysis, is therefore necessary. The research presented in this thesis is focused on the potential of using microfluidic discs for automated, miniaturized, parallel and rapid sample preparation for PTM characterization of therapeutic monoclonal antibodies. Paper I describes the method development for N-linked glycosylation profiling. Several sample preparation steps have been performed in an integrated process in the microfluidic compact disc (CD). Paper II demonstrates the use of the method presented in paper I in combination with multivariate statistics for discrimination of glycosylation profiles of different therapeutic antibodies and simulation of a real case of quality control. Paper III is focused on a method for monitoring changes in glycosylation profiles of therapeutic antibodies in serum over time by incubation with an exoglycosidase enzyme. Paper IV describes the method for peptide mapping of therapeutic antibodies. In addition, recent work (unpublished results) assesses the potential of this method for methionine oxidation detection. The developed methods were fast, robust with low sample/reagent consumption. Generation of glycosylation profile data for one sample was established in approximately 2 h. The amount of samples and antigens loaded into the CD platform for one replicate was less than 0.3 μg and approximately 0.06 μg, respectively. Furthermore, considering the parallel function of the CD, conducting the analysis for 54 samples can be completed within a day. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>
43

Integrated strategies to develop post-translationally modified proteins in extracellular vesicles as candidate disease markers

Hillary Andaluz Aguilar (9745967) 15 December 2020 (has links)
Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing proteins and nucleic acid cargo. These vesicles are released by almost all cell types and provide an effective and ubiquitous path for intercellular communication and transmission of pathogenic and signaling molecules among cells. Research into potential biomarkers isolated from EV has been propelled by the development of methods and tools to acquire them by minimally and non-invasive means, which reinforces their great diagnostic potential. In the context of cancer, this opens the door to apply EV based liquid biopsy for early detection prior to alternate, more prevailing diagnostic tools like imaging studies. In autoimmune diseases, EVs play a crucial role in immune responses and as immunomodulatory agents as they can modulate the function of a wide variety of immune cells, especially in antigen-presenting cells (APCs). Several efforts have been made to study EVs and their cargo in numerous disease models, but very few in autoimmunity. Autoimmune diseases are chronic, have been underexplored especially in the omics area, and their diagnosis and treatment rely on traditional therapy. Therefore, there is a need for efficient methods to elucidate biomarkers that could provide additional layers of information for treatment, diagnosis, and prognosis. Additionally, protein post-translational modifications (PTMs), such as phosphorylation, glycosylation, and acetylation, are involved in multiple essential cellular processes and represent an important mechanism of regulation for cellular physiological functions, leading to the development of effective and targeted therapeutics. Discovery and profiling PTMs have established the relevance of PTMs in EVs and associated EV functions and novel applications. This dissertation proposes integrated proteomic strategies to efficiently isolate and analyze EVs in human plasma from different types of pathologies like cancer and autoimmune diseases. The main focus is the development of the platforms, to not only isolate the proteome from EVs, but also PTMs including phosphorylation, glycosylation and acetylation, simultaneously. Chapter one, which is the core of this dissertation, describes the platform to sequentially isolate and analyze the EV proteome, phosphoproteome and glycoproteome from human plasma. Chapters two and three focus on the ongoing application of this platform with slight modifications into different disease models, in this case breast cancer subtypes and autoimmune diseases.
44

Regulation of the Drosophila Initiator Caspase Dronc through Ubiquitylation

Kamber Kaya, Hatem E. 17 January 2017 (has links)
Apoptosis is a programmed cell death mechanism that is evolutionary conserved from worms to humans. Apoptosis is mediated by initiator and effector caspases. The initiator caspases carry long pro-domains for their interaction with scaffolding proteins to form a cell-death platform, which is essential for their activation. Activated initiator caspases then cleave effector caspases that execute cell death through cleaving downstream targets. In addition to their apoptotic function, caspases also participate in events where caspase activity is not required for cell killing, but for regulating other functions, so-called non-apoptotic functions of caspases. The Drosophila initiator caspase Dronc, the ortholog of mammalian caspase-2 and caspase-9 has a CARD domain that is essential for its interaction with the scaffolding protein Dark to form the apoptosome. Apoptosome formation is crucial for activation of Dronc. Activity of both initiator and effector caspases are further kept in control by the ubiquitin system to avoid inappropriate caspase activity. However, mechanistic details of how the ubiquitin system regulates activation of Dronc are not clear. Therefore, I investigated the ubiquitylation status of Dronc and its function in Drosophila. I found that Dronc is mono-ubiquitylated at Lys78 (K78) in its CARD domain, which blocks its interaction with Dark and formation of the apoptosome. Furthermore, I demonstrated that K78 mono-ubiquitylation plays an inhibitory role in Dronc’s non-apoptotic functions, which may not require its catalytic activity but may be important for the survival of the fly. This thesis study unveils the link between the ubiquitin system and caspases through a regulatory mechanism where a single mono-ubiquitylation event could inhibit both apoptotic and non-apoptotic functions of a caspase.
45

L'Effet " Modifications Post-Traductionnelles" : petits groupements chimiques, grandes conséquences? Caractérisation de protéines modifiées chez Pseudomonas aeruginosa PA14 par analyse protéomique. / "Post-translational modifications" effect : small chemical groups, influencial consequences? Characterization of modified proteins in Pseudomonas aeruginosa PA14 by proteomic analysis.

Gaviard, Charlotte 18 December 2018 (has links)
Pseudomonas aeruginosa PA14 est une bactérie pathogène très résistante aux antibiotiques et impliquée dans de nombreuses infections nosocomiales. Toutefois, la disponibilité d'agents antibactériens efficaces contre cette bactérie manque cruellement à ce jour. Explorer la physiologie de P. aeruginosa au niveau des modifications post-traductionnelles (PTMs) pourrait fortement contribuer au développement de nouveaux agents thérapeutiques. En effet, il a été montré certaines corrélations entre les PTMs et la virulence, l’adaptation et la résistance bactérienne. De plus, les progrès récents en protéomique ont permis d’accéder à un nombre croissant des protéines modifiées. Pourtant, leur description reste un véritable challenge.Dans une première partie, nous avons étudié l'impact des kinases et des phosphatases sur la physiologie de P. aeruginosa PA14. Cependant, aucune différence de phénotype n'a été observée entre les 8 mutants de ces enzymes et la souche sauvage.Dans une deuxième partie, nous avons caractérisé le succinylome et l'acétylome de la lysine chez P. aeruginosa PA14 dans quatre sources de carbone (glucose, citrate, succinate et glutamate) par enrichissement par anticorps couplé à la spectrométrie de masse. Ainsi, 1 530 sites succinylés (617 protéines) et 1 109 sites acétylés (526 protéines) ont été identifiés. De façon intéressante, 622 sites (312 protéines) ont été observés acétylés ou succinylés sur la même lysine, révélant ainsi l'existence de protéoformes pour une même protéine. Les protéines modifiées sont impliquées dans tous les processus biologiques. Toutefois, certaines d'entre elles ont des fonctions dans la résistance aux antibiotiques, le chimiotactisme et la virulence.Nous avons également quantifié les peptides succinylés et/ou acétylés dans les 4 sources de carbone. Les peptides succinylés étaient principalement sur-exprimés en citrate, mais aucune différence significative n’a été observée pour les peptides acétylées.Dans une troisième partie, nous avons étudié par immunoprécipitation le succinylome et l’acétylome de la lysine des protéines extracellulaire de P. aeruginosa. Nous avons montré que certaines lysines des protéines LasB et CbpD, deux facteurs de virulence, sont modifiées par 9 PTMs différentes. Une approche d’électrophorèse bi-dimensionnelle (2D) a permis de révéler et de quantifier les protéoformes des protéines extracellulaires et plus spécifiquement de ces facteurs de virulence.Dans une quatrième partie, une approche quantitative « label-free » a permis de mettre en avant 581 protéines qui varient différemment selon la source de carbone. Parmi ces protéines, 67 biomarqueurs ont été identifiés par approche statistique.Ces travaux constituent un point de départ prometteur pour de futures études sur le rôle de la succinylation de la lysine et d'autres PTMs chez P. aeruginosa. / Pseudomonas aeruginosa PA14 is a multi-drug resistant human pathogen largely involved in nosocomial infections. Unfortunately, today, effective antibacterial agents lacked. Explore its physiology at the post-translational modification (PTMs) level may contribute to the renewal of combat tactics. Indeed, some correlations between PTMs and the bacterial virulence, adaptation and resistance have been shown. The recent improvements in proteomics have increased the number of modified proteins. However, their characterization believes a real challenge.In the first part, we focused on the impact of kinases and phosphatases on bacterial physiology of P. aeruginosa PA14. For this purpose, we compared different phenotypes of 8 mutants of kinase and phosphatase with the WT strain. Unfortunately, no difference was observed.In the second part, we characterized the lysine succinylome and acetylome in P. aeruginosa PA14 in 4 carbon sources (glucose, citrate, succinate and glutamate) by mass spectrometry. Overall, a total of 1 530 succinylated sites (617 proteins) and 1 109 acetylated sites (526 proteins) were identified. Interestingly, we noticed that 622 sites (312 proteins) can be either acetylated or succinylated on the same lysine. This reveals the existence of proteoforms for a same protein. As expected, many modified proteins are involved in a wide range of biological processes but some of these proteins have interesting functions like antibiotic resistance, chemotaxis and virulence.We also tried to quantify succinylated and/or acetylated peptides in the 4 carbon sources. Succinylated peptides were mainly over-represented in the citrate condition whereas no significant difference was observed for the acetylated forms.In the third part, we investigated the lysine succinylome and acetylome of P. aeruginosa in extracellular compartment by immunoprecipitation. We showed that some lysines of two virulence factors, LasB and CbpD, were modified by 9 different PTMs. We also used a 2-dimensional gel approach to reveal and quantify proteoforms of extracellular proteins and more specifically virulence factors. In the fourth part, we did a label-free quantitative approach to obtain protein abundance in each carbon source. In total, 581 proteins vary differently depending on the carbon source. Among these proteins, 67 biomarkers were identified by statistical approach.This work is a promising starting point for further investigations on the biological role of lysine succinylation, and others PTMs, in P. aeruginosa.
46

Molekulární mechanismy a geny podílející se na kontrole signální dráhy Wnt / Molecular mechanisms and components controlling the Wnt signaling pathway output

Krausová, Michaela January 2014 (has links)
Beyond its essential roles in embryonic development, the Wnt-mediated signal transduction cascade is critically implicated in homeostasis of adult tissues. In the gastrointestinal epithelium, the threshold of active Wnt signaling is kept in a physiological range by a spectrum of regulatory networks and loops, thereby balancing the opposing processes of cell fate determination, proliferation and stem cell self-renewal. Furthermore, compelling evidence undoubtedly link an aberrant Wnt activity to the onset of bowel cancer. Understanding the principle causes and effects secondary to excessive Wnt signaling can provide valuable insights into the pathology of the malignant transformation of the colorectum. The proposed thesis attempts to focus on novel modes of the Wnt pathway modulation; both general and context-specific nuances of the Wnt level adjustment are thereby delineated. The results are presented in three distinct research publications and one review article. The first study examines the contribution of the distinct post-translational modifications, which the Wnt proteins undergo, to their proper processing, secretion and signaling activity. First, we investigated the sequential order and mutual interdependence of cysteine and serine-linked fatty acylation and N-linked glycosylation of murine...
47

Caracterização bioquímica e avaliação in vitro da ativação de fibroblastos e do potencial leishmanicida de uma L-aminoácido oxidase (LAAO) da peçonha de Crotalus durissus terrificus / Biochemical characterization and in vitro evaluation of the fibroblast activation and the leishmanicide potential of an L-amino acid oxidase (LAAO) from Crotalus durissus terrificus venom

Wiezel, Gisele Adriano 02 September 2016 (has links)
Acidentes causados por animais peçonhentos representam um grave problema de saúde pública, principalmente em áreas de difícil acesso da população ao serviço de saúde. No Brasil, o gênero Crotalus é o gênero de serpente cuja peçonha apresenta o maior índice de letalidade. As L-aminoácido oxidases (LAAOs) estão presentes na peçonha crotálica e são flavoenzimas que catalisam a oxidação de L-aminoácidos, produzindo, concomitantemente, peróxido de hidrogênio e amônia. LAAOs têm demonstrado atividade citotóxica, antimicrobiana, antitumoral, antiparasitária e na agregação plaquetária. Os objetivos desse estudo incluíram o isolamento e a caracterização bioquímica da LAAO de C. d. terrificus, assim como a avaliação de seu potencial leishmanicida e da ativação de fibroblastos. Foram desenvolvidos dois protocolos para isolamento da LAAO. O primeiro consistiu em cromatografias de troca catiônica, filtração molecular e de interação hidrofóbica. O segundo protocolo diferiou do primeiro na terceira etapa (cromatografia de afinidade). Cromatografia de fase reversa da LAAO isolada demonstrou um alto grau de pureza e a separação do cofator FAD. A massa molecular da LAAO foi determinada por espectrometria de massas MALDITOF (58.702,196 Da). A caracterização estrutural dessa LAAO também incluiu a dedução da sua sequência primária e a localização do sítio de glicosilação e das ligações dissulfeto através de espectrometria de massas em equipamentos LC-MS/MS com diferentes tipos de fragmentação (HCD, ETD e EThcD). A sequência primária (498 resíduos) foi obtida após digestão da LAAO com diferentes proteases e o sítio de glicosilação foi localizado na Asn361. Análise por SDS-PAGE da LAAO em condições reduzida e reduzida/deglicosilada mostrou que cerca de 5% da massa da proteína é relativa à presença de açúcar. As ligações dissulfeto (Cys10-Cys171 e Cys331-Cys412) foram localizadas após digestão da enzima em pH ácido e análise por LC-MS/MS. A avaliação qualitativa da especificidade de substratos mostrou preferência por L-aminoácidos hidrofóbicos e, a ordem de especificidade (L-Phe>LLeu> L-Met>L-Trp>L-Ile) foi determinada através da cinética enzimática. A estabilidade da LAAO foi avaliada em diferentes temperaturas, tempos e condições de armazenamento. A enzima mostrou grande perda de atividade ao longo do tempo, sendo que a liofilização e o congelamento a -20 °C inibiram sua atividade completamente. A estabilidade térmica, avaliada pela técnica do Termofluor, mostrou que a LAAO é mais estável na presença de pH ácido, diferentes concentrações de substratos e ausência de NaCl. Promastigotas de Leishmania amazonensis foram estimulados com a LAAO (55 mUAE) e cerca de 30% dos parasitas foram mortos. Fibroblastos L929 também foram estimulados com a LAAO e em baixa concentração da enzima (1,83 mUAE) a viabilidade celular foi próxima de zero. Nas concentrações sem morte celular significativa, a ativação dos fibroblastos foi avaliada através da dosagem de óxido nítrico e citocinas, mas, em nenhum dos casos, houve ativação das células e maior produção desses compostos. Portanto, no presente estudo, foi isolada e caracterizada uma LAAO de C. d. terrificus que apresentou ação contra promastigotas de L. amazonensis e alta citotoxicidade para fibroblastos, sem causar a ativação dessas células / Acidents caused by venomous animals represent a serious publich health problem, mainly in remote areas where the acess to the health service is difficult. In Brazil, the genus Crotalus is the most lethal genus among the Brazilian snakes. The L-amino acid oxidases (LAAOs) are present in the venom from this genus and they are flavoenzymes that catalyze the oxidation of L-amino acids, producing hydrogen peroxide and ammonia concomitantly. LAAOs have been demonstrating many activities, including cytotoxic, antimicrobial, antitumor, antiparasitic and action on platelet aggregation. The main objectives of this study included the isolation and biochemical characterization of a LAAO from C. d. terrificus, and the evaluation of its leishmanicide potential and the fibroblasts activation. Two protocols were developed to the LAAO isolation from C. d. terrificus venom. First one consists in ionic exchange, gel filtration and hydrophobic interaction chromatographies. The second protocol has a modification in the third step which is affinity chromatography. Reverse-phase chromatography of the isolated LAAO showed high purity degree and the separation of FAD from the enzyme. The LAAO molecular mass was determined by MALDI-TOF mass spectrometry (58,702.196 Da). The structural characterization also included the deduction of primary sequence and the glycosylation site and disulfide bonds determinations through LCMS/ MS with different fragmentation modes (HCD, ETD, EThcD). The primary sequence (498 amino acid residues) was obtained after the LAAO digestion using different proteases. The glycosylation site was located in the Asn361. A SDS-PAGE analysis of reduced LAAO and reduced/deglycosylated LAAO showed that about 5% of the LAAO mass is due to the sugar presence. The disulfide bonds were determined after LAAO digestion at low pH and LC-MS/MS analysis. It showed bonds between Cys10-Cys171 and Cys331-Cys412. The qualitative evaluation of substrate specificity revealed preference for hydrophobic L-amino acids. The specificity order, determined through the kinetics evaluation, is L-Phe>L-Leu>LMet> L-Trp>L-Ile. The LAAO stability was evaluated at different temperatures, timecourse and storage conditions. The enzyme lost its activity over time, and lyophilization and freezing at -20 °C completely inhibited its activity. The thermal stability, evaluated by the Termofluor method, demonstrated that the best LAAO structural stability is achieved at acid pH, different substrate concentrations and at absence of NaCl. Leishmania amazonensis promastigotes were stimulated with LAAO (55 mEAU) and the parasites death was about 30%. The fibroblasts cell line L929 was also stimulated with LAAO, and at low concentration (1.83 mEAU) the cellular viability was close to zero. At lower concentrations, without significative cellular death, the fibroblast activation was evaluated through the nitric oxide e cytokines production, but none of the compounds were released. Therefore, in this study, a LAAO from C. d. terrificus venom was isolated and characterized. Moreover, this enzyme presented leishmanicide against L. amazonensis promastigotes and high cytotoxicity to fibroblasts, without the activation of these cells.
48

La galactosémie congénitale : la physiopathologie peut-elle être liée aux modifications post-traductionnelles des protéines ? / Congenital galactosemia : can the physiopathology be related to post-translationnal proteins modifications ?

Lacombe, Caroline 25 September 2013 (has links)
La galactosémie congénitale est une maladie métabolique affectant la voie du galactose. En effet, l'enzyme responsable de la transformation du galactose-1-phosphate en glucose-1-phosphate, la galactose-1-phosphate uridyltransférase, est déficiente et rend donc l'utilisation du galactose par l'organisme quasiment impossible. Ceci entraîne une accumulation de galactose ainsi que ses produits dérivés, le galactose-1-phosphate et le galactitol. Ainsi, notre hypothèse de travail est que les métabolites impliqués dans cette pathologie provoquent des modifications post-traductionnelles des protéines induisant ainsi leur vieillissement prématuré. Nous avons donc étudié l'impact de la « galactation » sur la structure du collagène de type I et montré que ces modifications structurales sont beaucoup plus importantes avec le galactose qu'avec le glucose à la même concentration, aussi bien sur la structure primaire que fibrillaire. Au contact du collagène « galacté », les fonctions des cellules inflammatoires sont modifiées. La technique de spectroscopie infrarouge a été utilisée pour caractériser les métabolites impliqués dans la galactosémie ainsi que les collagènes modifiés. Dans un but de dépistage, une étude en spectroscopie infrarouge de plasmas galactosémiques nous a permis de mettre en évidence le potentiel de cette technique, du fait de sa bonne sensibilité et de son faible coût de revient. En conclusion, les modifications post-traductionnelles des protéines semblent très fortement impliquées dans la physiopathologie de la galactosémie congénitale. / The congenital galactosemia is a metabolic disease involved in the galactose pathway. Indeed, the enzyme responsible of the galactose-1-phosphate transformation in glucose-1-phosphate, the galactose-1-phosphate uridyltransferase, is deficient and then leads to a use of galactose almost impossible. This leads to an accumulation of galactose and its derived products, the galactose-1-phosphate and the galactitol. Thus, our work hypothesis is that metabolites involved in this disease cause post-translational modifications of proteins inducing their premature aging. We then studied the impact of the « galactation » on the type I collagen and showed that the structural modifications are more important with galactose than with glucose at the same concentration, on both the primary and the fibrillar structure. On contact with « galacted » collagen, the inflammatory cells functions are also modified. The infrared spectroscopy technique has been used to characterize the metabolites involved in the galactosemia, just as the modified collagens. With the aim of screening, an infrared spectroscopy study of galactosemic plasmas allowed us to highlight the potential of this technique, with its good sensibility and its low cost price. To conclude, the post-translational modifications of proteins seem strongly involved in the physiopathology of the congenital galactosemia.
49

Characterization of Polypeptides by Tandem Mass Spectrometry Using Complementary Fragmentation Techniques

Nielsen, Michael Lund January 2006 (has links)
<p>In the growing field of proteomics identification of proteins by tandem mass spectrometry (MS/MS) is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein database. One problem with this approach is the false-positive identifications. MS-based proteomics experiments are further affected by a rather poor efficiency typical in the range of 10-15%, implicating that only a low percentage of acquired mass spectrometric data is significantly identified and assigned a peptide sequence.</p><p>In this thesis improvement in spectrum specificity is accomplished by using a combination of high-accuracy mass spectrometry and techniques that will yield complementary sequence information. Performing collision-activated dissociation (CAD) and electron capture dissociation (ECD) upon the same peptide ion will yield such complementary sequence information. Implementing this into a proteomics approach and showing the advantages of using complementary fragmentation techniques for improving peptide identification is shown. Furthermore, a novel database-independent score is introduced (S-score) based upon the maximum length of the peptide sequence tag derived from complementary use of CAD and ECD. The S-score can be used to separate poor quality spectra from good quality spectra. An-other aspect of the S-score is the development of the ‘reliable sequence tag’ which can be used to recover below threshold identifications and for a reliable backbone for de novo sequencing of peptides.</p><p>A novel proteomics-grade de novo sequencing algorithm has also been developed based upon the RST, which can retrieve peptide identification with the highest reliability (>95%). Furthermore, a novel software tool for unbiased identifications of any post-translational modifications present in a peptide sample is introduced (ModifiComb). Combining all the tools described in this thesis increases the identification specificity (>30 times), recovers false-negative identifications and increases the overall efficiency of proteomics experiements to above 40%. Currently one of the highest achieved in large-scale proteomics.</p>
50

High Content Analysis of Proteins and Protein Interactions by Proximity Ligation

Leuchowius, Karl-Johan January 2010 (has links)
Fundamental to all biological processes is the interplay between biomolecules such as proteins and nucleic acids. Studies of interactions should therefore be more informative than mere detection of expressed proteins. Preferably, such studies should be performed in material that is as biologically and clinically relevant as possible, i.e. in primary cells and tissues. In addition, to be able to take into account the heterogeneity of such samples, the analyses should be performed in situ to retain information on the sub-cellular localization where the interactions occur, enabling determination of the activity status of individual cells and allowing discrimination between e.g. tumor cells and surrounding stroma. This requires assays with an utmost level of sensitivity and selectivity. Taking these issues into consideration, the in situ proximity-ligation assay (in situ PLA) was developed, providing localized detection of proteins, protein-protein interactions and post-translational modifications in fixed cells and tissues. The high sensitivity and selectivity afforded by the assay's requirement for dual target recognition in combination with powerful signal amplification enables visualization of single protein molecules in intact single cells and tissue sections. To further increase the usefulness and application of in situ PLA, the assay was adapted to high content analysis techniques such as flow cytometry and high content screening. The use of in situ PLA in flow cytometry offers the possibility for high-throughput analysis of cells in solution with the unique characteristics offered by the assay. For high content screening, it was demonstrated that in situ PLA can enable cell-based drug screening of compounds affecting post-translational modifications and protein-protein interactions in primary cells, offering superior abilities over current assays. The methods presented in this thesis provide powerful new tools to study proteins in genetically unmodified cells and tissues, and should offer exciting new possibilities for molecular biology, diagnostics and drug discovery. 

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