Dissertations / Theses on the topic 'De novo Proteins'

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2015.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 107-119).
Biocatalysis has grown rapidly in recent decades as a solution to the evolving demands of industrial chemical processes. Mounting environmental pressures and shifting supply chains underscore the need for novel chemical activities, while rapid biotechnological progress has greatly increased the utility of enzymatic methods. Enzymes, though capable of high catalytic efficiency and remarkable reaction selectivity, still suffer from relative instability, high costs of scaling, and functional inflexibility. Herein, M13 bacteriophage libraries are engineered as a biochemical platform for de novo semisynthetic enzymes, functionally modular and widely stable. Carbonic anhydrase-inspired hydrolytic activity via Zn²+ coördination is first demonstrated. The phage clone identified hydrolyzes a range of carboxylic esters, is active from 25°C to 80°C, and displays greater catalytic efficacy in DMSO than in water. Reduction-oxidation activity is subsequently developed via heme and copper cofactors. Heme-phage complexes oxidize multiple peroxidase substrates in a pH-dependent manner. The same phage clone also binds copper(II) and oxidizes a catechol derivative, di-tert-butylcatechol, using atmospheric oxygen as a terminal oxidant. This clone could be purified from control phage via Cu-NTA columns, enabling future library selections for phage that coördinate Cu²+ ions. The M13 semisynthetic enzyme platform complements biocatalysts with characteristics of heterogeneous catalysis, yielding high-surface area, thermostable biochemical structures readily adaptable to reactions in myriad solvents. As the viral structure ensures semisynthetic enzymes remain linked to the genetic sequences responsible for catalysis, future work could tailor the biocatalysts to high-demand synthetic processes by evolving new activities, utilizing high-throughput screening technology and harnessing M13's multifunctionality.
by John P. Casey, Jr.
Ph. D.

While the advances of the scientific community have enabled extraordinary improvements in the capabilities of synthetic biology, there is a continued desire in biotechnology for enhanced or entirely novel biological functions. As proteins are either directly or indirectly responsible for the vast majority of naturally occurring biological activities, the modification of peptide structures constitutes a promising approach to address the ambitions of biotechnology. Central to the work in this thesis is the recognition that naturally occurring protein structures are intangibly complex due to the relics of evolutionary processes, accumulated from years of blind natural selection. Chapter 1 introduces de novo protein design strategies that circumvent the use of naturally occurring peptide scaffolds, offering examples of tractable systems that have been generated to perform various biological functions, thus forming the justification for the experimental approach undertaken here. The experimental work detailed in chapters 3 and 4 aimed to develop a system that would enable the incorporation of carotenoids and acenes into the internal cavity of de novo-designed 'maquette' proteins by hydrophobic partitioning alone. The results of these sections demonstrated that the protein chassis had little or no effect in the photophysical properties of the incorporated chromophores, whilst providing enhanced stability and solubility in entirely aqueous solutions. Conversely, the experimental strategy outlined in chapter 5 aimed to introduce nuclei of high atomic mass into the maquette proteins in order to directly affect the photophysical properties of the bound chromophores through the spin-orbit coupling interaction. The results of the final experimental chapter demonstrated that de novo designed proteins could effectively interface with native biological systems and provide a mechanism to enable cofactor incorporation in vivo. Where appropriate, the results of each experimental section are discussed in relation to their impact on specific areas of research and potential applications in biotechnology.

Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

Inhibition of protein synthesis serves as a general measure of cellular consequences of chemical stress. A few proteins are translated selectively and influence cell fate. How these proteins can bypass the general control of translation remains unknown. We found that low to mild doses of oxidants induce de novo translation of the NRF2 protein. Here we demonstrate the presence of a G-quadruplex structure in the 5' untranslated region (UTR) of NRF2 mRNA, as measured by circular dichroism, nuclear magnetic resonance, and dimethylsulfate footprinting analyses. Such a structure is important for 5'-UTR activity, since its removal by sequence mutation eliminated H2O2-induced activation of the NRF2 5' UTR. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics revealed elongation factor 1 alpha (EF1a) as a protein binding to the G-quadruplex sequence. Cells responded to H2O2 treatment by increasing the EF1a protein association with NRF2 mRNA, as measured by RNA-protein interaction assays. The EF1a interaction with small and large subunits of ribosomes did not appear to change due to H2O2 treatment, nor did post translational modifications, as measured by two-dimensional (2-D) Western blot analysis. Since NRF2 encodes a transcription factor essential for protection against tissue injury, our data have revealed a novel mechanism of cellular defense involving de novo NRF2 protein translation governed by the EF1a interaction with the G-quadruplex in the NRF2 5' UTR during oxidative stress.

The ability to design, synthesize and characterize de novo proteins can help facilitate the understanding of how individual amino acids contribute to the stability and structure of a protein. The de novo approach can be extended to include the use of templates, which assist in the organization of the peptides to form predetermined three-dimensional structures. These template assembled de novo proteins have been named "caviteins" (cavitand + protein).[See thesis for diagram]. One of the challenges in this area of research is the ability to design and synthesize native-like de novo proteins. Previously two caviteins, LG2 and LG3, had shown some nativelike characteristics, although the evidence for a completely native-like structure remained debatable. The approach to identify a native-like structure was to design a corresponding protein that would exhibit non native-like properties. The leucine residues of LG2 and LG3 were replaced with norleucine residues in NG2 and NG3, respectively. The norleucine-based caviteins were less native-like in structure, as speculated, than their leucine-based counterparts. In the past, the designed caviteins were limited to having only one type of peptide sequence attached within one bundle. Here, the design of a hetero-TASP, i.e. two different sequences within one bundle, was explored, and provided a means to create various de novo proteins, including an anti-parallel four-helix bundle. The hetero-TASPs were characterized and found to exhibit different native-like properties depending on the attached peptide sequences, and helix orientations. Lastly, the N - and C-capping efficiency of glycine was examined. Caviteins having, peptides linked to the cavitand template via their N - and C-termini, and with and without glycine caps were synthesized and characterized. It was found that the caviteins lacking glycine caps at their respective helix termini were comparable in stability with their capped-counterparts, which was contrary to what was hypothesized. It has been shown that subtle changes in the peptide sequence, linker and helix orientation have dramatic effects on the overall cavitein structure and stability. Since many of the factors underlying the stability and structure of four-helix bundles are now well understood, it would be exciting to undertake the challenges of designing caviteins with specific applications.
Science, Faculty of
Chemistry, Department of
Graduate

Redox cofactors and amino-acid free radicals play important roles in biology. Although many of the same cofactors and amino acids that form these radicals are found across a broad range of biological systems, identical cofactors can have different reduction potentials. The local environment plays a role in defining these redox potentials. An understanding of this local-environment effect can shed more light on how redox chemistry works in nature. Our laboratory has developed a library of model proteins that are well suited to study amino-acid radicals. a3X is a de novo designed protein that is composed of 67 residues. It forms a three-helix bundle connected by two glycine loops. The radical site is located at position 32 on the central a-helix. The a3X protein is designed to be well-folded and thermodynamically stable across a broad pH range. Paper 1 describes the structural and electrochemical characterization of a3Y, a tyrosine variant of a3X. We were able to obtain a unique Faradaic response from Y32 at both low and high pH, using differential pulse voltammetry. In addition, we successfully redesigned α3Y by introducing a histidine in close proximity to Y32, creating a tyrosine/histidine pair. Our goal in creating this pair was to study proton-coupled electron transfer (PCET) in a well-structured and solvent-sequestered protein environment.  In paper 2 we illustrated the redox reversibility of Y32 and produced the first ever Pourbaix diagram for a tyrosine radical in a protein. The formal potential of the Y32-OŸ/Y32-OH redox couple was determined to be 918 ± 2 mV vs. the normal hydrogen electrode (NHE) at pH 8.40.  While at pH 5.52, the formal potential of the Y32-OŸ/Y32-OH redox couple was recorded at 1.07 V. Papers 3 and 4 utilize a3W to study cation-π interactions. In paper 3, we showed how solvation can affect the strength of these interactions by -0.9 kcal/mol. In Paper 4, we were able to monitor the disruption of the cation-π interaction with the use of high-pressure fluorescence and were able to calculate the interaction energy for a solvent exposed cation-π. The aim of the work described in this thesis was to use model proteins to study tyrosine radicals to gain a broader perspective and better understanding of the versatility of biological electron transfer and to measure cation-π interactions and how they behave in different environments.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

Spiders produce multiple types of silk that exhibit diverse mechanical properties and biological functions. Most molecular studies of spider silk have focused on fibroins from dragline silk and capture silk, two important silk types involved in the survival of the spider. In this study we have focused on the characterization of egg case silk, a third silk fiber produced by the black widow spider, Latrodectus hesperus , whose DNA coding sequences have not been reported. Based upon solubility differences in 8 M guanidine hydrochloride, it is demonstrated by sodium dodecyl sulfate polyacrylamide gel electrophoresis and silver staining that the egg case silk is relatively complex at the molecular level, containing a large number of proteins with differing molecular weights. Protein components of egg case silk with a size about 100 kDa were obtained by a solubilization time course study, which indicates these proteins are likely to be embedded in the silk filament. Peptides in these 100 kDa proteins were released by tryptic in-gel and in-solution digestion. The peptides were sequenced using a MALDI tandem TOF mass spectrometer. Some of the de novo sequences were confirmed using a linear ion trap mass spectrometer equipped with a nanospray ion source. Combining the peptide sequences obtained, reverse genetics was employed to trace silk genes encoding proteins containing these de novo peptides. Three silk protein coding sequences were successfully discovered, which encode silk proteins named 3B, T1 and ECSP-1, respectively. 3B and T1 show the standard fibroin protein pattern. Amino acid repeat patterns were observed in these two silk clones. But the amino acid compositions of 3B and T1 show differences with the total amino acid composition of egg case silk, and also, the peptide sequences cannot be found in the primary amino acid sequences of 3B and T1. ECSP-1 protein represents one of the egg case silk proteins with a size of about 100 kDa. A number of peptide sequences obtained by mass spectrometric de novo sequencing were successfully located in ECSP-1's primary amino acid sequence. Sequence analysis demonstrates ECSP-1 represents a new class of silk proteins, with fibroin-like properties. The expression pattern of ecsp-1 is largely restricted to the tubuliform gland inside of the L. hesperus spider, with lower levels detected in the major and minor ampullate glands, which also confirms the identity of ECSP-1. It is also demonstrated that ECSP-1 assembles into higher aggregate structures through the formation of disulfide bonds. Peptide sequences from silk proteins from the Tarantula spider Grammostola rosea were also obtained. These sequences will be beneficial in obtaining genes encoding the silk from this spider species.

Orientador: Nilson Ivo Tonin Zanchin
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A resposta individual das células está na base da resistência do organismo à infecção viral. O principal mecanismo de resistência envolve a participação de inúmeros genes da via de sinalização dos interferons. Vários estudos vêm sendo conduzidos em larga escala para identificar genes que respondem aos mais variados tratamentos, assim como clusters gênicos relacionados a determinadas enfermidades, como a leucemia. A função do produto de muitos destes genes ainda não foi caracterizada. Numa ampla revisão destes artigos identificamos a proteína KIAA0082/ISG95 respondendo a interferon, à infecção pelo vírus da hepatite C (HCV), ao tratamento celular com oligodeoxinucleotídeos CpG, fazendo parte de um cluster de genes relacionados à leucemia e sendo super-expressa em linfócitos T ativados. Embora não possua função conhecida, esta proteína apresenta quatro domínios que indicam uma possível atividade relacionada ao metabolismo de RNA. Neste trabalho demonstramos que o promotor do gene ISG95 responde à estimulação por interferon num sistema repórter em células Vero. As atividades bioquímicas de ISG95 foram determinadas usando a proteína recombinante expressa em células de inseto Sf9. ISG95 interage com RNA e com S-adenosilmetionina, possuindo também atividade de metiltransferase in vitro. Ensaios de localização sub-celular demonstraram sua distribuição nuclear. Além disso, através do método duplo-híbrido de levedura e de ensaio de co-imunoprecipitação, foi possível identificar sua interação com o domínio C-terminal (CTD) da RNA polimerase II, o que é consistente com sua localização nuclear e com a função predita para o domínio WW localizado na extremidade C-terminal de ISG95. Os resultados indicam que ISG95 é parte da via de resposta a interferon e tem função associada possivelmente a eventos de processamento de prémRNA mediados pelo domínio CTD da RNA polimerase II
Abstract: A major mechanism of cellular resistance to viral invasion involves genes from the interferon signaling pathway, called ISGs (interferon stimulated genes). Global transcriptional profiling studies have linked increased expression of ISG95 (KIAA0082) to response to interferon treatment and to viral infection, suggesting that it may be part of the cellular defense against viral replication. In this work, we shown that the ISG95 promoter can drive interferoninduced transcription of a reporter gene in Vero cell cultures. The biochemical functions of ISG95 were assessed using recombinant protein. ISG95 shows RNA- and S-adenosyl-methionine binding and protein methyltransferase activity in vitro. ISG95 interacts with the C-terminal domain of RNA polymerase II, which is consistent with its nuclear localization and with the predicted function of the WW domain found in the C-terminal region of ISG95. The results presented in this work indicate that ISG95 is part of the interferon response pathway and functions in the pre-mRNA processing events mediated by the C-terminal domain of the RNA polymerase II
Doutorado
Genetica Animal e Evolução
Doutor em Genetica e Biologia Molecular

Nucleosides and nucleotides have a key role in cell physiology being implicated in crucial processes such as DNA and RNA synthesis, cell signaling and metabolic regulation. Purine and pyrimidine nucleotide balance is required for cell homeostasis, being imbalance and nucleotide depletion associated with metabolic dysregulation and cancer development. Understanding the molecular mechanisms behind these events appears to be a suitable approach to uncover novel drug anticancer targets and, eventually, improve therapy. De novo nucleotide biosynthesis is a highly energetic expensive process tightly regulated at different levels. PAICS (phosphoribosylaminoimidazole carboxylase / phosphoribosylaminoimidazole succinocarboxamide synthetase) gene encodes the bifunctional enzyme ADE2, which catalyzes steps 6 and 7 of de novo purine nucleotide biosynthesis. This enzyme has been reported to have an important role in carcinogenesis. Here we have analyzed how PAICS is regulated when nucleoside availability disturbances are induced using HT-29 cell lines. PAICS expression appears to be modulated in a challenging situation when the inhibitions of de novo pyrimidine nucleotide biosynthesis and salvage pathways were combined. Moreover when cells were cultured in a nucleoside depleted medium we observed a regulation of human Concentrative Nucleoside Transporters (hCNTs) expression. This type of modulation suggests that extracellular nucleoside availability and de novonucleotide biosynthesis are metabolically interconnected.

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Obesity is increasing, reaching epidemic levels in many regions of the world. Studies have shown that consumption of peanuts influences on weight control and this influence may be due to the action of trypsin inhibitors sacietog?nica that condition increased plasma colescistocinina (CCK). Moreover, the peanut has other health benefits, and these assignments are guaranteed to increase their production and consumption of several of its products, including the pa?oca peanut. The aim of this study was to identify the presence of a trypsin inhibitor in pa?oca peanut and evaluate its effect on food intake, weight gain and histomorphological changes in swiss mice (n = 8) and Wistar rats (n = 6). Experimental diets were prepared based on the AIN-93G and supplemented with tack or peanut trypsin inhibitor partially purified pa?oca peanut (AHTI). After each treatment, the animals were anesthetized and euthanized, their bloods were collected by cardiac puncture for the determination of CCK and other biochemical parameters (glucose, triglycerides, total cholesterol, high density lipoprotein, low density lipoprotein, glutamic-pyruvic transaminase, glutamic oxaloacetic transaminase and albumin) and their pancreas removed for histologic and morphometric analysis. The supplementation with pa?oca peanut and the AHTI showed a decrease of body weight gain and food intake in both mice and rats, due to the satiety, since the animals showed no evidence of impairment of nutritional status conditioned by consumption the AHTI. There were also observed biochemical or morphological important when compared with controls. However, AHTI led to increased secretion of CCK, a peptide sacietog?nico. Thus, these results indicate that AHTI present in pa?oca peanut, is able to enhance the secretion of plasma CCK and thereby reduce the weight gain associated with lower food intake of experimenta animals
A obesidade ? crescente, atingindo n?veis epid?micos, em muitas regi?es do mundo. Estudos t?m mostrado que o consumo de amendoins influencia no controle de peso e essa influ?ncia pode ser devido ? a??o sacietog?nica de inibidores de tripsina que condicionam o aumento plasm?tico de colecistocinina (CCK). Al?m disso, o amendoim apresenta outros benef?cios ? sa?de e essas atribui??es t?m garantido o aumento da sua produ??o e o consumo de v?rios de seus produtos, entre eles, a pa?oca de amendoim. O objetivo deste estudo foi identificar a presen?a de um inibidor de tripsina na pa?oca de amendoim e avaliar o seu efeito sobre o consumo alimentar, o ganho de peso e altera??es histomorfol?gicas em camundongos swiss (n=8) e ratos wistar (n=6). Dietas experimentais foram preparadas com base na AIN-93G e suplementadas com a pa?oca de amendoim ou com o inibidor de tripsina parcialmente purificado da pa?oca de amendoim (AHTI). Ao final de cada tratamento, os animais foram anestesiados, eutanasiados e tiveram seus sangues colhidos, por pun??o card?aca, para a dosagem de CCK e de outros par?metros bioqu?micos (glicose, triglicer?deos, colesterol total, lipoprote?nas de altadensidade, lipoprote?na de baixa-densidade, transaminase glut?mica pir?vica, transaminase glut?mica oxalac?tica e albumina) e seus p?ncreas extra?dos para an?lise histol?gica e morfom?trica. As suplementa??es com a pa?oca de amendoim e com o AHTI mostraram uma diminui??o do ganho de peso corporal e do consumo alimentar tanto em camundongos quanto em ratos, devido ? saciedade, uma vez que os animais n?o apresentaram ind?cios de comprometimento do estado nutricional condicionada pelo consumo do AHTI. N?o foram, tamb?m, observadas altera??es bioqu?micas, nem histomorfol?gicas importantes quando comparadas com os controles. No entanto, o AHTI levou ao aumento da secre??o de CCK, um pept?dio sacietog?nico. Assim, estes resultados sugerem que o AHTI, presente na pa?oca de amendoim, seria capaz de aumentar a secre??o plasm?tica de CCK e reduzir o ganho de peso associado com menor consumo alimentar de animais experimentais

INTRODUÇÃO: O linfoma difuso de grandes células B, sem outras especificaçoes (LDGCB, SOE) é uma neoplasia agressiva caracterizada pela heterogeneidade morfológica, imunofenotípica e molecular, porém o atual tratamento padrão utilizando imunoquimioterapia (R-CHOP) não considera tal diversidade. Há percentual significativo de pacientes que são refratários à terapia de primeira linha e alguns que apresentam recidiva precoce ou tardia, os quais representam as vítimas desta doença. O estudo imuno-histoquímico (IHQ), que é um método simples e universalmente disponível, vem sendo utilizado para reconhecer a diversidade biológica do LDGCB, SOE, identificando biomarcadores e subgrupos distintos da doença, que poderiam predizer a resposta terapêutica ao tratamento padrão e apontar possíveis candidatos a novas estratégias terapêuticas. OBJETIVOS: Este estudo avalia o valor prognóstico de cinco algoritmos para classificação do LDGCB segundo a célula de origem (COO) e da expressão de três biomarcadores (BCL2, CD30 e MYC) tendo como endpoint a sobrevida global. MÉTODOS: Foi realizado estudo retrospectivo com setenta e nove pacientes com LDGCB,SOE de novo tratados com imunoquimioterapia padrão, estadiados e acompanhados protocolarmente. Os casos foram classificados como subgrupo célula B centrogerminativa símile (GCB) ou como subgrupo célula B não-centrogerminativa símile (NGCB), de acordo com três algoritmos IHQ (Hans, Choi, e Visco-Young) pareados com estudo do perfil de expressão gênica (PEG) e dois algoritmos IHQ não-PEG pareados (Muris e Nyman). Foi estimado o valor prognóstico destes algoritmos e também avaliado a concordância entre eles. O valor prognóstico da expressão do BCL2, CD30 e MYC utilizando IHQ também foi analisado. RESULTADOS: Os algoritmos IHQ PEG pareados revelaram maior concordância entre si, porém nenhum deles revelou força prognóstica. A expressão do CD30 mostrou tendência a melhor prognóstico, porém a expressão de BCL2 e MYC avaliados isoladamente não revelaram impacto prognóstico. Contudo, a coexpressão do BCL2 e MYC, denominado como fenótipo linfoma duplo-expressor (LDE), revelou-se importante marcador prognóstico desfavorável. Foram identificados três subgrupos de risco baseado no fenótipo LDE e o Índice Prognóstico Internacional (IPI). CONCLUSÃO: Em pacientes com LDGCB, SOE de novo tratados com esquema terapêutico padrão, a pesquisa da expressão do fenótipo LDE é mais relevante do ponto vista prognóstico que a classificação em subgrupo GCB ou NGCB. Além disso, a expressão do CD30 pode ser relevante tanto para identificar subgrupo com tendência a melhor prognóstico como para identificar possíveis candidatos a nova terapia alvo
BACKGROUND: Diffuse large B-cell lymphoma, not otherwise specified (DLBCL, NOS) is an aggressive neoplasm characterized by morphological, phenotypic and molecular heterogeneity, but the current standard therapy using immunochemotherapy (R-CHOP) does not consider such diversity. There is a significant percentage of patients who are refractory to first-line therapy and those with early or late recurrence, whose represent the victims of this disease. Immunohistochemistry (IHC), a simple and universally available method, has been used to recognize the biological diversity of DLBCL, NOS, to identify biomarkers and distinct subgroups of the disease, which would predict the therapeutic response to standard treatment and point possible candidates for novel therapeutic strategies. OBJECTIVES: The current study was conducted to evaluate the prognostic value from five algorithms for classification of DLBCL based on cell of origin (COO) and the expression of three biomarkers (BCL2, CD30 and MYC) with overall survival (OS) as an endpoint. METHODS: We retrospectively evaluated seventy nine patients with de novo DLBCL, NOS treated with R-CHOP-like immunochemotherapy. The cases were assigned as germinal center B-cell like (GCB) or non-GCB subgroup (NGCB) according to five different IHC algorithms, including three algorithms based on gene expressing profile study (GEP), proposed by Hans, Choi, and Visco-Young, and two non-GEP based algoritms proposed by Muris, and Nyman. We evaluated their prognostic relevance and the concordance between these algorithms. The prognostic power of BCL2, CD30 and MYC expression were also assessed by IHC. RESULTS: None of the profiles assessed by IHC algorithms was able to predict overall survival (OS). The positive expression of CD30 showed a trend toward a better outcome. Neither the positive expression of BCL2 nor the positive expression of MYC were associated with outcome. However, the double-expressor lymphoma phenotype (DEL), represented by the concurrent expression of MYC and BCL2, exhibited a negative prognostic impact. Three different risk subgroups were identified based on the DEL phenotype and the International Prognostic Index (IPI) score. CONCLUSIONS: These data suggest that the DEL, rather than the cell of origin classification based on IHC, is a better predictor of OS in patients with DLBCL treated with R-CHOP-like immunochemotherapy. Besides, the CD30 expression may be a useful prognostic marker and a possible therapeutic target

Tese de Doutoramento em Ciências Veterinárias. Especialidade de Sanidade Animal
A modulação de imunidade específica por conjugação de antigénios com ligandos de receptores de reconhecimento de padrão (PRR) constitui uma estratégia emergente para o desenvolvimento de vacinas subunitárias. Neste trabalho, desenvolve-se um novo sistema de clonagem em Escherichia coli para expressão de antigénios em fusão com a lipoproteína OprI, um ligando TLR da membrana externa de Pseudomonas aeruginosa. O sistema permite um controlo apertado da expressão proteica e a purificação por cromatografia de afinidade com iões metálicos, ultrapassando as principais limitações de versões anteriores. Confirmou-se o processamento, translocação e triacilação da lipoproteína e desenvolveram-se protocolos para a produção de outras formulações recombinantes derivadas da parede bacteriana (fragmentos e vesículas de membrana externa) com potencial distinto para activação PRR. Como modelo, clonaram-se as sequências dos antigénios A104R do vírus da peste suína africana (VPSA), ovalbumina e EGFP. Demonstrou-se a capacidade adjuvante das três formulações, avaliando a resposta humoral e a indução de linfócitos T CD8+ in vivo e o perfil de citocinas e quimiocinas induzidas em células dendríticas estimuladas in vitro. Os resultados observados validam o sistema para a obtenção de formulações imunogénicas com aplicação no desenvolvimento de vacinas subunitárias experimentais e em estudos de modulação de resposta adaptativa.
ABSTRACT - A new cloning system based on the OprI lipoprotein for the production of bacterial cell wall-derived immunogenic formulations - The modulation of specific immunity through the conjugation of antigens with ligands of pattern recognition receptors (PRR) is emerging as a promising strategy for the development of subunit vaccines. Here, a new Escherichia coli cloning system for the expression of antigens in fusion with the OprI lipoprotein, a TLR ligand from the Pseudomonas aeruginosa outer membrane, is described. The system offers tight regulation of expression and allows for purification by metal affinity chromatography, circumventing the major drawbacks of former versions. Lipoprotein processing, translocation and triacylation were confirmed and protocols for the productions of other recombinant bacterial cell wall-derived formulations (outer membrane fragments and vesicles) with distinct potential for PRR activation were developed. As models, the sequences coding for the antigens A104R from African swine fever virus (ASFV), ovalbumin and EGFP were cloned. The adjuvant capacity of the three formulations was demonstrated evaluating the induction of humoral and CD8+ T cells responses in vivo and the cytokine and chemokine profile induced in dendritic cells stimulated in vitro. The results observed validate the system for the production of immunogenic formulations suitable for the development of experimental subunit vaccines and for studies on the modulation of adaptive immunity.
FCT-Fundação para a Ciência e Tecnologia. CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal da Faculdade de Medicina Veterinária-UTL.

Proteins are molecular machines of life in the truest sense. Being the expressors of genotype, proteins have been a focus in structural biology. Since the first characterization and structure determination of protein molecule more than half a century ago1, our understanding of protein structure is improving only incrementally. While computational analysis and experimental techniques have helped scientist view the structural features of proteins, our concepts about protein folding remain at the level of simple hydrophobic interactions packing side-chain at the core of the protein. Furthermore, because the rate of genome sequencing is far more rapid than protein structure characterization, much more needs to be achieved in the field of structural biology. As a step in this direction, my dissertation research uses computational analysis and experimental techniques to elucidate the fine structural features of the tertiary packing in proteins. With these set of studies, the knowledge of the field of structural biology extends to the fine details of higher order protein structure.

Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during fragment library generation. Using this information, we developed Flib and shown that it generates fragment libraries with higher precision and coverage than two other methods. We explored co-evolution to identify pairs of residues that are in contact, which were then used to improve model generation. We performed a comparative analysis of nine methods in terms of their precision and their usefulness to de novo structure prediction. Our results show that metaPSICOV stage 2 produces the most accurate predictions and that metaPSICOV stage 1 generates the best modelling results. In general, contact predictors are good at identifying contacts between β-strands and bad at identifying contacts between a-helices. We also show that the ratio of satisfied predicted contacts can be used to assess whether correct models were generated for a given target. We also investigated whether the biological process of cotranslational protein folding, the notion that proteins fold as they are being synthesized, can be used to improve de novo protein structure prediction. Our tool for this investigation is SAINT2. SAINT2 differs from conventional fragment-assembly approaches as it is able to perform predictions sequentially from N to C-terminus, starting with a small peptide that is extended as the simulation progresses (SAINT2 Cotranslational). SAINT2 is also able to generate decoys in a standard non-sequential fashion (SAINT2 In Vitro). We compared SAINT2 Cotranslational to SAINT2 In Vitro and shown that SAINT2 Cotranslational generally produces better answers, generating an individual decoy between 1.5 to 2.5 times faster than SAINT2 In Vitro. Our results suggest that biologically inspired structure prediction can improve search heuristics and final model quality.

Computational methods of analyzing, simulating, and modeling proteins are essential towards understanding protein structure and its interactions. Computational methods are easier as not all protein structures can be determined experimentally due to the inherent difficultly of working with some proteins. In order to predict, design, analyze, simulate or model a protein, data from experimentally determined proteins such as those located in the repository of the Protein Data Bank (PDB) are essential. The assumption here is that we can use pieces of known proteins to piece together a "new" protein hence, de novo protein design. The analysis of the geometric relationships between secondary structure elements in proteins can be extremely useful to protein prediction, analysis, and de novo design. This thesis project involves creating a database of protein secondary structure elements and geometric information for rapid protein assembly, de novo protein design, prediction and analysis.

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De novo protein structure prediction aims to find the 3D conformation of a protein from its amino acid sequence without the use of experimental templates. One of the most successful strategies consists in assembling models from a collection of small fragments of other proteins using a search algorithm. GAPF (Genetic Algorithms for Protein Folding) is a software for ab initio protein structure prediction developed by GMMSB/LNCC which uses a multiple minima genetic algorithms (GA) to search the energy landscape. The aim of this work is to incorporate a de novo methodology to GAPF to increase its predictiveness. The main strategy implemented is based on using fragment libraries. Fragments are selected based on sequence similarity and secondary structure prediction, and were used both to assemble the individuals of the initial population, and as mutation operators. We developed a strategy to insert fragments whose length was determined using the confidence of the secondary structure prediction. Additionaly, the structures with the highest hydrophobic compactness were favoured by a new form of parental selection. The test set comprises 20 proteins distributed among mainly-α, mainly-β and α/β classes, ranging from 20 to 146 aminoacids. The de novo method presented here was able to improve the prediction for 75% of the proteins of the test set, and the improvement was considered significative for 50% of the proteins of the test set. Besides the performance improvement (i.e., smaller number of evaluations of the energy function), a greater number of individuals with better hydrophobic compactness was generated. The results of this work point to important pathways to better de novo methods and aided setting the protocol that allowed GAPF to participate in the Critical Assessment of Protein Structure Prediction - CASP 11.
A predição de novo de estruturas de proteínas almeja encontrar a conformação tridimensional de uma proteína a partir de sua sequência de aminoácidos sem o uso de moldes/estruturas experimentais de referência. Uma das estratégias de maior sucesso consiste em construir modelos a partir de uma coleção de fragmentos de outras proteínas utilizando um algoritmo de otimização. O GAPF (Genetic Algorithms for Protein Folding) é um programa de predição ab initio, desenvolvido pelo GMMSB/LNCC, que utiliza um algoritmo genético (AG) de múltiplas soluções para a exploração da superfície de energia livre. O objetivo deste trabalho é o desenvolvimento de uma metodologia de novo para o programa GAPF objetivando o aumento da sua capacidade preditiva. A principal estratégia implementada baseia-se no uso de bibliotecas de fragmentos. Os fragmentos são escolhidos com base na similaridade de sequência e predição de estruturas secundárias e foram utilizados para compor os indivíduos da população inicial do AG e também através do uso de operadores de mutação específicos. Desenvolveu-se uma estratégia de inserção de fragmentos de tamanho variável, onde a determinação do tamanho utiliza informações obtidas da predição de estrutura secundária. Adicionalmente, foi incorporada uma estratégia de favorecimento da compactação hidrofóbica das estruturas preditas através do desenvolvimento de uma nova forma de seleção parental para a geração de novos indivíduos durante o AG. A metodologia foi testada em um conjunto de 20 proteínas, contendo de 20 a 146 resíduos de aminoácidos, pertencentes às classes principalmente-α, principalmente-β e α/β. Os resultados obtidos mostraram que a metodologia de novo desenvolvida foi capaz de melhorar a predição para 75% das proteínas do conjunto, sendo que foram verificadas melhorias consideradas significativas para 50% do conjunto. Além de uma melhora na performance computacional (i.e., menor número de avaliações da função energia), observou-se também a geração de indivíduos exibindo uma melhor compactação hidrofóbica. Os resultados deste trabalho apontam caminhos importantes para a melhoria da metodologia de novo no contexto do programa GAPF e viabilizaram a construção do protocolo utilizado pelo GMMSB em sua participação no evento Critical Assessment of Protein Structure Prediction - CASP 11.

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Soy protein concentrate (SPC) is used as an ingredient for food and animal feed. It is obtained from defatted soybean meal by extracting sugars and other soluble compounds. The main consequence of the extraction process is removal or inactivation of most anti-nutritional factors of soybean, which makes this product can be used in place of animal proteins in special diets. This work aimed to study the process of protein hydrolysis as an alternative to increase the value of the SPC through the improvement of their nutritional value. Hydrolysis process has been done many years ago with the purpose of improving physico-chemical, organoleptic and nutritional value of food proteins. Enzymatic hydrolysis is the most appropriate when the objective is to improve the nutritional value, because the chemical methods cause many unwanted effects. We studied two commercial alkaline proteases, Alcalase® and Novo-ProD®. Novo-ProD® showed superior activity than Alcalase® in all pH conditions tested. The process conditions that maximized efficiency of the hydrolysis of SPC by Novo-ProD® were: 55°C, pH 9 and enzyme/substrate ratio of 0.5% (enzyme mass / protein mass). The maximum degree of hydrolysis obtained in three hours reaction under these conditions was approximately 15.2% in bench scale and 12.8% in pilot scale. Increasing solid concentration of the reaction medium from 10 to 30%, maximum degree of hydrolysis of 11.2% was obtained in the same conditions. Digestibility trial was conducted with SPC hydrolyzate with 3,3% against SPC unhydrolyzed in adult dogs and turkeys in the initial growth phase. In dogs, hydrolysis increased apparent digestibility of dry matter from 76.5 to 86.2%, crude protein from 83.9 to 90.6% and metabolizable energy increased by approximately 5%. In turkeys, the increase was from 54.6 to 62.9% for dry matter digestibility and 9% increase in metabolizable energy.
O concentrado proteico de soja (SPC) é utilizado como ingrediente para alimentos e ração animal. É obtido a partir do farelo de soja desengordurado através da extração de açucares e outros compostos solúveis. A principal consequência do processo de extração é a remoção ou inativação de grande parte dos fatores antinutricionais da soja, o que faz com que este produto possa ser utilizado em substituição de proteínas de origem animal em dietas especiais. Este trabalho teve o objetivo de estudar o processo de hidrólise proteica como alternativa de aumentar a valor agregado do SPC através do melhoramento do seu valor nutricional. O processo de hidrólise tem sido feito há muitos anos com finalidade de melhorar propriedades físico-químicas, organolépticas e valor nutricional de proteínas alimentares. A hidrólise enzimática é a mais adequada quando o objetivo é melhorar o valor nutricional, pois os métodos químicos causam inúmeros efeitos indesejados. Foram estudadas duas proteases alcalinas comerciais: Alcalase® e Novo-Pro D®. A Novo-Pro D® apresentou atividades superiores às da Alcalase® em todas as condições de pH testadas. As condições de processo que maximizaram a eficiência da hidrólise do SPC pela Novo-Pro D® foram: 55°C, pH 9 e relação enzima/substrato de 0,5% (massa de enzima/massa de proteína). O grau de hidrólise máximo obtido, em três horas de reação nestas condições, foi de aproximadamente 15,2% em escala de bancada e 12,8% em escala piloto. Aumentando-se a concentração de sólidos do meio de reação de 10 para 30%, o grau de hidrólise máximo obtido foi de 11,2%, nas mesmas condições citadas. Avaliou-se a digestibilidade de nutrientes e metabolizabilidade da energia de um SPC hidrolisado com grau de hidrólise de 3,3% contra um SPC não hidrolisado em cães adultos e perus em fase inicial. Em cães, a hidrólise aumentou os coeficientes de digestibilidade aparente da matéria seca de 76,5 para 86,2%, da proteína bruta de 83,9 para 90,6% e a energia metabolizável aumentou em aproximadamente 5%. Em perus, o aumento foi de 54,6 para 62,9% para a digestibilidade da matéria seca e 9% de aumento da energia metabolizável.

Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.

Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.

Regrowth in the lesioned central nervous system is impeded by inhibitory molecules including myelin-associated inhibitors (MAIs) and chondroitin sulfate proteoglycans (CSPGs). Inhibitory molecules engage neuronal cell surface receptors and activate the small GTPase RhoA in injured neurons to mediate neurite outgrowth inhibition through targeted modifications to the cytoskeleton. Inhibition of RhoA with the ribosyltransferase C3 attenuates neurite outgrowth inhibition in vitro and in vivo but the ubiquitous expression and multifunctionality of RhoA may limit the specificity of therapeutic RhoA antagonists. The hypothesis of the thesis is that molecules that functionally interact with RhoA to mediate myelin-dependent inhibition may represent more specific targets for therapeutic intervention. We have explored the contribution of two RhoA interacting proteins to the neurite outgrowth inhibitory effects of MAIs. In Chapter 2 we describe the contribution of the rho effector, Rho kinase (ROCK) to MAI responses in neurons. In Chapter 3 we identify the cytosolic phosphoprotein CRMP4b (Collapsin Response Mediator Protein 4b) as a novel RhoA binding partner that mediates neuronal responses to CNS inhibitors. By structure function analysis we have developed a molecular antagonist of CRMP4b-RhoA binding that promotes neurite outgrowth on inhibitory substrates in vitro and has the potential to be a potent and specific molecular therapeutic for spinal cord injury. In Chapter 4 we identify glycogen sythase kinase 3b (GSK3b) as an important kinase in the MAI pathway that regulates protein interactions with RhoA. This thesis provides insights into the signal transduction machinery that is engaged in response to CNS inhibitors and suggests several novel therapeutic targets to promote axon regeneration following CNS injury.

Tato práce se zabývá vyhledáváním homologních enzymů v proteinových databázích, jejímž cílem je navrhnout nástroj poskytující takové vyhledávání. Čtenář se seznámí se základní teorií týkající se proteinů, enzymů, homologie, ale také s existujícími nástroji pro vyhledávání homologních proteinů a enzymů. Dále je popsáno ohodnocení nalezených existujících nástrojů pro vyhledávání homologních enzymů. Pro potřeby vyhodnocení byla vytvořena datová sada spolu s algoritmem pro vyhodnocení vyýsledků jednotlivých nástrojů. Další částí práce je návrh a implementace nové metody pro vyhledávání homologních enzymů společně s jejím vyhodnocením. Jsou popsány dva algoritmy (One-by-One a MSA) pro vyhledávání homologních enzymů, jejichž porovnání ukazuje, že MSA algoritmus je zanedbatelně lepší z hlediska přesnosti než One-by-One algoritmus zatímco z hlediska rychlosti vítězí One-by-One algoritmus.

The world's population is rapidly increasing and so is the demand for energy. Problems with increased CO2 production and global warming makes the need for clean and cheap energy one of the most important challenges facing the future human society. Solar energy is the most abundant energy source accessible to humankind and this energy could be captured and stored as chemical bonds with a device mimicking the process of light driven photosynthesis in plants. This work explains how an artificial protein could perform charge separation and first trials for synthesis of two different co factors, Azido Viologen and Tetra methyl azido viologen has been carried out. It also suggests a way of attaching the co factors to the protein by incorporating the unnatural amino acid Homopropargylglycine in the protein an use Huisgen cycloaddition for the attachment. Azido Viologen seems to have been successfully synthesized but needs to be further characterized by mass spectrometry and NMR bu the Tetra Methyl Azido Viologen was not. The Homopropargylglycine was not successfully incorporated in the protein but the likely reason for this seems to be the usage of the wrong expression system.

Rheumatoid arthritis (RA) is a chronic inflammatory, autoimmune disease, characterized by peripheral and symmetrical polyarthritis that leads to joint destruction and deformity due to erosion of cartilage and bone. This is a common disease that affects approximately 1% of the world population and is more common in women than men, however, its peak incidence occurs between the fourth and sixth decades of life. Large amounts of reactive oxygen species (ROS) have been identified in the synovial fluid of RA patients, and such large amounts may lead to oxidative damage of hyaluronic acid, lipid, cartilage matrix and DNA. The accumulation of ROS in the cells, also serves as major intracellular signaling molecules that amplify the inflammatory response synovium proliferative. The objective of this study was to evaluate the levels of ischemia-modified albumin (IMA) and also other markers of oxidative stress and inflammation in 16 patients with RA and 20 healthy controls. IMA levels were significantly higher in RA patients than healthy controls (0.495 ± 0.01 vs 0.433 ± 0.02 ABSU, P=0.038). No significant differences were observed for the other markers studied. Thus it was concluded that besides RA being related to inflammation, elevated levels of IMA in RA patients suggest that this pathology promotes increased oxidative stress.
A artrite reumatoide (AR) é uma doença inflamatória crônica, de caráter autoimune, caracterizada por poliartrite periférica e simétrica, que leva à deformidade e destruição das articulações devido à erosão da cartilagem e do osso. Esta é uma doença comum que afeta aproximadamente 1% da população mundial, sendo mais frequente em mulheres do que nos homens, no entanto, seu pico de incidência ocorre entre a quarta e sexta décadas de vida. Grandes quantidades de espécies reativas de oxigênio (EROs) foram identificadas no fluido sinovial de pacientes com AR, e essa grande quantidade pode levar a dano oxidativo ao ácido hialurônico, lipídios, matriz da cartilagem e ao DNA. O acumulo de EROs nas células, também serve como importantes moléculas sinalizadoras intracelulares que amplificam a resposta inflamatória - proliferativa sinovial. Assim, o objetivo deste estudo foi avaliar os níveis de albumina modificada pela isquemia (IMA) e outros marcadores de estresse oxidativo e inflamação em 16 pacientes com AR e 20 controles saudáveis. Os níveis de IMA foram significativamente maiores no grupo de pacientes com AR do que os controles saudáveis (0.495 ± 0.01 vs 0.433 ± 0.02 ABSU, P=0.038). Não foram observadas diferenças significativas para os outros marcadores estudados. Desta forma, foi possível concluir que além da AR estar relacionada com a inflamação, os níveis elevados de IMA em pacientes com AR, sugerem que esta patologia promova o aumento do estresse oxidativo.

The application of magnetic resonance imaging (MRI) to non-invasively assess disease biomarkers has been hampered by lack of desired contrast agents with high relaxivity, targeting capability, and optimized pharmacokinetics. We developed a novel MRI probe which targets HER2, a biomarker for various cancers and a target for anti-cancer therapies. This multimodal HER2-targeted MRI probe integrates a rationally designed protein contrast agent with a high affinity HER2 affibody and near IR dye. Our probe can differentially monitor tumors with different HER2 levels in both cells and xenograft mice. In addition to its 10-fold higher dose efficiency compared to clinically-approved agent DTPA, our developed agent also exhibits advantages in crossing the endothelial boundary, tissue distribution, and tumor tissue retention as demonstrated by even distribution of the imaging probe across the entire tumor mass. Additionally, a second series of protein contrast agents that included affibody against EFGR developed with the capability to specifically target EGFR. These contrast agents have been utilized to monitor drug treatments and quantitatively analyze biomarker expression level. Furthermore, we anticipate these agents will provide powerful tools for quantitative assessment of molecular markers, and improved resolution for diagnosis, prognosis and drug discovery.

Thesis (Ph. D.)--Indiana University, Dept. of Chemistry, 2006.
Source: Dissertation Abstracts International, Volume: 67-01, Section: B, page: 0249. Adviser: C. Cheng Kao. "Title from dissertation home page (viewed Feb. 9, 2007)."

Acquired cellular resistance to traditional chemotherapeutics is a common obstacle in the treatment of most cancer cell types. This resistance occurs as a result of changes in the underlying molecular mechanisms of disease progression. The development of novel chemotherapeutic approaches designed to enhance the efficacy of protypical anti-cancer drugs is important in order to overcome this issue. Such approaches will aid in understanding the biomolecular phenomena responsible for drug resistance and disease progression. Combining signaling pathway inhibitors has become an effective strategy for enhancing tumor cell death by targeting multiple pathways known to regulate cell survival. Pemetrexed, an FDA-approved anti-folate drug, targets thymidylate synthase (TS) and a secondary folate-dependent enzyme, 5’ aminoimidazole-carboximide ribonucleotide formyltransferase (AICART); both important for DNA synthesis. Studies performed by our collaborator demonstrated that TS inhibition causes intracellular accumulation of ZMP+ and activation of AMPK which is known to induce autophagy in mammalian cells. Previous studies from our lab and others showed that sorafenib, a multi-kinase inhibitor of Raf-1 and class III receptor tyrosine kinases, was able to induce a cytotoxic form of autophagy in a variety of tumor cell types. Combination treatment using pemetrexed and sorafenib in these cancer cells resulted in an enhancement of autophagy and cell lethality beyond that of individual drugs alone. Inhibition of autophagy suppressed the toxic interactions of these drugs in all cell types examined. Pemetrexed/sorafenib cotherapy also proved to be an effective treatment for triple negative breast cancer cells having advanced to a stage of estrogen independence. Fulvestrant-resistant MCF7 cells were more sensitive to the drug combination than parental, estrogen-dependent MCF7 cells. Breast cancer cells cotreated with pemetrexed and sorafenib exhibited enhanced MEK/ERK signaling, Src activation that was dependent on platelet-derived growth factor β (PDGFRβ) downregulation, elevated protein phosphatase 2A (PP2A) activity, and increased de novo ceramide synthesis. Studies using a mouse model of experimentally-induced breast cancer validated drug combination effectiveness through inhibition of tumor growth, while no deleterious effects on normal tissues were observed. The data presented demonstrates that pemetrexed/sorafenib cotreatment augments chemosensitivity in both in vitro and in vivo systems. Based upon these findings, a Phase I clinical trial involving pemetrexed and sorafenib in breast cancer patients with solid, recurrent tumors was begun in 2011. In conclusion, this work strongly supports a promising therapeutic utility for the pemetrexed/sorafenib combination in treatment of various cancer cell types.

Hoy en día, el cáncer sigue siendo la segunda causa de muerte en el mundo. Por lo tanto, existe una gran necesidad de encontrar nuevas terapias que resulten más efectivas para su tratamiento. Las terapias actuales, lejos de ser efectivas, producen una gran toxicidad sistémica y ofrecen un bajo porcentaje de supervivencia a los pacientes, siendo la principal causa de muerte la aparición de focos metastáticos, especialmente en el cáncer de colon. Por lo tanto, mejorar la especificidad celular y evitar la aparición de focos metastaticos son los mayores retos a los que se enfrentan las futuras terapias contra el cáncer. En este contexto, la terapia génica aparece como una alternativa muy prometedora ya que ofrece la posibilidad de personalizar las terapias además de disminuir su toxicidad. Dado que la bioseguridad es uno de los parámetros que más preocupa en este tipo de terapias, las proteínas multifuncionales aparecen como uno de los vectores de terapia génica más prometedores no solo por su alta biocompatibilidad y su baja toxicidad, sino también por su gran plasticidad. Por otro lado, la necesidad de controlar el tamaño de las partículas generadas para conseguir una adecuada biodistribucion in vivo ha sido ampliamente descrita en la literatura. En este trabajo, hemos explorado la posibilidad de modular el autoensamblaje de proteínas multifuncionales en nanoparticulas de un tamaño predefinido con tal de obtener el máximo potencial de su capacidad de entrega de ácidos nucleicos o drogas terapéuticas. En este contexto, hemos descrito parejas de tags arquitectónicos (de los cuales uno de ellos es una poli-histidina) que son capaces de inducir el autoensamblaje de las proteínas que las contienen en nanoparticulas con propiedades estructurales predefinidas. También hemos estudiado la interacción y el traffiking intracelular de estas nanoparticulas cuando las ponemos en contacto con células en cultivo, donde hemos visto que su internalización no resulta toxico para las células de mamíferos. Además, también hemos estudiado la estabilidad estructural que presentan estas nanoparticulas cuando se administra por vía intravenosa en modelos de ratón, mostrando que las interacciones intermoleculares que se generan durante el proceso de ensamblaje de las nanoparticulas in vitro, son suficientemente fuertes como para asegurar su estabilidad estructural in vivo. Se ha descrito que el receptor CXCR4 es un elemento clave en la formación de focos metastaticos durante el desarrollo tumoral de diferentes tipos de cáncer incluyendo el cáncer de colon, para el cual actualmente no existe todavía ningún vehículo que reconozca de forma específica las células metastaticas. En este contexto, en este estudio hemos explorado la posibilidad de funcionalizar las nanoparticulas proteicas con ligandos que reconocen el receptor CXCR4 con tal de dirigirlas de forma específica a las células que expresan este receptor. Entre los ligandos testados, hemos visto que el péptido T22 es un ligando inusualmente eficiente para el reconocimiento selectivo e internalización en células que expresan el receptor CXCR4 y que las nanoparticulas funcionalizadas con este ligando se biodistribuyen de forma selectiva a las células CXCR4+ in vivo en modelos murinos de cáncer colorectal. Finalmente, también hemos explorado la posibilidad de usar nanoparticulas proteicas funcionalizadas como virus artificiales para la entrega especifica de ácidos nucleicos en las células diana. Este trabajo muestra como las nanoparticulas que contienen dominios de unión a ácidos nucleicos, cuando son incubados junto a un DNA externo, son capaces de generar estructuras que imitan las estructuras virales, encapsulando el DNA en la parte interna de las estructura y protegiéndolo a su vez del ataque de nucleasas externas. Sin embargo, es necesario añadir un paso de hidrolisis con DNasa y RNasas en la purificación de nanoparticulas que contienen dominios de unión a ácidos nucleicos ya que se ha visto que unen ácidos nucleicos bacterianos provenientes del sistema de expresión bacteriano utilizado para su producción recombinante, afectando muy negativamente sobre su funcionalidad como virus artificiales. Por lo tanto, dado la gran biocompatibilidad que a priori se espera de las proteínas, sus propiedades arquitectónicas regulables y la posibilidad de funcionalizarlos con ligandos específicos, hace que las nanoparticulas proteicas autoensamblables sean una herramienta muy prometedora para la entrega dirigida de ácidos nucleicos y drogas terapéuticas en las células de cáncer metastatico de colon y en general en las células de mamífero.
Cancer is ranked as the second leading cause of death worldwide. Consequently there is a huge necessity of finding more effective cancer therapies. Currently available cancer therapies, far from being effective, present high systemic toxicity and low patient survival rates being the main mortality cause the appearance of metastatic foci, especially in colon cancer. Thus, improving cell specificity and avoiding metastases generation are the mayor challenges for future cancer therapies. In this context, gene therapy appears as very promising alternative therapy since cell targeted personalized therapies can be performed with low systemic toxicity. Since biosafety is the current mayor concern in this type of therapies, multifunctional proteins appear as the most promising gene therapy vectors because of their high biocompatibility and biosafety, low toxicity and really complete tuneability. Moreover, the necessity of effectively controlling nanoparticles size for their efficient biodistribution and delivery has been widely described in the literature. In the present work has been explored the possibility of effectively modulating the self-assembling of multifunctional protein building blocks into predefined size distribution nanoparticles in order to get the full potential of those protein-only nanoparticles for their application in therapeutic drugs and nucleic acids delivery approaches. In this regard, we have described cationic architectonic tag pairs ( one of them being a poly-histidine) that when incorporating to proteins, they induce the self-assembling of protein monomers into nanoparticles with predefined structural properties. It has also been studied the interaction and intracellular trafficking of these kind of protein nanoparticles in cultured cells proving not to be toxic for mammalian cells. Moreover, the structural stability of generated nanoparticles upon intravenous administration in mice has been also studied proving in vitro generated intermolecular interactions during protein assembling process strong enough to ensure nanoparticles structural stability in vivo. It has been shown that CXCR4 chemoquine receptor is a key element in metastasis formation during cancer evolution in different types of tumors, including colorectal cancer, for which metastatic intracellular targeting vehicles are currently missing. In this context, the possibility of effectively functionalizing protein nanoparticles with CXCR4 specific ligands has been deeply explored in this study. Among tested peptide ligands, T22 peptide has shown to be an unusually powerful tag for selective intracellular targeting in CXCR4+ cells having T22-empowered protein nanoparticles of optimal size selectively biodistribute in CXCR4+ cells in vivo. Finally, the suitability of functionalized self-assembling protein nanoparticles for their use as artificial viruses has been also extensively explored. Protein nanoparticles that contain nucleic acid binding domains have shown an appealing capacity to generate virus-like structures when combined with external DNA, completely shielding cargo DNA in the inner part of the structure and protecting it from external nucleases hydrolysis. However, the necessity of an additional DNase/RNase hydrolysis treatment during the nanoparticles purification process has been described since nanoparticles with nucleic acid binding domains have been shown to bind nucleic acids from the bacterial host used for their recombinant expression, resulting strongly detrimental for their functionality as artificial viruses. All together, the high biocompatibility expected for proteins, their regulatable architectonic properties and their efficient targeting possibility, make self-assembling protein-only nanoparticles a very promising material for the therapeutic delivery of drugs and nucleic acids in metastatic colorectal cancer cells and in general in mammalian cells.

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O receptor LRR-RLK (Leucine-rich repeat receptor-like kinase), designado NIK1 (NSP-interacting kinases), está envolvido na resposta imunológica em plantas contra Germinivirus. NIK1 foi inicialmente descrito por interagir com a proteína viral NSP (nuclear shuttle protein), proteína que participa do transporte de DNA viral do núcleo para o citoplasma de células infectadas. Com alta similaridade estrutural a NIK1, BAK1 (Brassinosteroid Insensitive Associated Kinase1), também conhecida como SERK3 (Somatic Embryogenesis Receptor Kinase3), é um receptor LRR-RLK de membrana que desempenha um duplo papel em vias de sinalização, podendo atuar como um coreceptor de BRI1 na presença de BR ou mediar respostas de defesa contra patógenos. Na via de crescimento desencadeada por brassinosteróides (BRs), BAK1 interage com BRI1 (Brassinosteroid-insensitive1) na membrana plasmática e ativa a função de cinase desta proteína. Recentemente, através de dados de RNA-seq, foi demonstrado que inativação da função de NIK1 no nocaute nik1 (Salk_060808) induz a expressão de genes envolvidos na resposta a BRs e desenvolvimento, indicando uma possível comunicação cruzada entre a via de sinalização antiviral mediada por NIK1 e vias de sinalização de desenvolvimento. Sendo assim, este trabalho teve como objetivo avaliar o papel de NIK1 na via de resposta a BRs. Arabidopissis thaliana, linhagem nik1 nocaute, foi transformada com as construções de DNA 35S:BAK-NIK1_GFP e 35S:NIK1-BAK1_GFP, sendo que a expressão dos transgenes e localização subcelular na membrana das proteínas quiméricas foram confirmadas por RT-PCR e microscopia confocal, respectivamente. Análises fenotípicas de plantas expressando as construções quiméricas BAK1-NIK1 e NIK1-BAK1 indicaram deficiência na via de desenvolvimento induzido por BR, uma vez que o fenótipo destas plantas transgênicas se assemelharam muito ao mutante bak1-4, deficiente na sinalização por BR. Além disso, a ativação da via de sinalização por BRs foi avaliada por meio de crescimento de hipocótilo e de análise da expressão de genes marcadores induzidos por brassinolídeo (BL). Em nik1, o tratamento com BL estimulou o crescimento do hipocótilo e induziu genes marcadores associados à sinalização por BR, embora em menor intensidade do que em Col-0, indicando funcionamento da via de desenvolvimento induzida por BR nesta linhagem nocaute. Expressão de ambas as proteínas quiméricas em nik1 mutante, que expressa os genes BAK1 e BRI1 normalmente, restaurou o fenótipo insensível a BL, típico do nocaute bak1-4. Claramente, a expressão dos genes quiméricos interferiu negativamente com a via de sinalização de BR, uma vez que nas linhagens transgênicas, BL não estimulou o alongamento do hipocótilo e tampouco a indução da expressão de genes marcadores associados à via de sinalização de BR. Estes resultados indicam que as proteínas quiméricas atuam como alelos mutantes transdominantes negativos na sinalização por BR. Esta hipótese foi fundamentada pela capacidade de NIK1 de interagir com BAK1, conforme previamente demonstrado, e com o domínio cinase de BRI1, demonstrado nesta investigação por meio de duplo híbrido em leveduras. Embora não se tenha observado uma ativação aumentada da resposta a BR no nocaute nik1, provavelmente devido a redundância funcional da subfamília NIK, os fenótipos resultantes da expressão das proteínas quiméricas, contendo ou o domínio LRR ou o domínio de cinase de NIK1, sugerem que NIK1 atue como um regulador negativo da sinalização por BR.
The LRR-RLK (Leucine-rich repeat receptor-like kinase) NIK1 (NSP-interacting kinase), is known to mediate immune response in plants against Germinivirus. NIK1 was initially described by interacting with the viral protein NSP (Nuclear shuttle protein), a protein that participates in viral DNA transport from the nucleus to the cytoplasm of infected cells. With high structural similarity with NIK1, BAK1 (Brassinosteroid Insensitive-Associated Kinase1), also known as SERK3 (Somatic embryogenesis receptor Kinase3), is a membrane LRR-RLK, which plays a dual role in signaling pathways and may act as a co-receptor of BRI1 in the presence of brassinosteroide (BR) or mediate defense responses against pathogens. In the BR- triggered growth pathway, BAK1 interacts with BRI1 (Brassinosteroid-Insensitive1) in the plasma membrane and activates the kinase function of this protein. Recently, RNA- seq data revealed that inactivation of NIK1 function in the nik1 mutant (Salk_060808), caused an up-regulation of genes involved in response to BRs and development, indicating a possible cross-talk between the NIK1-mediated antiviral signaling pathway and development signaling pathways. The goal of this investigation was to evaluate the role of NIK1 in the BR response pathway. Arabidopissis thaliana, nik1 line, was transformed with the DNA constructs 35S:BAK-NIK1_GFP and 35sNIK1-BAK1_GFP, and the expression of the transgenes and subcellular localization of the chimeric proteins were confirmed by RT-PCR and confocal microscopy, respectively. BAK1- NIK1- and NIK1-BAK1-expressing plants displayed a deficiency in the BR-induced growth pathway, as the phenotypes of these transgenic lines resemble the ones of the BR signaling deficient bak1-4 mutant. Furthermore, the activation of BR signaling was evaluated through brassinolide (BL)-induced hypocotyl growth and gene expression of BR signaling-associated marker genes. BL-induced stimulation of hypocotyl elongation and induction of marker genes were observed in nik1, although to a lesser extent than in Col-0, indicating a functional BR singling in this knockout line. Expression of both chimeric proteins in the nik1 mutant, which harbors BAK1 and BRI1 normal genes, mimicked the BL insensitive phenotype, typical of the bak1-4 knockout. Clearly, the expression of the chimeric genes impacted negatively the BR signaling, as in the transgenic lines, the BL treatment did not stimulated hypocotyl growth or the induction of BR signaling marker genes. These results indicate that the chimeric proteins function as transdominant negative mutant alleles in BR signaling. This hypothesis was substantiated by the capacity of NIK1 to interact with BAK1, as previously demonstrated, and with the BRI1 kinase domain, as demonstrated in the present investigation through a two-hybrid assay in yeast. Although nik1 did not display an enhancement of the BR-induced responses, most likely due to the functional redundancy of the NIK subfamily, the resulting phenotypes of the chimeric genes expression, harboring either the NIK1 LRR or kinase domain, implicate NIK1 as a negative regulator of BR signaling.

An in silico design algorithm has been developed to design binding ligands for protein targets of known three-dimensional structure. In this method, the binding energy of a candidate ligand is used to ascribe it a probability of binding. A sample of a virtual library of candidate ligands is then used to ascribe implicit weights to all the ligands in the library. These weights are used to obtain virtual sub-libraries which collectively carry a greater probability to bind to the target. This algorithm is presented along with validation studies on the different algorithmic components, demonstrating how optimization of the design method can be best achieved.

RODRIGUES, Marco Antônio de Magalhães. Expressão de proteínas do plasma seminal em carneiros das raças santa ines e morada nova: associações com parâmetros seminais , influência de fontes de proteínas e de nitrogênio não proteico nas dietas. 2011. 175 f. : Dissertação (mestrado) - Universidade Federal do Ceará, Programa de Pós-Graduação em Biotecnologia, Renorbio- Rede Nordeste de Biotecnologia, Fortaleza-CE, 2011.
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The Brazilian Northeast has about almost half of Brazilian sheep livestock, estimated at twenty million animals. The races created here, Santa Ines and Morada Nova stand out because they have good physical development, weight gain and good adaptation to the tropical climate. Recently showed the protein profile of mature rams through the techniques of two-dimensional electrophoresis associated with mass spectrometry, which several proteins have been identified, including those RSVPs 14 and 22 kDa, belonging to the family of BSPs and bodesinas - 1 and 2, that are part of the family of espermadesinas as well as the changes suffered by the protein profile of seminal plasma of animals during reproductive development, while changes in the parameters of sperm concentration and motility, although the association between the protein expression of these proteins with reproductive parameters testicular and measures have not yet been made in northeastern Brazil. Semen samples were collected from twenty-one adult sheep Santa Ines and eleven Morada Nova with normal reproductive and mean age of two years and seminal plasma was obtained by centrifugation and subjected to two-dimensional electrophoresis, and the spots that differed significantly between the groups of animals from high (G1) and low motility (G2) were digested with trypsin and subjected to mass spectrometry and research database for identification. The gels were stained with colloidal Cromassie, scanned and analyzed with PDQuest application and quantity of the spots quantitatively estimated. Evaluated, then, statistical associations between these variables and the reproductive parameters scrotal circumference (EC), percentage of motile cells (PEM) and total sperm defects (MDD) of the animals Santa Inês and scrotal circumference (EC) motility individual rogressive (MIP), percentage of motile cells (PEM), Sperm concentration (CONC) and Massal motility (MM) for the animails Morada Nova. Were detected on average 236 ± 7.65 spots per gel, according to the pairing generated by PDQuest application to the Santa Ines and 261 ± 15.09 spots per gel in the seminal plasma of animals Morada Nova, ranging between 182 and 375 spots gel. For Santa Inês a total of 63 spots were identified consistently in all gels, which represented 41.5% of all spots detected intensity. For Morada Nova animails, a total of 98 spots were detected consistently in all gels. The intensity of these spots amounted to 60.82% of the intensity of all spots shown on the master gel was observed a great expression of proteins of low molecular weight (14.5 to 18.4 kDa) and pI ranging from 4.2 to 5, 9. to Santa Ines. The average total of 236 spots found thirteen spots showed significant difference (p <0.05) between animals of high and low motility, being more intense ten spots in animals with high motility and three in animals with low motility. After digestion of spots and identification by mass spectrometry these spots were identified as proteins Arylsulfatase A and zinc alpha 2 glycoprotein more intense in G1and RSVP-22 and Bodesina with higher expression in G2. For the Morada Nova race, four spots showed significant difference (p <0.05) for the parameter percentage of motile cells (PEM). After digestion of spots and identification by MALDI-TOF-TOF, we identified as proteins, RSVP-14, RSVP-22, a protein α-1 of t-complex and aldose reductase, which are all more intense in animals with high motility (G1). In a second study, evaluated the influence of different sources of dietary protein (soybean meal, leucaena leaf hay and cottonseed meal) and non-protein nitrogen (urea) on body weight, testicular development and sperm quality of the animals studied and protein expression in the seminal plasma of the animals potentially related to the diets. We used 20 Morada Nova lambs aged between 24 and 39 weeks. For the testicular development criteria (cirrcunferência scrotal, testicular thickness, width and length testicular testicular) no significant difference (p <0.05) was observed at the end of experiment. Animals fed cottonseed meal had a significant increase in body weight (p <0.05) compared with Leucaena hay. In the same period, the body weight of animals fed leucaena hay, soybeans and urea was similar. Differences between treatments (p <0.05) were observed only for individual progressive motility and total defects. The semen of animals fed diets containing leucaena showed low motility individual when compared with those fed diets containing soybean meal. However, animals fed diets containing cottonseed meal and urea had similar values for progressive motility. When the total defects were analyzed, there was a significant difference between groups of leucaena hay and urea. Detected an amount of 246.6 ± 13.9, 236.0 ± 12.4, 261.2 ± 20.2 and 243.8 ± 20.5 spots per gel in groups of soybean meal, leucaena leaf hay, cottonseed meal and urea, respectively. No significant differences in the number of spots per gel, in both groups. Significant differences (p <0.05) were observed in the intensities of twelve spots in the proteic maps . An increased expression of spot S8707 (62.8 kDa, pI 6.9) in animals fed with hay and leaves of leucaena compared to those fed soybean meal, and a negative correlation with individual motility (MPI .) These observations indicate that factors present in hay sheets leucaena promote an increase in protein expression (S8707), the likely cause deleterious changes in the mechanism controlling the motility of sperm cells, as observed in this group lowest for MPI.
O Nordeste brasileiro possui aproximadamente quase metade do rebanho ovino brasileiro, estimado em vinte milhões de animais. Das raças aqui criadas, destacam-se as raças Santa Inês e Morada Nova que têm bom desenvolvimento corporal, ganho de peso e boa adaptação ao clima tropical. Recentemente mostrou-se o perfil protéico de carneiros maduros através das técnicas de eletroforese bidimensional associada à espectrometria de massa, onde várias proteínas foram identificadas, entre elas as RSVPs 14 e 22 kDa, pertencentes à família das BSPs e as bodesinas – 1 e 2, que fazem parte da família das espermadesinas, bem como as alterações que sofre o perfil protéico do plasma seminal dos animais durante o desenvolvimento reprodutivo, simultaneamente a mudanças nos parâmetros de motilidade e concentração espermática, embora a associação entre a expressão protéica dessas proteínas com parâmetros reprodutivos e medidas testiculares ainda não tenham sido feitas no nordeste do Brasil. Amostras de sêmen foram coletadas de 21 carneiros adultos Santa Inês e 11 da raça Morada Nova com normalidade reprodutiva e idade média de dois anos. O plasma seminal foi obtido através da centrifugação e submetido à eletroforese bidimensional, sendo os spots que diferiram estatisticamente entre os grupos de animais de alta (G1) e baixa motilidade (G2) foram digeridos com tripsina e submetidos a espectometria de massa e pesquisa em banco de dados para identificação. Os géis foram corados com Cromassie coloidal, digitalizados e analisados no aplicativo PDQuest e as quantidades dos spots estimados quantitativamente. Avaliaram-se, então, associações estatísticas entre estas variáveis e os parâmetros reprodutivos como, circunferência escrotal (CE), percentual de células móveis (PEM) e total de defeitos espermáticos maiores (TDM) dos animais Santa Inês e Circunferência escrotal (CE), Motilidade Individual Progressiva (MIP), Percentual de células móveis (PEM), Concentração espermática (CONC) e Motilidade Massal (MM) para os animais Morada Nova. Em média foram detectados 236±7,65 spots por gel, de acordo com o pareamento gerado pelo aplicativo PDQuest para a raça Santa Inês e 261± 15,09 spots por gel do plasma seminal dos animais Morada Nova, variando entre 182 e 375 spots por gel. Para a raça Santa Inês um total de 63 spots foi identificado consistentemente em todos os géis, o que representou 41,5% da intensidade todos os spots detectados. Para os animais Morada Nova, um total de 98 spots foram detectados de forma consistente em todos os géis. A intensidade desses spots somou 60,82% da intensidade de todos os spots mostrados no gel master. Foi observado a grande expressão de proteínas de baixo peso molecular (14,5 a 18,4 kDa) e pI variando de 4,2 a 5,9.para a raça Santa Inês. Do total médio de 236 spots encontrados, treze spots apresentaram diferença significativa (p<0,05) entre animais de alta e baixa motilidade, sendo dez spots mais intensos em animais de alta motilidade e três em animais de baixa motilidade. Após digestão dos spots e identificação por espectometria de massa esses spots foram identificados como as proteínas Arilsulfatase A e Zinco alfa 2 glicoproteína, mais intensas no G1 e RSVP-22 e Bodesina-2 com maior expressão no grupo G2. Para a raça Morada Nova , quatro spots apresentaram diferença significativa (p<0,05) para o parâmetro percentual de células móveis (PEM). Após digestão dos spots e identificação por MALDI-Tof-Tof, foram identificadas as proteínas RSVP-14, RSVP-22, Proteína α-1 do complexo-t e aldose redutase, sendo todas mais intensas em animais de alta motilidade (G1). Em um segundo estudo, foi avaliada a influência de diferentes fontes de proteína da dieta (farelo de soja, feno de folha de leucena e torta de algodão) e de nitrogênio não- protéico (uréia) sobre o peso corporal, desenvolvimento testicular e qualidade espermática dos animais estudados, bem como a expressão de proteínas no plasma seminal dos animais potencialmente relacionadas às dietas. Foram utilizados 20 cordeiros da raça Morada Nova com idade variando entre 24 e 39 semanas. Para os critérios de desenvolvimento testicular (cirrcunferência escrotal, espessura testicular, largura testicular e comprimento testicular) não houve diferença significativa (p<0,05). ao final do período experimental Animais alimentados com torta de algodão tiveram um aumento significativo do peso corporal (p<0,05), quando comparado com feno de leucena. No mesmo período, o peso corporal dos animais alimentados com feno de leucena, soja e uréia foi semelhante. Diferenças entre os tratamentos (p <0,05) foram observadas apenas para motilidade progressiva individual e defeitos totais. O sêmen dos animais alimentados com dietas contendo feno de leucena apresentou baixa motilidade progressiva individual quando comparados aqueles alimentados com dietas contendo farelo de soja. No entanto, animais alimentados com dietas contendo torta de algodão e uréia tinham valores semelhantes para a motilidade progressiva. Quando os defeitos totais foram analisados, houve uma diferença significativa entre os grupos de feno de leucena e uréia. Foi detectado uma quantidade de 246,6 ± 13,9, 236,0 ± 12,4, 261,2 ± 20,2 e 243,8 ± 20,5 spots por gel nos grupos de farelo de soja, feno de folhas de leucena, torta de algodão e uréia, respectivamente. Não houve diferenças significativas no número de spots por gel, entre os grupos. Diferenças significativas (p <0,05) foram observadas nas intensidades de doze spots dos mapas protéicos. Foi observado um aumento da expressão do spot S8707 (62,8 kDa, pI 6,9 ) em animais alimentados com feno de folhas de leucena, quando comparados àqueles alimentados com farelo de soja, bem como correlação negativa com a motilidade progressiva individual (MPI). Estas observações indicam que fatores presentes no feno de folhas de leucena promovem um aumento na expressão da proteína (S8707), o que provavelmente provoca alterações deletérias no mecanismo que controla a motilidade progressiva da célula espermática, já que neste grupo observou-se valores mais baixos para MPI.

Orientadores: Jorg Kobarg, Jose Andres Yunes
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Staniocalcinas (STCs) representam uma pequena família de hormônios glicoprotéicos, encontrados em todos os vertebrados e composta por STC1 e STC2, que foram inicialmente implicados na homeostase de cálcio e recentemente também foram implicados em vários outros processos. Stanniocalcina-1 (STC1), o primeiro membro encontrado, foi originalmente descoberto em peixes ósseos e posteriormente identificado em humanos onde parece ter um papel, embora ainda obscuro, na carcinogênese e angiogênese. Nos seres humanos STC1 pode ser encontrado em duas formas: um dímero ou um grupo de variantes de alto peso molecular coletivamente chamados bigSTC. Uma vez que ambas as células leucêmicas e os tumores sólidos dependem vascularização, a angiogênese é um passo fundamental na interação tumorhospedeiro e essencial para a progressão do câncer. Análises prévias de microarray resultaram na identificação de vários genes ativados em células endoteliais da medula óssea (BMEC) modulados pela presença de células leucêmicas. Apresentamos aqui STC1 como um marcador microambiente de medula óssea (BMM) durante leucemia linfoblástica aguda (LLA) pela validação dos dados prévios de microarray através de PCR em tempo real quantitativos. Em vista da falta de informações funcionais e estruturais sobre STC1 realizamos: (1) um screen no sistema de duplo híbrido em levedura, a fim de encontrar algumas das proteínas que interagem com a STC1 humana, e (2) uma caracterização estrutural inicial à baixa resolução desta proteína. Fomos capazes de construir um mapa interação proteína-proteína, obtido a partir dos 22 interactantes encontrados em screen de duplo híbrido em levedura. As proteínas encontradas apresentam-se em vários compartimentos celulares nos quais STC1 já foi demonstrada para estar presente, e essas novas informações podem ajudar a esclarecer como e qual o papel STC1 desempenha nesses locais. A fim de fornecer informação estrutural sobre STC1, realizamos análises bioquímicas e estruturais da proteína recombinante STC1 com 6xHis tag produzida em células de inseto utilizando o sistema baculovírus. A análise de dicroísmo circular confirmou a predição in silico do elevado conteúdo de alfa-helices. A análise por espectrometria de massas forneceu os dados experimentais que confirmaram o padrão conservado de pontes dissulfeto anteriormente descrito para STC1 de peixes. Finalmente, os dados de espalhamento de raios-X a baixo ângulo demonstraram que, STC1 adota uma estrutura dimérica, ligeiramente alongada em solução fornecendo deste modo os primeiros dados estruturais à baixa resolução desta família de proteínas. Além disso, foi possível obter proteína suficiente e de elevado grau de pureza para realizar ensaios cristalização que resultaram em cristais os quais difrataram a boa resolução.
Abstract: Staniocalcins (STCs) represent a small family of glycoprotein hormones found in all vertebrates composed by STC1 and STC2, which have been initially implicated in calcium homeostasis and also recently implicated in several other processes. Stanniocalcin-1 (STC1), the first member found, was originally discovered in bony fishes and later identified in humans were it seems to have a role, although still unclear, in carcinogenesis and angiogenesis. In humans STC1 can be found in two forms: a dimer or a group of higher molecular weigh variants collectively called bigSTC. Since both leukemic cells and solid tumors depend on vascularization, angiogenesis is a fundamental step in tumor-host interaction and essential to the cancer progression. Previous microarray analysis resulted in the identification of several activated genes in bone marrow (BM) endothelial cells (BMEC) modulated by presence of leukemic cells. Here we present STC1 as a BM microenvironment marker during acute lymphoblastic leukemia (ALL) by validating previous microarray data by quantitative RealTime-PCR. In view of the lack of functional and structural information on STC1 we performed (1) a yeast two hybrid screen in order to find some of the human STC1 interacting proteins and (2) a initial structural lowresolution characterization of this protein. We were able to construct a protein-protein interaction map, derived from the 22 interactants found in our yeast two-hybrid screen. The proteins found are located in several cellular compartments in which STC1 has already been shown to be present, and the new information might help to clarify how and which role it performs at these sites. As a means to provide structural information about STC1, we performed biochemical and structural analyses of recombinant STC1 6xHis tagged protein produced in insect cells by using the baculovirus system. Circular dichroism analysis confirmed the in silico predicted high alpha-helical content. By mass spectroscopy analysis we provided experimental data that confirmed the conserved disulfide pattern previously described for fish STC1. Finally Small Angle X-ray Scattering data demonstrated that STC1 adopts a dimeric, slightly elongated structure in solution, providing there by the first low resolution structural data of this family of proteins. Additionally, we could obtain enough protein of high purity to perform crystallization trials that resulted in crystals diffracting at good resolution.
Doutorado
Bioquimica
Doutor em Biologia Funcional e Molecular

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior
Amburana cearensis (cumaru) Ã uma leguminosa subutilizada da Caatinga. O alto teor proteico das sementes faz delas uma possÃvel nova fonte de proteÃnas alimentares. Foram determinadas as melhores condiÃÃes de extraÃÃo proteica para posterior produÃÃo do isolado proteico de cumaru (IPAc). As anÃlises tambÃm foram conduzidas com a farinha delipidada (FDAc) e com um isolado proteico de soja comercial (IPS). IPAc apresentou teor proteico > 90% e composiÃÃo de aminoÃcidos comparÃvel a IPS, com notÃvel deficiÃncia em metionina. Foram determinadas algumas propriedades funcionais para predizer sua adequaÃÃo como ingrediente na indÃstria alimentÃcia. Os resultados para FDAc, IPAc e IPS foram, respectivamente: solubilidade 20-79; 9-99 e 3-76%; capacidade de retenÃÃo de Ãgua 1,7; 3,9 e 7,5 g/g; capacidade de retenÃÃo de Ãleo 1,5; 6,3 e 1,6 g/g; capacidade emulsificante / estabilidade 52 / 46%; 55 / 51% e 53 / 21%; capacidade espumante / estabilidade 47 / 32%; 65 / 53% e 33 / 8 e menor concentraÃÃo geleificante 18, 16 e 12%. Para investigar se IPAc e IPS apresentam indÃcios de toxicidade, cÃlulas de adenocarcinoma humano foram expostas por 24 h aos isolados. Para comparaÃÃo, tambÃm foi realizada exposiÃÃo com os isolados de soja (IPGm), feijÃo comum (IPPv), feijÃo de porco (IPCe) e mamona (IPRc), a fraÃÃo proteica de mamona (FPRc), as lectinas PHA-E e ConA e o controle quÃmico (Crtl_Quim). O RNA das cÃlulas foi hibridizado em microarranjos contendo o genoma humano completo. Os perfis de expressÃo gÃnica apÃs exposiÃÃo Ãs proteÃnas foram comparados aos de PBS e Crtl_Quim e agrupados hierarquicamente. Crtl_Quim, IPAc e IPGm se mostraram inadequados para a continuaÃÃo das anÃlises por provocar um efeito superestimado. A anÃlise de vias e processos biolÃgicos afetados apontou que genes envolvidos com a biossÃntese de colesterol, estresse do RE e resposta imune foram superexpressos e genes envolvidos com o ciclo celular e replicaÃÃo do DNA foram subexpressos apÃs exposiÃÃo a IPPv, IPCe, PHA-E e ConA. As amostras IPRc e FPRc regularam para cima genes envolvidos com a apoptose e resposta imune e para baixo genes envolvidos com o ciclo celular e sinalizaÃÃo do cAMP. AnÃlise do mapa conectivo mostrou alta correlaÃÃo de ConA, PHA-E e IPCe com drogas bloqueadoras de canais de Ca2+ e de K+; enquanto IPRc e FPRc apresentam funÃÃo biolÃgica semelhante a pelo menos seis drogas inibitÃrias da sÃntese proteica. Conclui-se que IPAc tem grande potencialidade como novo alimento proteico com grande aplicabilidade na indÃstria de alimentos, devendo, no entanto, sofrer modificaÃÃes no mÃtodo de obtenÃÃo visando a melhora na solubilidade e a eliminaÃÃo do sal residual.
Amburana cearensis (cumaru) is an underutilized legume from Caatinga. Because of their high protein content its seeds are a possible novel source of food protein. Were determined the best conditions for protein extraction and preparation of protein isolate (IPAc).Analysis were carried out also with the defatted flour (FDAc) and with a marketed soybean protein isolate (IPS). IPAc showed protein content of 90% and amino acid composition compatible with the IPSâs composition, with remarkable low methionine content. Some functional properties were measured in order to predict the adequacy of the isolates as an ingredient for food industry. The results for FDAc, IPAc and IPS were, respectively: solubility 20-79; 9-99 e 3-76%; water holding capacity 1.7; 3.9 e 7.5 g/g; oil holding capacity 1.5; 6.3 e 1.6 g/g; emulsion formation / stability 52 / 46%; 55 / 51% e 53 / 21%; foamability / stability 47 / 32%; 65 / 53% e 33 / 8; least gelling concentration (LGC) 18, 16 and 12%. In order to investigate whether IPAc e IPS exhibit signs of toxicity, two cell lines of human adenocarcinoma (MCF-7 e Caco-2) were exposed to these isolates as well as to others prepared from soyabean (IPGm), white bean (IPPv), Jack bean (IPCe) and castor bean (IPRc), to the protein fraction from castor bean (FPRc), to the lectins PHA-E and ConA (50 Âg/mL) and to the chemical control (Crtl_Quim). Subcitotoxic doses were determined by viability test to later exposure assay for 24 h. The MCF-7 cellâs RNA were extracted and hybridized to a microarray containing the complete human genome. The expression profiles after the exposition to the proteins were compared to that ones generated after PBS and Crtl_Quim and hierarchicaly clustered. Crtl_Quim, IPAc and IPGm were unsuitable for further analysis by their overestimated effect. Analysis of biological pathways and process showed that genes involved with the cholesterol biosynthesis, ER stress and immune response were upregulated and genes involved with cell cycle and DNA replication were downregulated after exposure of cells to IPPv, IPCe, PHA-E and ConA. The samples IPRc and FPRc upregulated genes involved with apoptosis and immune response and downregulated genes involved with cell cycle and cAMP signaling. Connectivity Map analysis showed high correlation of ConA, PHA-E and IPCe with drugs that are Ca2+ and K+ channel blockers, while IPRc and FPRc showed biological function similar to at least six drugs inhibitors of protein synthesis. Itâs possible to conclude that the IPAc has a high potentiality as a novel protein food with wide applicability in the food industry and should, however, be modified in the method of obtaining aiming the improvement in its solubility and eliminating the residual salt.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
A quitosana (Chi), a (1-4)-amino-2-desoxi-ƒÒ-glicana, e a forma desacetilada da quitina, um polissacarideo das conchas de crustaceos. As suas caracteristicas unicas como a carga positiva, biodegradabilidade, biocompatibilidade, atoxicidade e estrutura rigida fazem com que esta macromolecula seja ideal para uso como sistema oral de entrega de vacinas. Foram preparadas vesiculas unilamelares grandes (REVs) envoltas por dentro e por fora (como um sanduiche) com quitosana (Chi) e poli-vinil alcool (PVA). Entretanto, existem alguns problemas as serem superados com relacao a estabilizacao da proteina durante este processo. Durante a fase de formacao de micelas reversas, no processo de nanoencapsulacao da proteina, expandem-se as interfaces hidrofobicas que entao levam as adsorcoes interfaciais seguidas por desenovelamento e agregacao das proteinas. Aqui, observaram-se atraves de tecnicas espectroscopicas e imunologicas, o uso dos sais da serie de Hoffmeister durante a fase de formacao de micela reversa para estudar a conformacao estavel do toxoide difterico (Dtxd). Foi estabelecida uma correlacao entre os sais usados na fase aquosa e as variacoes na solubilidade e conformacao de Dtxd. Como o conteudo em helice-ƒÑ foi praticamente estavel concluiu-se que a encapsulacao de Dtxd ocorreu sem agregacao ou sem exposicao de residuo hidrofobico na proteina. A agregacao de Dtxd foi evitada em 98 % quando se usou o cosmotropico PO2-4. Este ion foi usado para se preparar uma formulacao de Dtxd em REVs-Chi-PVA estavel e com identidade imunologica reconhecida na presenca de PO2-4. Entao, obteve-se uma solubilidade e estabilidade maxima de Dtxd depois de seu contacto com CH3CO2C2H5 para comecar a sua nanoencapsulacao em condicoes ideais. Este foi um avanco tecnologico importante porque uma solucao simples, como e a adicao de sais, evitou o uso de proteinas heterologas (Rescia et alii, 2009a). A proteina estabilizada foi entao encapsulada dentro de REVs como o descrito. Os lipossomas tem sido descritos como adjuvantes desde 1974 (Allison e Gregoriadis, 1974). A maior limitacao de seu uso em vacinas orais e a sua instabilidade estrutural causada pelas atividades enzimaticas do meio. O objetivo aqui foi combinar lipossomas, que podem encapsular antigenos (Dtxd, Diphtheria toxoid) com quitosana que protege estas particulas e promove a mucoadesibilidade. Empregaram-se tecnicas fisicas para se entender o processo pelo qual lipossomas (SPC: Cho, 3: 1) podem ser recobertos (interna e externamente) com quitosana (Chi) e PVA (poly-vinilic-alcohol) que sao polimeros biodegradaveis e biocompativeis. Obtiveram-se particulas de REVs-Chi (vesiculas preparadas por evaporacao de fase reversa recobertas interna e externamente com Chi) redondas e com as superficies rugosas e estabilizadas ou nao com PVA. As eficiencias de encapsulacao (Dtxd foi usada como antigeno) foram diretamente dependentes da presenca de Chi e PVA na formulacao. A adsorcao de Chi a superficie de REVs foi acompanhada por um aumento no potencial ƒê. Em contraste, a adsorcao de PVA a surperficie de REVs-Chi foi acompanhada por uma diminuicao do potencial . A presenca de Dtxd aumentou a eficiencia de adsorcao de Chi as superficies. A afinidade de PVA pela mucina foi 2000 vezes maior do que a observada somente com Chi e nao depende se a molecula esta em solucao ou se esta adsorvida a superficie lipossomal. A liberação do Dtxd foi retardada por sua encapsulação dentro de REVs-Chi-PVA. Concluiu-se que estas novas vesículas estabilizadas foram hábeis em se adsorverem às superfícies intestinais, resistiram às degradações e controlaram a liberação do antígeno. Assim, as partículas de REVs-Chi-PVA podem ser usadas como um veículo oral com capacidade adjuvante (Rescia et alii, 2009b). Os lipossomas revstidos por quitosana (REVs-Chi) como veículos orais para transporte de vacinas foram bem caraterizados neste laboratório. Estas partículas foram desenhadas para serem capturadas pelo muco, para interagirem com surperfícies orais e para resistirem às enzimas do trânsito gástrico. Foram usadas três formulações diferentes contendo o Dtxd (toxoide diftérico) para imunizar camundongos: REVs [Vesículas unilamelares obtidas por evaporação de fase reversa produzidas com SPC: Cho (3:1)]; REVs-Chi (REVs recobertas por Chi) e REVs-Chi-PVA (REVs recobertas por Chi e estabilizadas por PVA). Através do teste de adesibilidade e dos experimentos com anti-toxoide diftérico observou-se que houve uma correlação direta entre a complexidade da partícula (antígeno livre < REVs < REVs-Chi < REVs-Chi-PVA) e a produção de anticorpos (IgA, IgG1 and IgG2a) em todos os ensaios (R= 0,91766- 0,99718). O resultado mais interessante foi a total ausência da produção de IgA nos camundongos imunizados com o antígeno livre, provando então a excelência das partículas engenheiradas. Além do aumento da produção dos anticorpos de mucosa, ambas formulações com Chi ou com Chi-PVA estimularam tanto a produção de anticorpos humorais quanto a seletividade. Demonstrou-se que é possível de se estabelecer uma correlação entre REVs-Chi/Dtxd and REVs-Chi-PVA/Dtxd e o aumento da imunidade de mucosa. Estas partículas podem ser usadas como veículo geral tanto para transporte de drogas quanto de vacinas (Rescia et alli, 2009c).
Chitosan, - (1-4)-amino-2-deoxy-D-glucan) is a deacetylated form of chitin, a polysaccharide from crustacean shells. Its unique characteristics such as positive charge, biodegradability, biocompatibility, non-toxicity, and rigid structure make this macromolecule ideal for oral vaccine delivery system. We prepared reverse phase evaporation vesicles (REVs) sandwiched by chitosan (Chi) and polyvinylic alcohol (PVA). However, in this method there are still some problems to be circumvented related to protein stabilization. During the inverted micelle phase of protein nanoencapsulation, hydrophobic interfaces are expanded leading to interfacial adsorption followed by protein unfolding and aggregation. Here, spectroscopic and immunological techniques were used to ascertain the effects of the Hoffmeister series ions on Diphtheria toxoid (Dtxd) stability during the inverted micelle phase. A correlation was established between the salts used in aqueous solutions and the changes in Dtxd solubility and conformation. Dtxd α-helical content was quite stable what led us to conclude that encapsulation occurred without protein aggregation or without exposition of hydrophobic residues. Dtxd aggregation was 98 % avoided by the kosmotropic PO2-4. This ion was used to prepare a stable Dtxd and immunologically recognized REVs-Chi-PVA formulation in the presence of 50 mM PO42-. Under these conditions the Dtxd retained its immunological identity. Therefore, we could obtain the maximum Dtxd solubility and stability after contact with CH3CO2C2H5 to begin its nanoencapsulation within ideal conditions. This was a technological breakthrough because a simple solution like salt addition avoided heterologous proteins usage (Rescia et al., 2009a). The stabilized protein was as encapsulated within REVs as described. Liposomes have been used as adjuvants since 1974 (Allison and Gregoriadis, 1974). One major limitation for the use of liposomes in oral vaccines is the lipid structure instability caused by enzyme activities. Our goal was to combine liposomes which can encapsulate antigens (Dtxd, diphtheria toxoid) with chitosan which protects the particles and promotes mucoadhesibility. We employed physical techniques to understand the process by which liposomes (SPC: Cho, 3:1) can be sandwiched with chitosan (Chi) and stabilized by PVA (Poly-vinylic alcohol) which are biodegradable and biocompatible polymers. Round and smooth surfaced particles of REVs-Chi (Reversed phase vesicles sandwiched by Chi) stabilized by PVA were obtained. The REVs encapsulation efficiencies (Dtxd was used as the antigen) were directly dependent on the Chi and PVA present in the formulation. Chi adsorption on REVs surface was accompanied by an increase of  otential. In contrast, PVA adsorption on REVs-Chi surface was accompanied by a decrease of potential. The presence of Dtxd increased the Chi surface adsorption efficiency. The PVA affinity by mucine was 2000 higher than that observed with Chi alone and did not depend on the molecule being in solution or adsorbed on the liposomal surface. The liberation of encapsulated Dtxd was retarded by encapsulation within REVs-Chi-PVA. These results lead us to conclude that these new and stabilized particles were to able to adsorb to intestinal surfaces, resisted degradation and controlled the antigen release. Therefore, REVs-Chi-PVA particles can be used as an oral delivery adjuvant (Rescia et al., 2009b). Liposomes sandwiched by chitosan (REVs-Chi) as vehicles for oral vaccines have been well characterized in our laboratory. These particles were designed to be captured by mucus, to interact with oral surfaces and to withstand the enzymes of the gastric transit. Three different formulations containing Dtxd (diphtheria toxoid): REVs [reverse phase evaporation vesicles of SPC: Cho (3: 1)]; REVs-Chi (REVs sandwiched by chitosan) and REVs-Chi-PVA were used to immunize mice. Through adhesibility assays and antibody anti-diphtheria experiments we observed a direct correlation between particle complexity (free antigen < REVs < REVs-Chi < REVs-Chi-PVA) and antibody production (IgA, IgG1 and IgG2a) in all the assays (R= 0,91766- 0,99718). The most striking result was the absence of IgA production in those mice immunized with the free antigen, proving the excellence of the engineered particles. In addition to enhancement of mucosal antibodies production, the formulations with Chi and PVA stimulated both, humoral antibody production and selectivity. We have shown that it was possible to establish a correlation between REVs-Chi/Dtxd and REVs-Chi-PVA/Dtxd and the enhancement of mucosal immunity. These particles can be used as a general vehicle for oral drug or vaccine delivery systems (Rescia et al., 2009c).
TEDE
BV UNIFESP: Teses e dissertações

A proteólise limitada de certas proteínas leva à liberação de peptídeos opióides endógenos. Vários relatos apontam que peptídeos derivados da hemoglobina como hemorfinas e hemopressinas têm efeito antinociceptivo, pela atividade de modulação de receptores acoplados a proteínas G. No presente estudo, um ensaio de captura do substrato (ECS) foi combinado com a marcação isotópica e LC-MS/MS para identificar e caracterizar um novo fragmento da hemoglobina que se liga à EP24.15. O peptídeo AGH, identificado neste trabalho, inibe respostas de hipernocicepção periféricas através de receptores opióides do tipo m . A persistência do peptídeo AGH no tecido nervoso perfundido sugere relevância fisiológica. Embora o AGH seja derivado de hemoglobina e tenha atividade opióide, falta-lhe a sequência chave das hemorfinas (YPWT), indicando que ele pode pertencer a uma nova classe de peptídeos derivados da hemoglobina. Adicionalmente, o AGH modula as interações entre as proteínas 14-3-3e e EP24.15 in vitro, podendo estar relacionado com a secreção não convencional da EP24.15.
Limited proteolysis of certain proteins leads to the release of endogenous opioid peptides. Several reports have shown that hemoglobin-derived peptides such as hemorphins and hemopressins have an antinociceptive effect by modulating GPCR activity. In the present study, a substrate capture assay (SCA) was combined with isotopic labeling and LC-MS/MS to identify and characterize a new bioactive hemoglobin fragment that binds to EP24.15. AGH, a new peptide identified in this work, inhibits peripheral hyperalgesic responses through m opioid receptors (MOR). The persistence of AGH peptide in perfused nervous tissue suggests its physiological relevance. Although AGH is derived from hemoglobin and it is a peptide with opioid activity, it lacks the key sequence of hemorphins (YPWT), indicating that it is part of a new class of peptides derived from hemoglobin. Additionally, the AGH modulates interactions between 14-3-3e and EP24.15 proteins in vitro and may be related to the unconventional EP24.15 secretion.