Ubiquilin (UBQLN) is a member of type2 ubiquitin-like (UBL) protein family characterized by an UBL domain at the N-terminus and an ubiquitin associated (UBA) domain at the C-terminus. This protein has been shown to play an important role in the regulation of the levels, aggregation and degradation of various neurodegenerative disease-associated proteins. However, the specific functions and mechanisms of UBQLN regulation still remain to be elucidated. In this study, we investigate the effect of UBQLN expression on α-Amino-3-hydroxy-5-methyl-isoxazole-4-propionic acid receptor (AMPAR) degradation and the underlying molecular mechanisms. We show that UBQLN overexpression decreases AMPAR levels in neurons and also reduces GluA1 expression in HEK 293T cells. Moreover, our results indicate that UBQLN can form a complex with GluA1, and this interaction is related to the ubiquitination of AMPARs. In addition, we find a higher expression of UBQLN2 in Alzheimer’s disease (AD) patient brains, which might be a potential pathological mechanism of GluA1 reduction in AD. Given the crucial effect of UBQLN in AMPAR regulation, UBQLN may play an important role in synaptic transmission, brain functions as well as neurodegenerative diseases. / 2018-07-21T00:00:00Z

Neste trabalho serão apresentados resultados sobre três sistemas proteícos diferentes: Lisozima, Crioglobulina e Proteassomo, analisados a partir, principalmente, da técnica de espalhamento de Raios X a baixos ângulos. Técnicas como microscopia eletrônica de transmissão e espalhamento de luz dinâmico foram utilizadas como técnicas complementares. Os resultados apresentados demonstram o potencial único que a técnica de espalhamento a baixos ângulos possui no estudo de sistemas em solução. Os dados correspondem a um estudo em um grande intervalo de tamanhos para as proteínas estudadas (15kDa to 750 kDa), requerendo diferentes abordagens em cada caso. Como será mostrado, para casos onde se tem um meio monodisperso, diversas metodologias de modelagem podem ser utilizadas. Para o sistema composto de Lisozima, por se tratar de uma proteína amplamente estudada na literatura, é interesante poder comparar os resultados encontrados com os já publicados e observar sua estabilidade em solução. O peso molecular calculado a partir dos dados de espalhamento foi 15kDa, que está em bom acordo com a esperado para esta proteina (14,6 kDa). Além disso, ao variar-se a concentração da proteína em solução, é possível observar um fator de interação entre as partículas para maiores concentrações. Esse fator de interação pode ser considerado próximo ao de esferas rígidas. Para o sistema de Crioglobulinas, houve uma dificuldade na purificação da amostra, mas ainda assim apresentaremos alguns resultados interessantes, em que a técnica de SAXS fornece informações sobre a flexibilidade de proteínas e as análises para as amostras de um pool de imunoglobulinas indicou que com a diminuição da temperatura a dispersão de raios de giro aumenta, indicando a formação de agregados. Para o sistema do Proteassomo, diversas análises se mostraram possível e resultados novos puderam ser obtidos e publicados. Dos estudos utilizando MET,com as micrografias obtidas tem-se a indicação de diferenças na estrutura, quando a molécula está em condições diferentes. Das análises feitas por SAXS, é possível utilizar duas modelagens diferentes, uma simples, outra mais avançada, em que se pode concluir que a redução do Cys-PT glutatiolado induz mudanças conformacionais. Além disso, resultados de SAXS e MET estão em concordância e fornecem informações complementares. / In this work results will be presented on three different protein system: Lysozime, Cryoglobulin and Proteasome, analyzed mainly by Small Angle X-ray scattering technique. Techniques such as transmission electron microscopy and dynamic light scattering were used as complementary techniques. The results show that an unic potential Small Angle X-ray scattering technique around the study of systems in solution. The data correspond to a study of a wide range of sizes for the studied proteins (15kDa to 750 kDa), requiring different approaches in each case. As will be shown for cases where there is a monodisperse system, different modeling methodologies may be used. For the system composed of Lysozyme, because it is a protein widely studied in the literature, it is interesting to compare the results with those already published and observe its stability in solution. The molecular weight calculated from the scattering data was 15kDa, which is in good agreement with the expected for this protein (14.6kDa). Futhermore by varying the concentration of the protein in solution, it is possible to observe a factor of interaction between the particles for higher concentrations. This interaction factor can be considered close to the rigid spheres. For Cryoglobulins system, there was a difficulty in the sample purification, but still present some interesting results, where the SAXS technique provides information on the flexibility of proteins and the analysis for the samples from a pool of immunoglobulin indicated that with decreasing temperature, the dispersion of radius of gyration increases, indicating the formation of aggregates. For the proteasome system, various analyzes have proved possible and new results could be obtained and published. From studies using TEM, with the micrographs we have the indication of differences in the structure, when the molecule is in different conditions. From the analyzes made by SAXS, it is possible to use two different modeling, a simple one, and other more advanced, where it can be concluded that the reduction of the Cys-PT glutathiolated induces conformational changes. Moreover, SAXS and TEM results are in agreement and provide additional information.

Calcium ions have important roles in cellular processes including intracellular signaling, protein folding, enzyme activation and initiation of programmed cell death. Cells maintain low levels of calcium in their cytosol in order to regulate these processes. When activation of calcium-dependent processes is needed, cells can release calcium stored in the endoplasmic reticulum (ER) into the cytosol to initiate the processes. This can also initiate formation of plasma membrane channels that allow entry of additional calcium from the extracellular milieu. The change in calcium levels is referred to as calcium flux. A key protein involved in initiation of calcium flux is Stromal Interaction Molecule 1 (STIM1), which has recently been identified as a sensor of ER calcium levels. STIM1 is an ER transmembrane protein that is activated by a drop in ER calcium levels. Upon activation, STIM1 oligomerizes with a plasma membrane protein, ORA1, to form calcium-selective plasma membrane channels. Dysregulation of calcium flux has been reported in cancers, autoimmune diseases and other diseases. STIM1 is a promising target in drug discovery due to its key role early in calcium flux. Here we review the involvement and importance of STIM1 in diseases and we discuss STIM1 as a viable target for drug discovery using computational chemistry methods to rapidly identify new molecules to target STIM1. Herein, computational techniques were used to understand the mechanistic role of STIM1 and virtual screening is in process to discover potential inhibitors of STIM1 activity. Also mutational analysis on STIM1 was performed computationally to see the effect it had on the protein computationally. It has been found that tumor cells and tissues, compared to normal cells, have higher levels of copper and possibly other metal ions. This presents a potential vulnerability of tumor cells that can serve as a physiological difference between cancer cells and normal cells and allows design of compounds that selectively target tumor cells while sparing normal cells. Recently we have identified compounds that have potential to inhibit the proteasome in tumor cells and induce cell death by mobilizing endogenous tumor copper resulting in in cellulo activation of the compound. These compounds hence act as pro-drugs, becoming active drugs in tumor cells with high copper content but remaining essentially inactive in normal cells, thereby greatly reducing adverse effects in patients. Such use would be of significant benefit in early detection and treatment of cancers, in particular, aggressive cancers such as pancreatic cancer which is usually not detected until it has reached an advanced stage. Six compounds were identified following virtual screening of the NCI Diversity Set with our proteasome computer model followed by confirmation with a biochemical assay that showed significant inhibition of the proteasome by the compounds in the presence of copper ions. In a dose response assay, NSC 37408 (6, 7-dihydroxy-1-benzofuran-3-one), our best compound, exhibited an IC50 of 3µM in the presence of 100 nM copper. Chagas’ Disease, a parasitic disease caused by the parasite Trypanosma Cruzi, is endemic to Latin America. The disease manifests itself in a short acute phase and a long chronic phase. Current treatments are effective only in the acute phase and are not used in the chronic phase due to toxicity of the drugs. Hence a new drug discovery approach was chosen for this disease. Cruzain is the major etiologic enzyme involved in the disease and is only present in the parasite. It is also an enzyme expressed by the parasite in both phases. Herein, a novel peptoid library containing hydromethylketones was constructed and screened against a virtual structure of cruzain. The peptoids thus found through this drug discovery effort can be used as potential drug candidates against cruzain. Computational techniques will help achieve a high degree of specificity and aid in proposing assays for determining compounds with high activity Alzheimer disease is the most common form of dementia. Its pathogenesis incorporates many potential targets for treatment. Among the targets identified, Apolipoprotein E4 (apoE4) is especially interesting due to its catalytic role in the degradation and clearance of amyloid beta (Aβ), a risk factor for Alzheimer disease. ApoE exists in 3 isoforms which directly impact its functionality in the body. There are characteristic structural differences between them. In ApoE4 ionic interactions exist between Arg-61 and Glu-255 residues, unlike the other isoforms. Hence interruption of this interaction by inhibitors may change the structure of apoE4 to a more linear structure as observed in the other isoforms. Virtual screening of the NCI diversity set on an energy minimized protein virtual structure was performed to identify potential small molecule inhibitors and to gain further understanding of interactions that can be targeted to inhibit this protein. From the top ligands in the NCI diversity set, a peptide library was designed to target the protein. Previous research has indicated that liquid assisted grinding (LAG) is efficient and reliable for cocrystal formation when compared to solvent crystallization and dimethyl formamide is the best solvent for grinding. Herein, we report the comparison of four screening processes: Slurry, solvent crystallization, LAG and dry grinding. Thirty-eight crystal forms containing the Narom··· COOH, Narom···OH supramolecular heterosynthons were screened in the process, and it was observed that slurry methodology is as efficient and reliable in forming cocrystals as solution crystallization. Twenty-four new crystal forms were also isolated herein. LAG was found to be more efficient as compared to dry grinding and was successful in the formation of twenty-five crystal forms of the thirty-eight screened. Dimethyl formamide still remains the best solvent for LAG. All our slurry experiments were performed in water and it was found that water can be used reliably for this method for compounds within a wide range of solubility, thereby increasing the versatility and usability of this method for future screening procedures.

<a>The 20S proteasome, a multi-subunit protease complex, present in all domains of life and some orders of bacteria, is involved in degradation of the majority of cellular proteins. Structurally, it is made of α and β subunits arranged in four heptameric rings, with inner two β-rings sandwiched between outer two α-rings. The 20S proteasome in prokaryotes usually has one type of α and one type of β subunits, whereas eukaryotes have seven distinct types of α and seven distinct types of β subunits. Unlike the highly conserved structure of proteasome, its assembly pathway is different across the domains. In archaea and eukaryotes, proteasome assembly begins with α subunit interactions leading to the α-ring formation. By contrast, bacterial proteasome assembly pathway bypasses the α-ring formation step by initiating assembly through an α and β subunit interaction first. These early interactions are not well understood due to their highly rapid and dynamic nature. This dissertation focused on understanding the early events in proteasome assembly and contributed three significant findings. First, the archaeal proteasome assembly can also begin without formation of α-rings, demonstrating the coexistence of a bacterial-like assembly pathway. Second, a novel assembly intermediate was identified in yeast, and its composition argues for the presence of a similar α-ring independent assembly pathway. Third, the assembly chaperone Pba3-Pba4 prevents the formation of high molecular weight complexes arising from spontaneous and non-productive interactions among the α subunits. These findings provide a broader understanding of proteasome biogenesis and suggest considering proteasome assembly event as a network of interactions rather than a linear pathway. The results also shed light on assembly chaperone’s contribution in increasing the efficiency of proteasome assembly by streamlining the productive interactions.</a>

Indiana University-Purdue University Indianapolis (IUPUI) / The ubiquitin-proteasome system is responsible for the targeted degradation of proteins within the cell. The 26S proteasome, which is the protease of this system, is a high molecular weight complex consisting of 33 subunits that arrange to form two smaller complexes the 19S regulatory particle (RP) and the 20S core particle (CP). The 19S RP can bind one or both ends of the 20S CP and is responsible for recognizing the ubiquitinated substrates. After recognition, the 19S RP will subsequently deubiquitinate, unfold, and translocate the substrates into the proteolytic 20S CP. The 20S CP consists of seven unique alpha and seven unique beta subunits that arrange into four stacked rings, with two alpha rings capping two beta rings. Assembly of the alpha(1-7)beta(1-7)beta(1-7)alpha(1-7) structure begins with the formation of an alpha ring and proceeds through specific assembly intermediates. This process is assisted by assembly chaperone proteins that promote on pathway interactions to efficiently construct the 20S CP. In this dissertation, three new findings are described which further characterize the proteasome assembly pathway. First, novel non-canonical complexes comprised of proteasome subunit alpha4 were identified in vivo, revealing proteasome subunits can assemble into complexes outside of the proteasome. Second, Hsp70 proteins, Ssa1/2, were shown to assist in the assembly of 20S CPs, adding to the growing list of proteins guiding proteasome assembly. Third, a novel complex was identified which is believed to represent a new proteasome assembly intermediate.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19764号 / 農博第2160号 / 新制||農||1039(附属図書館) / 学位論文||H28||N4980(農学部図書室) / 32800 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 阪井 康能, 教授 植田 和光, 教授 三芳 秀人 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

No description available.

Omi, also known as HtrA2, is a mammalian pro-apoptotic mitochondrial protein and a member of the HtrA (high temperature requirement A) family of serine proteases. Omi promotes the caspase-dependent apoptotic pathway through cleavage of IAPs (inhibitor of apoptosis proteins); this cleavage inactivates IAPs and facilitates caspase activity. Omi's proteolytic activity is necessary and essential for its pro-apoptotic function. This study is aimed to further understand the role of Omi in the cytoplasm by using the yeast two-hybrid system to identify novel Omi interactors/substrates. A HeLa (cervical carcinoma cell line) cDNA library was screened using Omi as a "bait" protein. One of the proteins indentified in this screen as a strong Omi interactor was the S5a protein and was selected for further analysis. S5a is a soluble cytosolic mammalian protein and a component of the proteasome's 19S regulatory subunit. The proteasome is a large cytosolic protein complex responsible for the controlled degradation of damaged or denatured cellular proteins. Further characterization of the interaction through an in vitro proteolytic assay demonstrated that Omi can cleaves recombinant S5a protein. This data suggests that S5a is a bona fide substrate of Omi that is degraded upon induction of apoptosis. It also provides a new mechanism that leads to the inactivation of the proteasome during cell death.

No description available.

Obesity is a major health condition in which little is known about the molecular mechanisms that drive it. The hypothalamus is the primary control center for controlling both food intake and energy expenditure in order to maintain the body's energy balance and dysregulation of molecular processes in this region have been implicated in the development and progression of obesity. Recently, several studies have shown altered DNA methylation of critical appetite genes, including the satiety gene Pomc, in the hypothalamus of rodents fed a high fat obesogenic diet. However, it has not previously been studied whether diet-induced changes in DNA methylation of critical appetite genes in the hypothalamus contributes to the development and persistence of the obesity phenotype. Further, DNA 5-hydroxymethylation (5-hmC) is one type of DNA methylation that is 10 times more abundant in the brain than peripheral tissues. However, to date, no study has been conducted examining whether DNA 5-hmC becomes altered in the brain following weight gain and/or contributes to the obesity phenotype. Additionally, there is also evidence to support that exposure to a high fat diet dysregulates the activity of the ubiquitin-proteasome system, the master regulator of protein degradation in cells, in the hypothalamus of male rodents. Despite this, whether this can occur in both sexes and directly contributes to abnormal weight gain has not been investigated. Here, we used a rodent diet-induced obesity model in combination with quantitative molecular assays and CRISPR-dCas9 manipulations to test the role of hypothalamic 1) DNA 5-hmC levels, 2) Pomc methylation, and 3) dysregulated ubiquitin-proteasome signaling in abnormal weight gain following exposure to obesogenic diets. We found that males, but not females, have decreased levels of DNA 5-hmC in the hypothalamus following exposure to a high fat diet, which tracked body weight. Short-term exposure to a high fat diet, which does not result in significant weight gain, resulted in decreased hypothalamic DNA 5-hmC levels, suggesting these changes occur prior to obesity development. Moreover, decreases in DNA 5-hmC persist even after the high fat diet is removed. Importantly, CRISPR-dCas9 mediated upregulation of DNA 5-hmC enzymes in the male, but not female, hypothalamus significantly reduced the percentage of weight gained on the high fat diet relative to controls. Next, we used the CRISPR-dCas9-TET1 and dCas9-DNMT3a systems to test the role of Pomc DNA methylation in the hypothalamus in abnormal weight gain following acute exposure to a high fat diet in male rats. We found that exposure to a high fat diet increases Pomc DNA methylation and reduces gene expression in the hypothalamus. Despite this, we found that CRISPR-dCas9-TET1-mediated demethylation of Pomc was not sufficient to prevent abnormal weight gain following exposure to a high fat diet. Moreover, CRISPR-dCas9-DNMT3a-mediated methylation of Pomc did not alter weight gain following exposure to standard or high fat diets. Finally, we found that both males and females showed dynamic downregulation of proteasome activity, decreases in proteasome subunit expression and an accumulation of degradation-specific K48 polyubiquitinated proteins in the hypothalamus. However, while the CRISPR-dCas9 system was able to selectively increase some forms of proteasome activity, it was unable to prevent diet-induced proteasome downregulation or abnormal weight gain. Collectively, this data reveals novel, sex-specific differences in the engagement of the ubiquitin proteasome system and role of DNA 5-hydroxymethylation in the hypothalamus during the development of the obesity phenotype. / Doctor of Philosophy / Obesity affects 34% of the American population at an annual cost of more than $340 billion in healthcare and is a risk factor for the development of diabetes and certain cancers. Genetic and environmental factors have also been shown to influence the expression of genes that play a role in the development of obesity. The hypothalamus coordinates many integral activities such as hormone regulation and feed intake and numerous studies have observed altered hypothalamic gene regulation in obesity models. Recently, several studies have shown altered DNA methylation of critical appetite genes, including the satiety gene Pomc, in the hypothalamus of rodents fed a high fat obesogenic diet. However, it has not previously been studied whether diet-induced changes in DNA methylation of critical appetite genes in the hypothalamus contributes to the development and persistence of the obesity phenotype. Further, DNA 5-hydroxymethylation (5-hmC) is one type of DNA methylation that is 10 times more abundant in the brain than peripheral tissues. However, to date, no study has been conducted examining whether DNA 5-hmC becomes altered in the brain following weight gain and/or contributes to the obesity phenotype. Additionally, there is also evidence to support that exposure to a high fat diet dysregulates the activity of the ubiquitin-proteasome system, the master regulator of protein degradation in cells, in the hypothalamus of male rodents. Despite this, whether this can occur in both sexes and directly contributes to abnormal weight gain has not been investigated. In this document, I outline a series of experiments designed to elucidate novel, sex-specific differences in the role of the ubiquitin proteasome system and DNA 5-hydroxymethylation in the hypothalamus during the development of the obesity phenotype.