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Analysis of the Cellular Proteins, TIA-1 and TIAR, and their Interaction with the West Nile Virus (WNV) 3' SL Minus-Strand RNAEmara, Mohamed Maged 03 May 2008 (has links)
The 3' terminal stem loop of the WNV minus-strand [WNV3'(-) SL] RNA was previously shown to bind the cell protein, T-cell intracellular antigen-1 (TIA-1), and the related protein, TIAR. These two proteins are known to bind AU-rich sequences in the 3' UTRs of some cellular mRNAs. AU stretches are located in three single-stranded loops (L1, L2, and L3) of the WNV3'(-) SL RNA. The RNA binding activity of both proteins was reduced when L1 or L2, but not L3, AU sequences were deleted or substituted with Cs. Deletion or substitution with Cs of the entire AU-rich sequence in either L1 or L2 in a WNV infectious clone was lethal for the virus while mutation of some of these nt decreased the efficiency of virus replication. Mutant viral RNAs with small plaque or lethal phenotypes had similar translational efficiencies to wildtype RNA, but showed decreased levels of plus-strand RNA synthesis. These results correlated well with the efficiency of TIA-1 and/or TIAR binding in in vitro assays. In normal cells, TIA-1 and TIAR are evenly distributed in the cytoplasm and nucleus. Between 6 and 24 hr after WNV infection, TIAR concentrated in the perinuclear region and TIA-1 localization to this region began by 24 hr. Similar observations were made in DV2 infected cells but at later times after infection. In infected cells, both proteins colocalized with dsRNA, a marker for viral replication complexes, and with viral non-structural proteins. Anti-TIAR or anti-TIA-1 antibody coimmunoprecipitated viral NS3 and possibly other viral nonstructural proteins. In response to different types stress, TIA-1 and TIAR recruit cell mRNA poly(A)+ into cytoplasmic stress granules (SG) leading to general translational arrest in these cells. SG were not induced by flavivirus infection and cells became increasingly resistant to arsenite induction of SG with time after infection. Processing Body (PB) assembly was also decreased beginning at 24 hr. These data suggest that the sequestration of first TIAR and then TIA-1 via their interaction with viral components in flavivirus infected cells inhibits SG formation and prevents the shutoff of host translation.
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Muscarinic Receptor Modulation of the Phospholipid Effect in Cardiac MyocytesMattern, Janet 05 1900 (has links)
The muscarinic agonist carbachol stimulates a rapid increase in ^32Pi incorporation into phosphatidic acid (PA) and phosphatidylinositol (PI) in calcium tolerant myocytes prepared from heart tissue. The density of muscarinic receptors, determined by [^3H]-QNB binding, is greater in the atria than in the ventricles. 250 uM carbachol decreased specific [^3H]-QNB binding to muscarinic receptors on myocyte membranes by fifty percent. Trifluoperazine, also a phospholipase C inhibitor, inhibited the carbachol stimulated increase in ^32Pi incorporation into PA and PI and did not interfere with muscarinic receptor binding. Therefore, isolated canine myocytes provide a suitable model system to further study the muscarinic receptor stimulated phospholipid effect, and its role in mediating biochemical processes and physiological function in the heart.
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Structural and functional study of efflux pumps involved in drug resistance / Étude structurale et fonctionnelle des pompes à efflux impliqués dans la résistance aux médicamentsMartinez Jaramillo, Lorena Marcela 14 February 2014 (has links)
L’efficacité des chimiothérapies est limitée par la surexpression de pompes d’efflux adressées à la membrane plasmique des cellules cibles. En effet, celles-ci réduisent le taux intracellulaire des médicaments anticancéreux, antiviraux, antifongiques et antibactériens. La P-gp/ABCB1 est la plus impliquée dans ce phénomène, suivie de MRP1/ABCC1 et de BCRP/ABCG2. Une approche pour surmonter ce phénomène est de développer des médicaments qui ne soient pas expulsés par ces pompes. Dans ce contexte, nous avons développé une nouvelle classe d’inhibiteurs de la protéase du VIH-1 qui ne sont ni transportés par P-gp ni par BCRP. Ils sont ainsi des candidats intéressants aux trithérapies contre le SIDA. Un point clé pour comprendre comment ces transporteurs font traverser les médicaments à travers la membrane est d’identifier des nouvelles structures. Ainsi, nous avons résolu trois structures de P-gp de souris. Une d’entre-elles est complexée à un nano-anticorps lié au premier NBD («nucleotide-binding domain»), qui fige la P-gp dans une nouvelle conformation ouverte vers l'intérieur. Pour finir, nous avons localisé deux sites de liaison de P-gp en caractérisant les modes d'inhibition de deux inhibiteurs précédemment cocristallises avec la pompe. Ceci permet de mieux comprendre le mécanisme de translocation et offre la possibilité de cibler plus précisément ces sites pour développer des modulateurs de cette pompe / Resistance to chemotherapy is partly due to efflux pumps expressed in the plasma membrane which prevents the accumulation of anticancer, antiviral, antifungal and antibacterial drugs in target cells. Three human ABC transporters are particularly involved in MDR phenotype: P-gp/ABCB1, MRP1/ABCC1 and BCRP/ABCG2. Among the different approaches used to overcome the resistance linked to these transporters, the development of non-substrate drugs MDR-ABC transporters has been described. Here, new class of HIV-1 protease inhibitors not recognized by P-gp/BCRP were identified, promising to be attractive candidates to HAART therapy. Since the determination of the X-ray structures in different conformations is a key point to understand how MDR-ABC transporters translocate drugs across the plasma membrane, the crystal structures of three inward-facing conformations of mouse P-gp were resolved. One structure has a camel nanobody bound to the C-terminal side of the first nucleotide-binding domain, revealing a unique epitope on P-gp and freezing a new open-inward conformation. Finally, the enzymatic characterization of two inhibitors co-crystallized with the mouse P-gp has allowed to localize two main binding sites by which drugs efflux occurs. These results bring new findings of the drug-efflux mechanism and offer the possibility to target more precisely those sites to develop modulators of this pump
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Raman and surface-enhanced raman spectroscopy of G-quadruplexesUnknown Date (has links)
G-quadruplexes (G4s) are nucleic acid structures formed from π-stacked planar sets of four Hoogsteen hydrogen bonded guanine bases. G4s emerged as potential therapeutic targets based on their ability to modulate gene expression and inhibit the ability of telomerase to elongate chromosomal telomeres. Raman spectroscopy, polarized Raman spectroscopy, surface-enhanced Raman spectroscopy (SERS), and other optical spectroscopic techniques were used to characterize the G4s formed by four different DNA sequences: human telomeric (HT), thrombin-binding aptamer (TBA), nuclease hypersensitive element III1 region of the c- Myc gene promoter (Myc), and a single loop-isomer of Myc (MycL1). / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2015. / FAU Electronic Theses and Dissertations Collection
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Clues of identification of protein-protein interaction sites.January 2005 (has links)
Leung Ka-Kit. / Thesis submitted in: November 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 67-71). / Abstracts in English and Chinese. / Abstract / Chapter CHAPTER 1. --- INTRODUCTION --- p.1 / Chapter 1.1 --- Background of protein structures --- p.1 / Chapter 1.2 --- Background of protein-protein interaction (PPI) --- p.4 / Chapter 1.2.1 --- Quaternary structure and protein complex --- p.4 / Chapter 1.2.2 --- Previous related work --- p.4 / Chapter 1.2.3 --- The kinetic and thermodynamic formalism --- p.6 / Chapter CHAPTER 2. --- MATERIALS AND METHODS --- p.10 / Chapter 2.1 --- Amino acid composition representative power modeling --- p.10 / Chapter 2.1.1 --- Propensity level modeling --- p.10 / Chapter 2.1.2 --- Polar atoms visualization --- p.17 / Chapter 2.2 --- Rigid structure representative power modeling --- p.17 / Chapter 2.3 --- Electrostatic potential modeling --- p.17 / Chapter 2.3.1 --- Charge residence --- p.17 / Chapter 2.3.2 --- Minimum Ribbon (MR) --- p.19 / Chapter 2.4 --- Examination of interface --- p.23 / Chapter 2.5 --- Identification procedures of a binding site --- p.24 / Chapter 2.6 --- System requirements --- p.24 / Chapter CHAPTER 3. --- RESULTS AND DISCUSSIONS --- p.24 / Chapter 3.1 --- Polar atoms --- p.25 / Chapter 3.2 --- Minimum Ribbon (MR) --- p.27 / Chapter 3.3 --- "Charge complementarity, propensity level and rigid structure orientation" --- p.31 / Chapter 3.4 --- Identification of interacting site --- p.36 / Chapter CHAPTER 4. --- CONCLUSIONS --- p.64 / System requirements --- p.65 / Basic operation --- p.65 / Limitation --- p.66
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Identification Of Key DNA Elements Involved In promoter Recognition By Mxr1p , A key Regulator Of Methanol Utilisation Pathway In Pichia PastorisKranthi, Balla Venkata 01 1900 (has links)
The methylotrophic yeast Pichia pastoris is widely used for recombinant protein production due to its ability to grow to high cell densities as well as possession of an inducible methanol utilization pathway (MUT). The expression of genes encoding enzymes of the MUT pathway is very tightly regulated. These genes are turned on when methanol but not glucose is used as the sole carbon source. Thus, P. pastoris cells can be grown to high densities in glucose containing medium and expression of genes of MUT pathway can be turned on by changing the carbon source to methanol. This strategy is widely used for recombinant protein production wherein the gene of interest is cloned downstream of the methanol-inducible promoter of the gene encoding the first enzyme of the MUT pathway, alcohol oxidase I (AOXI). Despite production of a large number of recombinant proteins using the AOXI promoter, the mechanism of transcriptional activation of AOXI is not very well understood. It is only recently that a zinc finger protein known as Mxr1p (methanol expression regulator 1) was shown to play a key role in the regulation of AOXI as well as other genes of methanol utilization pathway (1) P. pastoris strains that do not express Mxr1p (mxr1) are unable to grow on peroxisomal substrates such as methanol and oleic acid. Methanol-inducible expression of genes involved in MUT pathway as well as those involved in peroxisome biogenesis (peroxins,) is severely impaired in mxr1 strains. While Mxr1p is constitutively expressed in cells cultured on glucose as well as methanol, it is cytosolic in glucose-grown cells, but nuclear in methanol-grown cells (1). The exact nucleotide sequence to which Mxr1p binds and regulates the expression of genes of MUT pathway is not known. The aim of this thesis is to map the Mxr1p binding sites in the promoters of methanol-inducible genes of P. pastoris.
As a first step towards understanding the mechanism of transcriptional regulation of AOXI and other methanol inducible genes of P. pastoris by Mxr1p, the N-terminal region comprising of 150 amino acids, including the zinc finger DNA binding domain of Mxr1p was cloned into an E. coli expression vector and the recombinant protein was purified from E. coli cells. This recombinant protein (referred to as Mxr1p in this study) was used in an electrophoretic mobility shift assay (EMSA) to identify Mxr1p binding sites in the AOXI promoter. EMSA was carried out with sixteen different oligonucleotides spanning AOXI promoter region between -940 and -114 bp. Such studies led to the identification of six Mxr1p binding sites in AOXI promoter. Using a combination of DNase I footprinting as well as EMSA with chimeric double stranded oligonucleotides, the minimal Mxr1p binding site was identified as a 20 bp DNA sequence containing a core 5’CYCC 3’ sequence. Using methylation interference as well as extensive mutagenesis studies, nucleotides critical for Mxr1p binding were identified.
Comparative analysis of Mxr1p binding sites identified in our study with the AOXI promoter deletion studies of Hartner et al (2) suggested that the Mxr1p binding sites identified in our study are likely to function as methanol-inducible enhancers in vivo, since deletion of AOXI promoter regions comprising Mxr1p binding sites results in a significant loss of methanol-inducible promoter activity. Thus, Mxr1p binding sites are likely to function as Mxr1p response elements (MXREs) in vivo.
Mxr1p is considered to be the P. pastoris homologue of S. cerevisiae Adr1p (alcohol dehydrogenase II [ADH2] synthesis regulator). Adr1p is a key regulator of S. cerevisiae genes involved in the metabolism of glycerol, ethanol and oleic acid. The DNA binding domains of Adr1p and Mxr1p share 82% similarity and 70% identity. We therefore examined whether Mxr1p can bind to the Adr1p binding site of ADH2 promoter(ADH2-UAS1). Our studies indicate that Mxr1p does not bind to ADH2-UAS1. Interestingly, a single point mutation restores Mxr1p binding to ADH2-UAS1.
Since Mxr1p is involved in the regulation of a number of genes including AOXI, we examined whether promoters of other Mxr1p-regulated genes also harbour MXREs similar to those identified in AOXI promoter. The promoters of genes encoding dihydroxyacetone synthase (DHAS) and peroxin 8 (PEX8) were chosen for this purpose. A detailed analysis of Mxr1p binding to these promoter sequences led to the conclusion that DHAS and PEX8 promoters also harbour Mxr1p binding sites similar to those of AOXI promoter. Based on these studies, we have derived a consensus sequence for Mxr1p binding.
This study is the first report on detailed characterization of Mxr1p binding sites in three methanol-inducible promoters of P. pastoris and thus provides the molecular framework by which this transcription factor functions as a master regulator of genes involved in methanol utilization pathway of P. pastoris. Our study provides the blue print for mapping Mxr1p binding sites in the promoters of other Mxr1p-regulated genes.
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Structural and functional study of efflux pumps involved in drug resistanceMartinez Jaramillo, Lorena Marcela 14 February 2014 (has links) (PDF)
Resistance to chemotherapy is partly due to efflux pumps expressed in the plasma membrane which prevents the accumulation of anticancer, antiviral, antifungal and antibacterial drugs in target cells. Three human ABC transporters are particularly involved in MDR phenotype: P-gp/ABCB1, MRP1/ABCC1 and BCRP/ABCG2. Among the different approaches used to overcome the resistance linked to these transporters, the development of non-substrate drugs MDR-ABC transporters has been described. Here, new class of HIV-1 protease inhibitors not recognized by P-gp/BCRP were identified, promising to be attractive candidates to HAART therapy. Since the determination of the X-ray structures in different conformations is a key point to understand how MDR-ABC transporters translocate drugs across the plasma membrane, the crystal structures of three inward-facing conformations of mouse P-gp were resolved. One structure has a camel nanobody bound to the C-terminal side of the first nucleotide-binding domain, revealing a unique epitope on P-gp and freezing a new open-inward conformation. Finally, the enzymatic characterization of two inhibitors co-crystallized with the mouse P-gp has allowed to localize two main binding sites by which drugs efflux occurs. These results bring new findings of the drug-efflux mechanism and offer the possibility to target more precisely those sites to develop modulators of this pump
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Probing metal and substrate binding to metallo-[beta]-lactamase ImiS from Aeromonas sobria using site-directed mutagenesisChandrasekar, Sowmya. January 2004 (has links)
Thesis (M.S.)--Miami University, Dept. of Chemistry and Biochemistry, 2004. / Title from first page of PDF document. Includes bibliographical references (p. 57-64).
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Probing the dNTP Binding Region of <em>Bacillus subtilis</em>: DNA Polymerase III with Site-Directed Inhibitors: A DissertationButler, Michelle Marie 13 March 1992 (has links)
6-(p-Hydroxyphenylhydrazino) uracil (H2-HPUra) is a selective and potent inhibitor of the replication-specific DNA polymerase III (pol III) of Gram+ bacteria such as Bacillus subtilis. Although a pyrimidine, H2-HPUra derives its inhibitory activity from its specific capacity to mimic the purine nucleotide, dGTP. The project described in this thesis dissertation involves the use of H2-HPUra-like inhibitors to probe the structure and function of the pol III active site. It consists of two separate problems which are summarized below.
Production of a potent bona fide dGTP form of inhibitor. A method was devised to successfully convert the H2-HPUra inhibitor prototype to a bona fide purine, using N2-benzyl guanine as the basis. Structure-activity relationships of benzyl guanines carrying a variety of substituents on the aryl ring identified N2-(3,4-dichlorobenzyl) guanine (DCBG) as a compound equivalent to H2-HPUra with respect to potency and inhibitor mechanism. DCBdGTP, the 2'-deoxyribonucleoside 5'-triphosphate form of DCBG, was synthesized and characterized with respect to its action on wild-type and mutant forms of pol III. DCBdGTP acted on pol III by the characteristic inhibitor mechanism and formally occupied the dNTP binding site with a fit which permitted its polymerization. The latter experiment identified the site for the binding of the inhibitor's aryl moiety as a distinct site located at a distance of approximately 6-7 Å from the base-paired 2-NH group of a bound dGTP.
Attempt to covalently label amino acid residue 1175, a putative participant in inhibitor binding. Azp-12, a point mutation of serine 1175, yields a form of pol III whose inhibitior sensitivity varies specifically as a function of the composition of the para substituent of the inhibitor's aryl ring. On the basis of the latter behavior, residue 1175 was hypothesized to be a residue directly involved in the binding of the inhibitor's aryl moiety. To test this hypothesis, residue 1175 was specifically mutated to either cysteine or lysine, each of which presents a side chain amenable to covalent bond formation with appropriately reactive inhibitor forms. Of the two mutant pol III forms, only the cysteine form (pol III-cys) was catalytically active. The kinetic properties and inhibitor sensitivity profile of pol III-cys identified it as a target suitable for potentially irreversible inhibitor forms containing the following groups in the meta position of the aryl ring: -CH2Br, -CH2C1, and -CH2SH. None of the several inhibitors tested selectively or irreversibly inactivated pol III-cys. Possible bases for the failure of this group of inhibitors and for the redesign of more useful covalently reactive inhibitor forms are considered.
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Efeito de 2-aril(heteroaril)-4,5-diidro-1h-imidazóis sobre a atividade da enzima monoamina oxidase in vitro / Effect of 2-aryl-heteroaryl-4,5-dihydro-1h-imidazoles on monoamine oxidase activity in vitro.Anna, Gabriela da Silva Sant 05 August 2008 (has links)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Monoamine oxidase (MAO) is a flavin adenine dinucleotide (FAD)-containing enzyme attached to the mitochondrial outer membrane of neurons, glia, and other cells. Its roles include regulation of the levels of biogenic and xenobiotic amines in the brain and peripheral tissues by catalyzing their oxidative deamination. On the basis of their substrate and inhibitor specificities, two isoforms of MAO have been described (A and B). Due to their role in the metabolism of catecholamines neurotransmitters, MAO-A and MAO-B have long been of pharmacological interest. Accordingly, and reversible and irreversible inhibitors of MAO-A and MAO-B have been used in the clinics to treat
neurological disorders including depression and Parkinson´s disease. Since the demonstration that I2-
imidazoline sites are associated with mitochondrial membranes 15 years ago, several studies have provided evidence that these sites represent regions on MAOs. In line with this view, it has been demonstrated that imidazoline derivatives inhibit MAO activity. This effect has been attributed to a high affinity I2 binding site on MAO-B (I2B) and to a similar lower affinity site on MAO-A (I2A). This study investigated the effect of 4,5-dihydro-1H-imidazole-2-substituted compounds on MAO activity in vitro by spectrophotometric and fluorimetric methods using kynuramine as substrate. Among the compounds that inhibited MAO-A (3c-e, 3j), compound 3d was 73-fold more selective towards MAO-A than MAO-B. Among the compounds that selectively inhibited MAO-B (3g-I, 3k, 3o), imidazoline 3g was shown to be potent with Ki value of 5,3 μM. Some of compounds that selectively bind to I2-sites,
such as 3l (benazoline), 3n (2-BFI), and 3p (BU224) showed good inhibitory activity especially against MAO-B. Imidazolines inhibited MAO-A and MAO-B activities in liver with less selectively than in rat brain. The compounds 3d and 3g reversibly inhibited MAO, and kinetics studies showed that compound 3d and 3g inhibited MAO in a mixed manner (decreased Vmax and increased Km values).
These results confirm that imidazolines inhibit MAO activity and suggest a relationship between I2 binding site and modulation of central MAO / A monoamina oxidase (MAO) é uma enzima que contém o dinucleotídeo adenina-flavina (FAD) e que está presente na membrana externa da mitocôndria de células neuronais, glia e outras células. Seu papel inclui a regulação dos níveis de aminas biogênicas e xenobióticas no cérebro e em
tecidos periféricos pela desaminação oxidativa. Com base na especificidade a substrato e inibidores, são descritas duas isoformas da MAO (A e B). Devido aos seus papéis no metabolismo das catecolaminas neurotransmissoras, a MAO-A e a MAO-B são consideradas farmacologicamente
interessantes, e inibidores reversíveis e irreversíveis destas isoformas são usados clinicamente para tratar doenças neurológicas incluindo depressão e doença de Parkinson. Nos últimos 15 anos, desde a demonstração que sítios I2 estão associados com frações da membrana mitocondrial, muitos
estudos provem evidências de que estes sítios representam regiões da MAO. Além disso, alguns estudos têm demonstrado que derivados imidazolínicos são capazes de inibir a atividade da MAO. Este efeito tem sido atribuído a sítios I2 de alta afinidade na MAO-B (I2B) e a um sítio similar de baixa
afinidade na MAO-A (I2A). Assim, este estudo teve como objetivo investigar o efeito in vitro de compostos 4,5-diidro-1H-imidazol-2-substituídos sobre a atividade da enzima monoamina oxidase através de métodos espectrofotométricos e fluorimétricos usando quinuramina como substrato. Entre
os compostos estudados que inibiram preferencialmente a MAO-A (3c-e, 3j) apenas o composto 3d foi seletivo, apresentando um Ki para a MAO-A de aproximadamente 73 vezes menor do que seu Ki para MAO-B. Entre os compostos obtidos que seletivamente inibiram MAO-B (3g-l, 3K, 3o), apenas a imidazolina 3g mostrou ser potente, com valores de Ki de 5,3 μM. Alguns compostos que exercem ligação potente e seletiva à sítios I2, como o 3l (benazolina), 3n (2-BFI) e 3p (BU224) mostraram boa atividade inibitória especialmente contra MAO-B. Em fígado de ratos, as imidazolinas inibiram com
menos seletividade a MAO-A e MAO-B quando comparado com cérebro de ratos. Os compostos 3d e 3g inibiram a MAO de maneira reversível e apresentaram inibição de natureza mista (diminuindo o valor de Vmáx e aumentando o valor de Km) sobre a enzima MAO. Estes resultados confirmam que
drogas imidazolinas podem inibir a atividade da MAO e sugerem uma relação entre sítios I2 e a modulação da atividade da enzima.
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