Modelagem molecular da Chiquimato quinase de Mycobacterium leprae

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Bioinformática estrutural aplicada ao estudo de proteínas alvo do genoma do Mycobacterium tuberculosis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Suscetibilidade e interação de proteínas Cry1 e Vip3A de Bacillus thuringiensis para o controle de lepidópteros-praga

Pós-graduação em Agronomia (Genética e Melhoramento de Plantas) - FCAV

Structural and functional evidence for membrane docking and disruption sites on phospholipase A2-like proteins revealed by complexation with the inhibitor suramin

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The study the properties structurals and elastics of phases lamellar of lipid.

Lamellar systems composed of lipid bilayers have been widely used as model system for investigating properties of biological membranes, interactions between membranes and with biomolecules. The composition of the membrane determines its three dimensional shape and its properties such as rigidity and compressibility which play an important role on membrane fusion, protein adhesion, interactions between proteins, etc. We present a systematic study of a lamellar system composed of lecithin and a commercial co-surfactant (Simusol), which is a mixture of ethoxylated fatty acids. Using X ray scattering and a new procedure to fit X-ray experimental data, we determine relevant parameters characterizing the lamellar structure, varying membrane composition from 100% of lecithin to 100% of Simulsol. We present experimental data illustrating the swelling behavior for the membrane of different compositions and the respective behavior of the Caillé parameter. From and GISAXS experiments on oriented films under controlled humidity we investigate the compressibility of the lamellar phase and the effect of incorporating co-surfactant. Combining the Caillé parameter and compressibility studies we determine the bending rigidity of membranes. The results obtained with this experimental approach and new procedure to fit X-ray experimental allows us to identify structural changes in the bilayer depending both on hydration and co-surfactant content, with implications on elastic properties of membranes.

Modulation of epidermial growth factor receptor signaling in colon adenocarcinoma

The use of agents targeting EGFR represents a new frontier in colon cancer therapy. Among these, monoclonal antibodies (mAbs) and EGFR tyrosine kinase inhibitors (TKIs) seemed to be the most promising. However they have demonstrated low utility in therapy, the former being effective at toxic doses, the latter resulting inefficient in colon cancer. This thesis work presents studies on a new EGFR inhibitor, FR18, a molecule containing the same naphtoquinone core as shikonin, an agent with great anti-tumor potential. In HT-29, a human colon carcinoma cell line, flow cytometry, immunoprecipitation, and Western blot analysis, confocal spectral microscopy have demonstrated that FR18 is active at concentrations as low as 10 nM, inhibits EGF binding to EGFR while leaving unperturbed the receptor kinase activity. At concentration ranging from 30 nM to 5 μM, it activates apoptosis. FR18 seems therefore to have possible therapeutic applications in colon cancer. In addition, surface plasmon resonance (SPR) investigation of the direct EGF/EGFR complex interaction using different experimental approaches is presented. A commercially available purified EGFR was immobilised by amine coupling chemistry on SPR sensor chip and its interaction to EGF resulted to have a KD = 368 ± 0.65 nM. SPR technology allows the study of biomolecular interactions in real-time and label-free with a high degree of sensitivity and specificity and thus represents an important tool for drug discovery studies. On the other hand EGF/EGFR complex interaction represents a challenging but important system that can lead to significant general knowledge about receptor-ligand interactions, and the design of new drugs intended to interfere with EGFR binding activity.

Selektiv deblockierbare 2,6-Diamino-2,6-didesoxy-D-glucose-Scaffolds für die kombinatorische Synthese potentieller RNA-Liganden

Aminoglydosid-Antibiotika wie Neomycin B oder Cyclopeptid-Antibiotike wie Viaomycin sind dafür bekannt, daß sie selektiv an RNA binden können. Diese Interaktionen beruhen sowohl auf elektrostatischen Wechselwirkungen als auch auf H-Brücken-Bindungen. Des weiteren ist die definierte räumliche Anordnung von Donor- und Akzeptor-Resten in den Strukturen der RNA-Liganden wichtig für die Affinität. Eine Möglichkeit natürliche RNA-Liganden zu imitieren ist der Einsatz polyfunktioneller Template wie zum Beispiel das 2,6-Diamino-2,6-didesoxy-D-glucose-Scaffold. Mit Hilfe dieser Scaffolds können dann verschiedene positv geladene Reste und Donatoren sowie Akzeptoren für H-Brücken-Bindungen oder auch Interkalatoren räumlich definiert präsentiert werden. Für die unabhängige Funktionalisierung einer jeden Position ist ein Satz orthogonal stabiler Schutzgruppen nötig, wobei eine Hydroxylguppe durch einen Anker ersetzt wird, der eine Anbindung des Scaffolds an einen polymeren Träger ermöglicht. Das neu entwickelte 2,6-Diamino-2,6-didesoxy-D-glucose-Scaffold ist das erste Monosaccharid-Templat, das in allen fünf Positionen mit orthogonal stabilen Schutzgruppen blockiert ist. Alle Positionen könne in beliebiger Reihenfolge selektiv deblockiert und anschließend derivatisiert werden. Das Scaffold kann mit Aminosäuren, Guanidinen oder Interkalatoren umgesetzt werden, um so natürlich vorkommende RNA-bindende Aminoglycoside oder Peptide zu imitieren. Aufbauend auf diesem Monosaccharid-Templat wurde eine Bibliothek von über 100 potentiellen RNA-Liganden synthetisiert, die im Rahmen des Sonderforschungsbereichs 579 (RNA-Liganden-Wechselwirkungen) in Zellassays auf ihre Fähigkeit zur Hemmung der Tat/TAR-Wechselwirkung untersucht wurden, wobei bis jetzt 9 Verbindungen mit einer hemmenden Wirkung im micromolaren Bereich gefunden wurden.

Nanoscale effects and applications of self-organized nanostructured thin films

A nanostructured thin film is a thin material layer, usually supported by a (solid) substrate, which possesses subdomains with characteristic nanoscale dimensions (10 ~ 100 nm) that are differentiated by their material properties. Such films have captured vast research interest because the dimensions and the morphology of the nanostructure introduce new possibilities to manipulating chemical and physical properties not found in bulk materials. Block copolymer (BCP) self-assembly, and anodization to form nanoporous anodic aluminium oxide (AAO), are two different methods for generating nanostructures by self-organization. Using poly(styrene-block-methyl methacrylate) (PS-b-PMMA) nanopatterned thin films, it is demonstrated that these polymer nanopatterns can be used to study the influence of nanoscale features on protein-surface interactions. Moreover, a method for the directed assembly of adsorbed protein nanoarrays, based on the nanoscale juxtaposition of the BCP surface domains, is also demonstrated. Studies on protein-nanopattern interactions may inform the design of biomaterials, biosensors, and relevant cell-surface experiments that make use of nanoscale structures. In addition, PS-b-PMMA and AAO thin films are also demonstrated for use as optical waveguides at visible wavelengths. Due to the sub-wavelength nature of the nanostructures, scattering losses are minimized, and the optical response is amenable to analysis with effective medium theory (EMT). Optical waveguide measurements and EMT analysis of the films’ optical anisotropy enabled the in situ characterization of the PS-b-PMMA nanostructure, and a variety of surface processes within the nanoporous AAO involving (bio)macromolecules at high sensitivity.

Structural characterisation of tBLMs

Biological membranes are one of the vital key elements of life but are also highly complex architectures. Therefore, various model membrane systems have been developed to enable systematic investigations of different membrane related processes. A biomimetic model architecture should provide a simplified system, which allows for systematic investigation of the membrane while maintaining the essential membrane characteristics such as membrane fluidity or electrical sealing properties. This work has been focused on two complementary parts. In a first part, the behaviour of the whey protein ß-lactoglobulin (ßlg) at a membrane interface has been investigated. Protein-lipid interactions have been studied using Langmuir monolayers at the air-water interface and tethered bilayer lipid membranes. A combination of different surface analytical techniques such as surface plasmon spectroscopy, neutron reflectivity and electrochemical techniques allowed for a detailed analysis of the underlying processes. Those experiments showed that the protein adsorbed in native confirmation, slightly flattened, to hydrophobic monolayers. If hydrophilic bilayers with defects were present, ßlg penetrated the upper layer. Interactions with phospholipids were only observed if the protein was denatured beforehand. Experiments at the air-water interface showed a more rigid conformation of the protein at acidic pH compared to alkaline pH. In the second part of this work, the structure of different model membrane systems has been investigated. Solid supported membrane systems have been established as powerful biomimetic architectures, which allow for the systematic investigation of various membrane related processes. Additionally, these systems have been proposed for biosensing applications. Tethered bilayer lipid membranes (tBLMS) are one type of solid supported membranes. The structure of the anchor lipid that tethers the membrane to the solid support has a significant impact on the membrane properties. Especially the sub-membrane part, which is defined by the spacer group, is important for the biological activity of incorporated membrane proteins. Various anchor lipids have been synthesised with different spacer and anchor groups. An increase of the spacer length led to a direct increase of the water reservoir beneath the membrane. However, this elongation also resulted in an amplified roughness of the monolayer and subsequently to diminished mechanical and electrical bilayer qualities. Additionally, a cholesterol-spacer had been designed to modulate the membrane fluidity. Model membrane systems with additional cholesterol-spacer or upper bilayer leaflets with additional cholesterol also exhibited an increased water reservoir with only slightly diminished mechanical and electrical abilities. Both parts show that tBLMs are very effective model systems that can be applied as biomimetic platforms to study for example lipid-protein interactions. They also enable the incorporation of ion channels and allow for potential biosensing application.

Synthese von Sialyl-Lewis-X-Mimetika durch stereoselektive ortho-C-Glycosylierung von Phenolen

Ziel der Arbeit war es, Sialyl-LewisX-Mimetika auf Basis ortho-C-glycosylierter Phenole als Inhibitoren für die Selektin-Ligand-Wechselwirkungen zu synthetisieren. Dazu wurde zunächst die Stereoselektivität der ortho-C-Mannosylierung untersucht. Dabei wurde gezeigt, dass bei der Umsetzung von Phenolen mit dem benzylgeschützten Mannosyl-trichloracetimidat in Gegenwart von TMSOTf selektiv das β-C-Mannosid erhalten wurde. Gleichzeitig konnte anhand der NMR-spektroskopischen Untersuchungen nachgewiesen werden, dass die in der Literatur beschriebenen α-C-Mannoside von Phenolen tatsächlich β-konfiguriert sind. Wenn Naphthole als Glycosylakzeptoren verwendet wurden, konnten durch Modifikation des Promotors auch die für die Synthese der Mimetika benötigten α-C-Mannoside erhalten werden, wobei ZnCl2 als Promotor die besten Ergebnisse lieferte. Allerdings zeigten die synthetisierten α-C-Mannoside und α-C-Galactoside eine Inversion des Pyranoseringes und lagen in der ungewöhnlichen 1C4-Konformation vor.rnAnschließend konnte auf diese Weise das durch Docking-Studien gefundene Mimetikum (2S)-3-Cyclohexyl-2-[7-hydroxy-8-(α-D-mannosyl)naphthalin-2-yloxy]propionsäure syntheti-siert werden. Es besaß jedoch in Zelladhäsionstests keine ausreichende Aktivität bei der Inhibierung der Selektin-Ligand-Wechselwirkung. Bei den ursprünglichen Dockingstudien war allerdings von der gewohnten 4C1-Konformation ausgegangen worden. Spätere NMR-Experimente und DFT-Berechnungen zeigten, dass das Mimetikum tatsächlich in der 1C4-Konformation vorlag und es deshalb nicht aktiv war. Die synthetisierten Stereo- und Regioisomere zeigten in Zelladhäsionstests ebenfalls keine Aktivität.rnVersuche, die α-1-C-Mannosylnaphthole zu den benötigten 1-C-2-O-Diglycosyl-naphthalinen umzusetzen waren nicht erfolgreich, da die phenolische OH-Gruppe sterisch zu sehr abgeschirmt war, um unter milden Reaktionsbedingungen glycosyliert zu werden, bzw. die α-1-C-Mannosylnaphthaline unter drastischeren Reaktionsbedingungen nicht stabil waren. Daher wurde 1-(2′,3′,4′,6′-Tetra-O-benzyl-β-D-galactopyranosyl)-2-naphthol mit 2,3,4,6-Tetra-O-acetyl-α-D-mannopyranosyl-trichloracetimidat in Gegenwart von TMSOTf zum ersten synthetischen 1-C-2-O-Diglycosyl-phenol umgesetzt. Nach Abspaltung der Schutzgruppen sollte das erhaltene 1-Galactosyl-2-O-mannosyl-naphthalin enzymatisch zum Sialyl-LewisX-Mimetikum verlängert werden. Es wurde vom Enzym jedoch nicht als Substrat erkannt. Versuche zur chemischen Anbindung des Säurebausteins stehen noch aus.rn

Modulation of signal transduction by vitamin E

The ability of vitamin E to modulate signal transduction and gene expression has been observed in numerous studies; however, the detailed molecular mechanisms involved are often not clear. The eight natural vitamin E analogues and synthetic derivatives affect signal transduction with different potency, possibly reflecting their different ability to interact with specific proteins. Vitamin E modulates the activity of several enzymes involved in signal transduction, such as protein kinase C, protein kinase B, protein tyrosine kinases, 5-, 12-, and 15-lipoxygenases, cyclooxygenase-2, phospholipase A2, protein phosphatase 2A, protein tyrosine phosphatase, and diacylglycerol kinase. Activation of some these enzymes after stimulation of cell surface receptors with growth factors or cytokines can be normalized by vitamin E. At the molecular level, the translocation of several of these enzymes to the plasma membrane is affected by vitamin E, suggesting that the modulation of protein-membrane interactions may be a common theme for vitamin E action. In this review the main effects of vitamin E on enzymes involved in signal transduction are summarized and the possible mechanisms leading to enzyme modulation evaluated. The elucidation of the molecular and cellular events affected by vitamin E could reveal novel strategies and molecular targets for developing similarly acting compounds.

Deregulated ephrin-B2 expression in the mammary gland interferes with the development of both the glandular epithelium and vasculature and promotes metastasis formation

Eph receptor tyrosine kinases and their membrane-bound ephrin ligands play key roles during morphogenesis and adult tissue homeostasis. Receptor-ligand interactions result in forward and reverse signalling from the receptor and ligand respectively. To delineate the role(s) of forward and reverse signalling in mammary gland biology we have established transgenic mice exhibiting mammary epithelial-specific overexpression of either the native ephrin-B2 or a dominant negative ephrin-B2 mutant incapable of reverse signalling. During pregnancy and lactation overexpression of the native ephrin-B2 resulted in precocious differentiation, whereas overexpression of mutated ephrin-B2 caused delayed epithelial differentiation and in disturbed tissue architecture. Both transgenes affected also mammary vascularisation. Whereas ephrin-B2 induced superfluous but organised capillaries, mutant ephrin-B2 overexpression resulted in an irregular vasculature with blind-ending capillaries. Mammary tumours were not observed in either transgenic line, however, the crossing with NeuT transgenic animals revealed that mutated ephrin-B2 expression significantly accelerated tumour growth and imposed a metastatic phenotype.

An Sp1/Sp3 binding polymorphism confers methylation protection.

Hundreds of genes show aberrant DNA hypermethylation in cancer, yet little is known about the causes of this hypermethylation. We identified RIL as a frequent methylation target in cancer. In search for factors that influence RIL hypermethylation, we found a 12-bp polymorphic sequence around its transcription start site that creates a long allele. Pyrosequencing of homozygous tumors revealed a 2.1-fold higher methylation for the short alleles (P<0.001). Bisulfite sequencing of cancers heterozygous for RIL showed that the short alleles are 3.1-fold more methylated than the long (P<0.001). The comparison of expression levels between unmethylated long and short EBV-transformed cell lines showed no difference in expression in vivo. Electrophorectic mobility shift assay showed that the inserted region of the long allele binds Sp1 and Sp3 transcription factors, a binding that is absent in the short allele. Transient transfection of RIL allele-specific transgenes showed no effects of the additional Sp1 site on transcription early on. However, stable transfection of methylation-seeded constructs showed gradually decreasing transcription levels from the short allele with eventual spreading of de novo methylation. In contrast, the long allele showed stable levels of expression over time as measured by luciferase and approximately 2-3-fold lower levels of methylation by bisulfite sequencing (P<0.001), suggesting that the polymorphic Sp1 site protects against time-dependent silencing. Our finding demonstrates that, in some genes, hypermethylation in cancer is dictated by protein-DNA interactions at the promoters and provides a novel mechanism by which genetic polymorphisms can influence an epigenetic state.

Studies on gene expression within germinal centers

During T cell dependent immune responses, the acquisition of B cell memory from naïve cells takes place within a highly specialized microenvironment: The germinal centers (GC) of the secondary lymphoid organs. The GC reaction is a tightly regulated process in which the balance between survival and death is mediated by signals transduced through ligation of critical costimulatory molecules such as CD40 and CD154. While most cognate receptor-ligand interactions occur between T-cells and antigen (Ag)-presenting cells (APC) such as B-cells, evidence of homotypic B cell interactions has emerged. Despite the progress in our understanding of the reaction, several questions remain: (1) What determines the concomitant expression of CD40 and its ligand CD154 by GC B-cells? (2) Which molecules are responsible for inducing GC-B cell survival? and (3) how can cognate T-cell help be recruited into the organized structure of GCs? ^ Because the expression of costimulatory and survival molecules is predominant at distinct Ag-dependent maturation stages, we hypothesized the existence of stage specific gene expression responsible for the regulation of the GC reaction. Our studies reveal several novel genes whose expression may be critical for the GC reaction. The discovery of AKNA reveals the mechanism behind homotypic B cell CD40 and CD40 ligand interactions, which can explain the costimulatory signaling to GC B cells in the absence of T cells. Additionally, the identification of the pro-survival molecule PRELI may provide a novel mechanism for the survival of Ag-selected B cells. We propose that PRELI and its phylogenic homologues represent a novel family of proteins responsible for the protection of cells against caspase-independent apoptosis. Furthermore, we show that GC B cells actively participate in the recruitment of T cells through the secretion of CC and CxC chemokines, thus supporting their mutual involvement in cognate interactions. ^

The role of plasmacytoid dendritic cells in the regulation of adaptive immunity

Plasmacytoid dendritic cells (pDCs) selectively express TLR7 which allows them to respond to RNA viruses and TLR9 which allows them to respond to DNA viruses and CpG oligonucleotides. Upon exposure to virus pDCs produce vast amounts of type I interferon (IFN) directly inhibiting viral replication and contributing to the activation of other immune cells. The ability of pDCs to promote B and T cell differentiation through type I IFN has been well documented although the role of additional factors including tumor necrosis factor (TNF) family members has not been thoroughly addressed. Here the expression of selected TNF family members in pDCs was examined and the role of TNF receptor-ligand interactions in the regulation of B and T lymphocyte growth and differentiation by pDCs was investigated. Upon stimulation with CpG-B, pDCs exhibit strong and stable expression of CD70, a TNF family ligand that binds to its receptor CD27 on memory B cells and promotes plasma cell differentiation and Ig secretion. Using an in vitro pDC/B cell co-culture system, it was determined that CpG-B-stimulated pDCs induce the proliferation of CD40L-activated human peripheral B cells and Ig secretion. This occurs independently of IFN and residual CpG, and requires physical contact between pDCs and B cells. CpG-stimulated pDCs induce the proliferation of both naive and memory B cells although Ig secretion is restricted to the memory subset. Blocking the interaction of CD70 with CD27 using an antagonist anti-CD70 antibody reduces the induction of B cell proliferation and IgG secretion by CpG-B-stimulated pDCs. Published studies have also indicated an important role for CD70 in promoting the expansion of CD4+ and CD8+ T cells and the development of effector function. CpG-B-stimulated pDCs induce naïve CD4+ T cell proliferation and production of multiple cytokines including IFN-γ, TNF-α, IL-10, IL-4, IL-5 and IL-13. Blocking the function of CD70 with an antagonist anti-CD70 antibody significantly reduced the induction of naïve CD4+ T cell proliferation by CpG-B-stimulated pDCs and the production of IL-4 and IL-13. Collectively these data indicate an important role for CD70 in the regulation of B and T lymphocyte growth and differentiation by pDCs. ^