Acyclic permutants of naturally occurring cyclic proteins - Characterization of cystine knot and beta-sheet formation in the macrocyclic polypeptide kalata B1

Kalata B1 is a prototypic member of the unique cyclotide family of macrocyclic polypeptides in which the major structural features are a circular peptide backbone, a triple stranded beta-sheet, and a cystine knot arrangement of three disulfide bonds. The cyclotides are the only naturally occurring family of circular proteins and have prompted us to explore the concept of acyclic permutation, i.e. opening the backbone of a cross-linked circular protein in topologically permuted ways. We have synthesized the complete suite of acyclic permutants of kalata B1 and examined the effect of acyclic permutation on structure and activity. Only two of six topologically distinct backbone loops are critical for folding into the native conformation, and these involve disruption of the embedded ring in the cystine knot. Surprisingly, it is possible to disrupt regions of the p-sheet and still allow folding into native-like structure, provided the cystine knot is intact. Kalata B1 has mild hemolytic activity, but despite the overall structure of the native peptide being retained in all but two cases, none of the acyclic permutants displayed hemolytic activity. This loss of activity is not localized to one particular region and suggests that cyclization is critical for hemolytic activity.

Stabilization of native protein fold by intein-mediated covalent cyclization

A mutant version of the N-terminal domain of Escherichia coli DnaB helicase was used as a model system to assess the stabilization against unfolding gained by covalent cyclization. Cyclization was achieved in vivo by formation of an amide bond between the N and C termini with the help of a split mini-intein. Linear and circular proteins were constructed to be identical in amino acid sequence. Mutagenesis of Phe102 to Glu rendered the protein monomeric even at high concentration. A difference in free energy of unfolding, DeltaDeltaG, between circular and linear protein of 2.3(+/-0.5) kcal mol(-1) was measured at 10degreesC by circular dichroism. A theoretical estimate of the difference in conformational entropy of linear and circular random chains in a three-dimensional cubic lattice model predicted DeltaDeltaG = 2.3 kcal mol(-1), suggesting that stabilization by protein cyclization is driven by the reduced conformational entropy of the unfolded state. Amide-proton exchange rates measured by NMR spectroscopy and mass spectrometry showed a uniform, approximately tenfold decrease of the exchange rates of the most slowly exchanging amide protons, demonstrating that cyclization globally decreases the unfolding rate of the protein. The amide proton exchange was found to follow EX1 kinetics at near-neutral pH, in agreement with an unusually slow refolding I measured by stopped-flow circular dichroism. rate of less than 4 min(-1) The linear and circular proteins differed more in their unfolding than in their folding rates. Global unfolding of the N-terminal domain of E. coli DnaB is thus promoted strongly by spatial separation of the N and C termini, whereas their proximity is much less important for folding. (C) 2005 Elsevier Ltd. All rights reserved.

Síntese e fotosensibilização de nanotubos de titanatos

Nesta tese é descrita a preparação de nanotubos de titanatos (TNT) via síntese hidrotérmica alcalina, usando uma nova metodologia que evita a utilização de TiO2 cristalino como precursor. Foi estudada a influência da substituição sódio/protão na estrutura, morfologia e propriedades ópticas dos materiais preparados. Os resultados mostraram que a substituição Na+ → H+ resulta numa redução na distância intercamadas dos TNTs, tendo sido medidos valores entre 1.13±0.03 nm e 0.70±0.02 nm para aquele parâmetro. O comportamento óptico dos TNTs foi estudado na região UV-vis, estimando-se um hiato óptico de energia 3.27±0.03 eV para a amostra com maior teor de sódio enquanto que para a amostra protonada foi determinado um valor de 2.81±0.02 eV. Estes valores mostram que a troca iónica Na+ → H+ teve influência no desvio da banda de absorção dos TNTs para a região do visível próximo. A actividade fotocatalítica dos TNTs na degradação do corante rodamina 6G (R6G) foi posteriormente estudada. Verificou-se que, apesar de a amostra com maior teor de sódio ter sido a que exibiu maior capacidade para adsorver o R6G, foi a amostra protonada que apresentou a actividade catalítica mais elevada na fotodegradação deste corante. Numa segunda fase, e com o objectivo de preparar novos materiais nanoestruturados fotosensíveis, procedeu-se à decoração dos TNTs protonados com semicondutores (SC) nanocristalinos usando um método novo. Para o efeito os TNTs foram decorados com nanocristalites de ZnS, CdS e Bi2S3. Foi estudada a influência do tipo de semicondutor na estrutura, morfologia e propriedades ópticas dos SC/TNTs obtidos. Verificou-se que, para qualquer dos semicondutores usados no processo de decoração, a estrutura dos TNTs é preservada e não ocorre segregação do SC. Verificou-se ainda que a morfologia dos nanocompósitos preparados depende fortemente da natureza do semicondutor. No que respeita ao comportamento óptico destes materiais, foram determinados hiatos ópticos de energia 3.67±0.03 eV, 2.47±0.03 eV e 1.35±0.01 eV para as amostras ZnS/TNT, CdS/TNT e Bi2S3/TNT, respectivamente. Estes resultados mostram que através do processo de decoração de TNTs com semicondutores podem ser preparados materiais nanocompósitos inovadores, com propriedades ópticas novas e/ou pré-definidas numa gama alargada do espectro electromagnético.

Desenvolvimento de processo de depilação de pele caprina sem destruição do pêlo e avaliação do seu impacto ambiental

O meio ambiente é uma grande preocupação mundial existindo cada vez mais imposições legais no sentido de o proteger. Torna-se assim necessário que as indústrias adoptem e desenvolvam processos alternativos mais limpos. A indústria de curtumes transforma a pele animal em couro, material resistente à putrefacção e com estabilidade térmica suficiente para ser manufacturado nas indústrias do calçado, estofos, vestuário e marroquinaria. A transformação referida é efectuada através duma série de processos entre os quais o caleiro, processo que visa depilar a pele e promover o relaxamento da estrutura fibrilar, tem um papel importante. O processo de caleiro produz um efluente bastante poluente. Tendo em conta esse facto, este trabalho teve como objectivo desenvolver processos de depilação de pele caprina sem destruição do pêlo, com vista à redução da quantidade de sulfureto e sulfidrato de sódio utilizada e da carga poluente do efluente. Além disso, o processo permite a recuperação do pêlo e este pode ser reaproveitado como fertilizante orgânico, hidrolisado de queratina, compostagem, etc. Todo o trabalho foi realizado tomando por base um processo de caleiro padrão utilizado industrialmente, alterando-o de forma a obter um processo de caleiro óptimo de depilação sem destruição do pêlo com e sem utilização de enzimas. Numa primeira fase, desenvolveu-se um processo de depilação sem destruição do pêlo normalmente utilizado para a pele de bovino que foi adaptado com resultados positivos, designado de processo sem enzimas. Numa segunda fase, desenvolveu-se um processo enzimático em que se utilizou uma protease (Erhavit DMC), uma lipase (Defat 50) e uma amilase (Mayzme SD-L); este processo deu bons resultados tal como o anterior. A redução da quantidade de sulfureto de sódio foi de 33% e 53% para o processo sem enzimas e processo com enzimas, respectivamente, em relação ao processo padrão. O efeito dos processos na carga poluente, à escala piloto, comprova uma redução de 37% nos SST, 37% nos SDT, 60% na CQO, 9% no S2- e 73% no Azoto para o processo sem enzimas e uma redução de 93% nos SST, 63% nos SDT, 69% na CQO, 69% no S2- e 83% no Azoto para o processo com enzimas, quando comparados com o processo padrão. . Uma análise de custos, com incidência apenas nos agentes químicos utilizados, permitiu concluir a existência de uma redução de custos anuais de 30% para o processo com enzimas e de 13% para o processo sem enzimas, quando comparados com o processo padrão. Como conclusão, os processos desenvolvidos apresentam um grande potencial para serem explorados industrialmente.

Innovative method for carbon dioxide determination in human postmortem cardiac gas samples using headspace-gas chromatography-mass spectrometry and stable labeled isotope as internal standard.

A novel approach to measure carbon dioxide (CO2) in gaseous samples, based on a precise and accurate quantification by (13)CO2 internal standard generated in situ is presented. The main goal of this study was to provide an innovative headspace-gas chromatography-mass spectrometry (HS-GC-MS) method applicable in the routine determination of CO2. The main drawback of the GC methods discussed in the literature for CO2 measurement is the lack of a specific internal standard necessary to perform quantification. CO2 measurement is still quantified by external calibration without taking into account analytical problems which can often occur considering gaseous samples. To avoid the manipulation of a stable isotope-labeled gas, we have chosen to generate in situ an internal labeled standard gas ((13)CO2) on the basis of the stoichiometric formation of CO2 by the reaction of hydrochloric acid (HCl) with sodium hydrogen carbonate (NaH(13)CO3). This method allows a precise measurement of CO2 concentration and was validated on various human postmortem gas samples in order to study its efficiency.

Molecular modeling study of the binding and signaling properties of the TCRpMHC complex

The activation of the specific immune response against tumor cells is based on the recognition by the CD8+ Cytotoxic Τ Lymphocytes (CTL), of antigenic peptides (p) presented at the surface of the cell by the class I major histocompatibility complex (MHC). The ability of the so-called T-Cell Receptors (TCR) to discriminate between self and non-self peptides constitutes the most important specific control mechanism against infected cells. The TCR/pMHC interaction has been the subject of much attention in cancer therapy since the design of the adoptive transfer approach, in which Τ lymphocytes presenting an interesting response against tumor cells are extracted from the patient, expanded in vitro, and reinfused after immunodepletion, possibly leading to cancer regression. In the last decade, major progress has been achieved by the introduction of engineered lypmhocytes. In the meantime, the understanding of the molecular aspects of the TCRpMHC interaction has become essential to guide in vitro and in vivo studies. In 1996, the determination of the first structure of a TCRpMHC complex by X-ray crystallography revealed the molecular basis of the interaction. Since then, molecular modeling techniques have taken advantage of crystal structures to study the conformational space of the complex, and understand the specificity of the recognition of the pMHC by the TCR. In the meantime, experimental techniques used to determine the sequences of TCR that bind to a pMHC complex have been used intensively, leading to the collection of large repertoires of TCR sequences that are specific for a given pMHC. There is a growing need for computational approaches capable of predicting the molecular interactions that occur upon TCR/pMHC binding without relying on the time consuming resolution of a crystal structure. This work presents new approaches to analyze the molecular principles that govern the recognition of the pMHC by the TCR and the subsequent activation of the T-cell. We first introduce TCRep 3D, a new method to model and study the structural properties of TCR repertoires, based on homology and ab initio modeling. We discuss the methodology in details, and demonstrate that it outperforms state of the art modeling methods in predicting relevant TCR conformations. Two successful applications of TCRep 3D that supported experimental studies on TCR repertoires are presented. Second, we present a rigid body study of TCRpMHC complexes that gives a fair insight on the TCR approach towards pMHC. We show that the binding mode of the TCR is correctly described by long-distance interactions. Finally, the last section is dedicated to a detailed analysis of an experimental hydrogen exchange study, which suggests that some regions of the constant domain of the TCR are subject to conformational changes upon binding to the pMHC. We propose a hypothesis of the structural signaling of TCR molecules leading to the activation of the T-cell. It is based on the analysis of correlated motions in the TCRpMHC structure. - L'activation de la réponse immunitaire spécifique dirigée contre les cellules tumorales est basée sur la reconnaissance par les Lymphocytes Τ Cytotoxiques (CTL), d'un peptide antigénique (p) présenté à la suface de la cellule par le complexe majeur d'histocompatibilité de classe I (MHC). La capacité des récepteurs des lymphocytes (TCR) à distinguer les peptides endogènes des peptides étrangers constitue le mécanisme de contrôle le plus important dirigé contre les cellules infectées. L'interaction entre le TCR et le pMHC est le sujet de beaucoup d'attention dans la thérapie du cancer, depuis la conception de la méthode de transfer adoptif: les lymphocytes capables d'une réponse importante contre les cellules tumorales sont extraits du patient, amplifiés in vitro, et réintroduits après immunosuppression. Il peut en résulter une régression du cancer. Ces dix dernières années, d'importants progrès ont été réalisés grâce à l'introduction de lymphocytes modifiés par génie génétique. En parallèle, la compréhension du TCRpMHC au niveau moléculaire est donc devenue essentielle pour soutenir les études in vitro et in vivo. En 1996, l'obtention de la première structure du complexe TCRpMHC à l'aide de la cristallographie par rayons X a révélé les bases moléculaires de l'interaction. Depuis lors, les techniques de modélisation moléculaire ont exploité les structures expérimentales pour comprendre la spécificité de la reconnaissance du pMHC par le TCR. Dans le même temps, de nouvelles techniques expérimentales permettant de déterminer la séquence de TCR spécifiques envers un pMHC donné, ont été largement exploitées. Ainsi, d'importants répertoires de TCR sont devenus disponibles, et il est plus que jamais nécessaire de développer des approches informatiques capables de prédire les interactions moléculaires qui ont lieu lors de la liaison du TCR au pMHC, et ce sans dépendre systématiquement de la résolution d'une structure cristalline. Ce mémoire présente une nouvelle approche pour analyser les principes moléculaires régissant la reconnaissance du pMHC par le TCR, et l'activation du lymphocyte qui en résulte. Dans un premier temps, nous présentons TCRep 3D, une nouvelle méthode basée sur les modélisations par homologie et ab initio, pour l'étude de propriétés structurales des répertoires de TCR. Le procédé est discuté en détails et comparé à des approches standard. Nous démontrons ainsi que TCRep 3D est le plus performant pour prédire des conformations pertinentes du TCR. Deux applications à des études expérimentales des répertoires TCR sont ensuite présentées. Dans la seconde partie de ce travail nous présentons une étude de complexes TCRpMHC qui donne un aperçu intéressant du mécanisme d'approche du pMHC par le TCR. Finalement, la dernière section se concentre sur l'analyse détaillée d'une étude expérimentale basée sur les échanges deuterium/hydrogène, dont les résultats révèlent que certaines régions clés du domaine constant du TCR sont sujettes à un changement conformationnel lors de la liaison au pMHC. Nous proposons une hypothèse pour la signalisation structurelle des TCR, menant à l'activation du lymphocyte. Celle-ci est basée sur l'analyse des mouvements corrélés observés dans la structure du TCRpMHC.

Preparação e propriedades de zeólitas faujasita contendo cátions amônio

Sodium faujasite zeolites with Si/Al ratio of 1.4 and 2.5 were exchanged with methylammonium cations. The influence of framework aluminum and ion exchange degree in their basic properties were evaluated. These properties were assessed in the Knoevenagel catalytic condensation. The sodium ion exchange was restricted to the supercavity and the exchange degree depended on the cation volume and on the Si/Al ratio. The higher catalytic activity is achieved for the zeolite with the lower Si/Al ratio exchanged with the monomethylammonium cation. The best performance of this catalyst is attributed to the higher basicity in combination with elevated micropore volume.

Studies of nucleophilic attack on tris (pentafluorophenyl) phosphine and its oxides

The reaction of tris(pentafluorophenyl)phosphine [5] with the nucleophiles dimethyl formamide (DMF), hexamethylphosphoric triamide (HMPA), diethyl formamide (DEF), hexaethylphosphoric triamide (HEPA), hydrazine, N,N-dimethyl hydrazine (in presence and/or absence of KF), phenylhydrazine, ammonium hydroxide, formamide, aniline, sodium hydrogen sulfide, and hexaethylphosphorous triamide was investigated. The reaction of [5] with DMF and HMPA gave the same product, namely tris-[4-(N,N-dimethylamino)-2,3,5,6-tetrafluorophenyl]phosphine [12] but in higher yield in the case of HMPA. Compound (5] also reacted with DEF to give tris[4-(N,N-diethylamino)-2,3,5,6-tetrafluorophenyl] phosphine [14]. When [51 was treated with HEPA, it gave a mixture of bis(pentafluorophe~yl)-(N,N-diethylamino-tetrafluorophenyl)phosphine, pentafluorophenyl-bis-(N,N-diethylamino-tetrafluorophenyl)phosphine and tris (N,N-diethylamino-tetrafluorophenyl)phosphine. Treatment of [5] with aqueeus hydrazine solution in excess ethanol gave tris(4-hydrazo-2,3,4,6-tetrafluorophenyl)phosphine [1s1 in high yield while reaction with aqueous hydrazine led to C-P cleavage and production of tetrafluorophenyl hydrazine. With N,N-dimethyl hydrazine, [5] gave tris(4-N,N-dimethylhydrazine-2,3,5,6-tetrafluorophenyl) phosphine {20j. The latter could be obtained in higher yield and shorter reaction time, by the addition of KF. The reaction of compound {51 with phenylhydrazine in THF gave bis(pentafluorophe~yl)-4-S-phenylhydrazino- 2,3,5,6-tetrafluorophenyl phosphine [22] in low yield. Reaction of [5] with ammonium hydroxide in THF at high pressure in the presence of KF gave tris-~4-amino-2,3,5,6-tetrafluorophenyl)phosphine [25]. Similarly, formamide led to a mixture of (C6F4NHZ)3P, (C6F4NHZ)ZPC6FS, (C6F4NHZ)ZPC6F4NHCHO, and C6F4NHZP(C6Fs)(C6F4NHCHO). When [5] was treated with aniline, a mixture of mono-, di-, and tri-substituted products was obtained. Sodium hydrogen sulfide in ethylene glycol/ pyridine led to C-P cleavage and the isolation of pentafluorobenzene and tetrafluorothiophenol. Reaction of [5] and its oxide [35] with different alkoxides in the corresponding alcohols led mainly to C-P bond cleavage products, with the exception of one case where sodium methoxide was used in ether, and which led to tris-(4-methoxy-2,3,9,6-tetrafluorophenyl)phosphine [37]. On the basis of various spectroscopic data, it was concluded that the para position in compound [5] was generally the favoured site of attack.

A novel medium for the development of in vitro cell culture system from Penaeus monodon

Lack of a valid shrimp cell line has been hampering the progress of research on shrimp viruses. One of the reasons identified was the absence of an appropriate medium which would satisfy the requirements of the cells in vitro. We report the first attempt to formulate an exclusive shrimp cell culture medium (SCCM) based on the haemolymph components of Penaeus monodon prepared in isosmotic seawater having 27 % salinity. The SCCM is composed of 22 amino acids, 4 sugars, 6 vitamins, cholesterol, FBS, phenol red, three antibiotics, potassium dihydrogen phosphate and di-sodium hydrogen phosphate at pH 6.8–7.2. Osmolality was adjusted to 720 ± 10 mOsm kg-1 and temperature of incubation was 25 8C. The most appropriate composition was finally selected based on the extent of attachment of cells and their proliferation by visual observation. Metabolic activity of cultured cells was measured by MTT assay and compared with that in L-15 (29), modified L-15 and Grace’s insect medium, and found better performance in SCCM especially for lymphoid cells with 107 % increase in activity and 85 ± 9 days of longevity. The cells from ovary and lymphoid organs were passaged twice using the newly designed shrimp cell dissociation ‘‘cocktail’’.

Effects of stabiliser addition and in-container sterilisation on selected properties of milk related to casein micelle stability

Different stabilising salts and calcium chloride were added to raw milk to evaluate changes in pH, ionic calcium, ethanol stability, casein micelle size and zeta potential. These milk samples were then sterilised at 121 °C for 15 min and stored for 6 months to determine how these properties changed. Addition of tri-sodium citrate (TSC) and di-sodium hydrogen phosphate (DSHP) to milk reduced ionic calcium, increased pH and increased ethanol stability in a concentration-dependent fashion. There was relatively little change in casein micelle size and a slight decrease in zeta potential. Sodium hexametaphosphate (SHMP) also reduced ionic calcium considerably, but its effect on pH was less noticeable. In contrast, sodium dihydrogen phosphate (SDHP) reduced pH but had little effect on ionic calcium. In-container sterilisation of these samples reduced pH, increased ethanol stability and increased casein micelle size, but had variable effects on ionic calcium; for DSHP and SDHP, ionic calcium decreased after sterilisation but, for SHMP, it remained little changed or increased. Milk containing 3.2 mM SHMP and more than 4.5 mM CaCl2 coagulated upon sterilisation. All other samples were stable but there were differences in browning, which increased in intensity as milk pH increased. Heat-induced sediment was not directly related to ionic calcium concentration, so reducing ionic calcium was not the only consideration in terms of improving heat stability. After 6 months of storage, the most acceptable product, in appearance, was that containing SDHP, as this minimised browning during sterilisation and further development of browning during storage.

Rosiglitazone reverses tenofovir-induced nephrotoxicity

Tenofovir disoproxil fumarate (TDF) is a first-line drug used in patients with highly active retroviral disease; however, it can cause renal failure associated with many tubular anomalies that may be due to down regulation of a variety of ion transporters. Because rosiglitazone, a peroxisome proliferator-activated receptor-gamma agonist induces the expression of many of these same transporters, we tested if the nephrotoxicity can be ameliorated by its use. High doses of TDF caused severe renal failure in rats accompanied by a reduction in endothelial nitric-oxide synthase and intense renal vasoconstriction; all of which were significantly improved by rosiglitazone treatment. Low-dose TDF did not alter glomerular filtration rate but produced significant phosphaturia, proximal tubular acidosis, polyuria and a reduced urinary concentrating ability. These alterations were caused by specific downregulation of the sodium-phosphorus cotransporter, sodium/hydrogen exchanger 3 and aquaporin 2. A Fanconi`s-like syndrome was ruled out as there was no proteinuria or glycosuria. Rosiglitazone reversed TDF-induced tubular nephrotoxicity, normalized urinary biochemical parameters and membrane transporter protein expression. These studies suggest that rosiglitazone treatment might be useful in patients presenting with TFV-induced nephrotoxicity especially in those with hypophosphatemia or reduced glomerular filtration rate.

Síntese, caracterização e estudo termoanalítico dos succinatos de alguns metais de transição bivalentes no estado sólido

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Síntese, caracterização e estudo do comportamento térmico dos 2-metoxibenzoatos de Mn(II), Co(II), Ni(II), Cu(II) e Zn(II) no estado sólido

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Preparação e propriedades de zeólitas faujasita contendo cátions amônio

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)