Structure and function of the Bacillus hybrid enzyme GluXyn-1: Native-like jellyroll fold preserved after insertion of autonomous globular domain

The 1,3–1,4-β-glucanase from Bacillus macerans (wtGLU) and the 1,4-β-xylanase from Bacillus subtilis (wtXYN) are both single-domain jellyroll proteins catalyzing similar enzymatic reactions. In the fusion protein GluXyn-1, the two proteins are joined by insertion of the entire XYN domain into a surface loop of cpMAC-57, a circularly permuted variant of wtGLU. GluXyn-1 was generated by protein engineering methods, produced in Escherichia coli and shown to fold spontaneously and have both enzymatic activities at wild-type level. The crystal structure of GluXyn-1 was determined at 2.1 Å resolution and refined to R = 17.7% and R(free) = 22.4%. It shows nearly ideal, native-like folding of both protein domains and a small, but significant hinge bending between the domains. The active sites are independent and accessible explaining the observed enzymatic activity. Because in GluXyn-1 the complete XYN domain is inserted into the compact folding unit of GLU, the wild-type-like activity and tertiary structure of the latter proves that the folding process of GLU does not depend on intramolecular interactions that are short-ranged in the sequence. Insertion fusions of the GluXyn-1 type may prove to be an easy route toward more stable bifunctional proteins in which the two parts are more closely associated than in linear end-to-end protein fusions.

Caracterização in vitro do metabolismo e da absorção intestinal da casearina X

As principais propriedades farmacológicas da Casearia sylvestris, uma espécie de árvore cujas folhas são utilizadas na medicina popular, já foram descritas na literatura. Recentemente foi demonstrada a potente atividade citotóxica in vitro da casearina X (CAS X), o diterpeno clerodânico majoritário isolado das folhas de C. sylvestris, contra linhagens de células tumorais humanas. Apesar dos resultados promissores, sua potente atividade citotóxica in vitro não pode ser extrapolada para uma potente atividade in vivo, a menos que possua boa biodisponibilidade e duração desejável do seu efeito. Tendo em vista que o avanço nas pesquisas de produtos naturais requer a avaliação pré-clínica de propriedades farmacocinéticas, no presente trabalho foi realizada a caracterização in vitro do metabolismo e da absorção intestinal da CAS X, com o objetivo de prever sua biodisponibilidade in vivo. Para os estudos de metabolismo in vitro, foi utilizado o modelo microssomal hepático de ratos e de humanos. Foi desenvolvido um método analítico para a quantificação da CAS X em microssomas, empregando a precipitação de proteínas com acetonitrila no preparo das amostras e a cromatografia líquida de alta eficiência para as análises. O método foi validado de acordo com os guias oficiais da Agência Nacional de Vigilância Sanitária e da European Medicine Agency (EMA). A CAS X demonstrou ser substrato para as reações de hidrólise mediada pelas carboxilesterases (CES) e apresentou um perfil cinético de Michaelis-Menten. Foram estimados os parâmetros de Vmax e KM, demonstrando que o clearance intrínseco em microssomas hepático de humanos foi 1,7 vezes maior que o de ratos. O clearance hepático foi estimado por extrapolação in vitro-in vivo, resultando em mais de 90% do fluxo sanguíneo hepático em ambas as espécies. Um estudo qualitativo para a pesquisa de metabólitos foi feito utilizando espectrometria de massas, pelo qual foi possível sugerir a formação da casearina X dialdeído como produto de metabolismo. Nos estudos de absorção intestinal in vitro foi utilizado o modelo de monocamadas de células Caco-2. Um método analítico por cromatografia líquida acoplada a espectrometria de massas foi desenvolvido e validado de acordo com o EMA, para as etapas de quantificação da CAS X no sistema de células. Os parâmetros cinéticos de permeabilidade aparente absortiva e secretória da CAS X foram estimados em um sistema celular, no qual a atividade hidrolítica da CES foi inibida. Assim, a CAS X foi capaz de permear a monocamada de células Caco-2, provavelmente por transporte ativo, sem a ocorrência de efluxo, mas com significativa retenção do composto dentro das células. Em conjunto, os ensaios in vitro realizados demonstraram a susceptibilidade da CAS X ao metabolismo de primeira passagem, como substrato para as CES específicas expressas no fígado e intestino.

Therapeutic drug monitoring of cefepime with micellar electrokinetic capillary chromatography: Assay improvement, quality assurance, and impact on patient drug levels

The improvement and performance of a micellar electrokinetic capillary chromatography assay for cefepime in human serum and plasma with a 50 μm id fused-silica capillary elongated from 40 to 60 cm is reported. Sample preparation with dodecylsulfate protein precipitation at pH 4.5, the pH 9.1 separation medium and the applied voltage were as reported previously[16]. The change resulted in a significant lower current, higher resolution and increased detection time intervals. The performance of the assay with multi-level internal calibration was assessed with calibration and control samples. Quality assurance data of a two year period assessed under the new conditions demonstrated the robustness of the assay. In serum samples of patients who received both cefepime and sulfamethoxazole, cefepime could not be detected due to the inseparability of the two compounds. The presence of an interference can be recognized by an increased peak width (width > 0.2 min), the appearance of a shoulder or an unresolved double peak. The patient data gathered during a three year period reveal that introduction of therapeutic drug monitoring led to a 50% reduction of the median drug level. The data suggest that therapeutic drug monitoring can help to minimize the risk of major adverse reactions and to increase drug safety on an individual basis. This article is protected by copyright. All rights reserved.

Synthesis and electrochemical properties of mesoporous nickel oxide

Mesoporous Ni(OH)(2) is synthesized using sodium dodecyl sulfate as a template and urea as a hydrolysis-controlling agent. Mesoporous NiO with a centralized pore-size distribution is obtained by calcining Ni(OH)(2) at different temperatures. The BET specific surface area reaches 477.7 m(2) g(-1) for NiO calcined at 250 degreesC. Structure characterizations indicate a good mesoporous structure for the nickel oxide samples. Cyclic voltammetry shows the NiO to have good capacitive behaviour due to its unique mesoporous structure when using a large amount of NiO to fabricate the electrode. Compared with NiO prepared by dip-coating and cathodic precipitation methods, mesoporous NiO with a controlled pore structure can be used in much larger amounts to fabricate electrodes and still maintain a high specific capacitance and good capacitive behaviour. (C) 2004 Elsevier B.V. All rights reserved.

Synthesis and characterization of mesoporous nickel oxide and its application to electrochemical capacitor

Mesoporous Ni(OH)(2) was synthesized using cationic surfactant as template and urea as hydrolysis-controlling agent. Mesoporous NiO with centralized pore size distribution was obtained by calcining Ni(OH)(2) at different temperatures. The BET specific surface area reaches 477.7 m(2).g(-1) for NiO calcined at 523 K. Structure characterizations indicate the polycrystalline pore wall of mesoporous nickel oxide. The pore-formation mechanism is also deduced to be quasi-reverse micelle mechanism. Cyclic voltammetry shows the good capacitive behavior of these NiO samples due to its unique mesoporous structure when using large amount of NiO to fabricate electrode. Compared with NiO prepared by dip-coating and cathodic precipitation methods, this mesoporous NiO with controlled pore structure can be used in much larger amount to fabricate the electrode and still maintains high specific capacitance and good capacitive behavior.

Investigação da rota biohidrometalúrgica com Acidithiobacillus ferrooxidans/thiooxidans para recuperação do cobalto de baterias de íons lítio descartadas

The recycling of metals from secondary sources can be advantageous. Among the metals of interest, we have cobalt, a metal used for various purposes. As regards the secondary sources of cobalt, the lithium-ion batteries can be considered, since they contain cobalt oxide in their composition (LiCoO2). This way, the objective of this work was to use the microorganism strains (Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans) to bioleach the LiCoO2 extracted from discarded lithium ion batteries with emphasis on the recovery of cobalt for synthesis of new materials of interest. The lineage growth occurred in T&K medium and the growth investigation was made by observing the media, by platelet growth and microscope analysis. Then, the inoculum was standardized on 5 x 106 cells mL-1 and used in bioleaching tests. The bioleaching was investigated: the microorganism nature: separate strains and A. ferrooxidans and A. thiooxidans consortium, bioleaching time (0 to 40 days), inoculum proportion (5 to 50% v/v), energy source (iron and sulfur) and residue concentration (1063 to 8500 mg L-1 of cobalt). The cobalt concentration in the media was found by atomic absorption spectrometry and the medium pH was monitored during the bioleaching. The results show that the amount of bioleached cobalt increases with time and the iron concentration. The bioleaching with A. thiooxidans was not influenced by the addition of sulfur. The use of the two lineages together did not improve the bioleaching rates. Among the lineages, the A. thiooxidans presented better results and was able to bioleach cobalt amounts above 50% in most of the experiments. A. thiooxidans presented lower bioleaching rates, with a maximum of 50% after 24 days of experiment. After reprocessing by bioleaching, the cobalt in solution was used for synthesis of new materials: such as LiCoO2 cathode and as adsorbent pesticide double lamellar hydroxide (HDL Co-Al-Cl) by the Pechini and co-precipitation methods. The reprocessed LiCoO2 presented a unique stoichiometric phase relative to the HT-LiCoO2 structure similar to the JCPDS 44-0145, presenting electrochemical activity when tested as a cathode material. The double lamellar hydroxide Co-Al-Cl was tested as pesticide adsorbent, being possible to adsorb around 100% of the pesticide. The bioleaching was efficient in the recovery of cobalt present in lithium-ion batteries and microorganisms presented high tolerance to the residue, being able to bioleach even at higher LiCoO2 concentrations. The cobalt bioleaching medium did not impair the synthesis phases and the obtained materials presented structure and activity similar to the sintered materials from the reagents containing cobalt.

Produção enzimática de biodiesel a partir de resíduos agro-industriais usando a lipase imobilizada de origem microbiana

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Química e Biológica

Development and validation of sensitive methods for determination of sibutramine hydrochloride monohydrate and direct enantiomeric separation on a protein-based chiral stationary phase

Sibutramine hydrochloride monohydrate, chemically 1-(4-chlorophenyl)-N,N-dimethyl-alpha-(2-methylpropyl) hydrochloride monohydrate (SB center dot HCl center dot H2O), was approved by the U.S. Food and Drug Administration for the treatment of obesity. The objective of this study was to develop, validate, and compare methods using UV-derivative spectrophotometry (UVDS) and reversed-phase high-performance liquid chromatography (HPLC) for the determination of SB center dot HCl center dot H2O in pharmaceutical drug products. The UVDS and HPLC methods were found to be rapid, precise, and accurate. Statistically, there was no significant difference between the proposed UVDS and HPLC methods. The enantiomeric separation of SB was obtained on an alpha-1 acid glycoprotein column. The R- and S-sibutramine were eluted in < 5 min with baseline separation of the chromatographic peaks (alpha = 1.9 and resolution = 1.9).

Protein partitioning in poly(ethylene glycol)/sodium polyacrylate aqueous two-phase systems

The partition of hemoglobin, lysozyme and glucose-6-phospate dehydrogenase (G6PDH) in a novel inexpensive aqueous two-phase system (ATPS) composed by poly(ethylene glycol) (PEG) and sodium polyacrylate (NaPA) has been studied. The effect of NaCl and Na2SO4, pH and PEG molecular size on the partitioning has been studied. At high pH (above 9), hemoglobin partitions strongly to the PEG-phase. Although some precipitation of hemoglobin occurs, high recovery values are obtained particularly for lysozyme and G6PDH. The partitioning forces are dominated by the hydrophobic and electrochemical (salt) effects, since the positively charged lysozyme and negatively charged G6PDH partitions to the non-charged PEG and the strongly negatively charged polyacrylate enriched phase, respectively. (c) 2007 Elsevier B.V. All rights reserved.

Correlation between turbidimetric and nephelometric methods of measuring C-reactive protein in patients with unstable angina or non-ST elevation acute myocardial infarction

OBJECTIVE: To evaluate the performance of the turbidimetric method of C-reactive protein (CRP) as a measure of low-grade inflammation in patients admitted with non-ST elevation acute coronary syndromes (ACS). METHODS: Serum samples obtained at hospital arrival from 68 patients (66±11 years, 40 men), admitted with unstable angina or non-ST elevation acute myocardial infarction were used to measure CRP by the methods of nephelometry and turbidimetry. RESULTS: The medians of C-reactive protein by the turbidimetric and nephelometric methods were 0.5 mg/dL and 0.47 mg/dL, respectively. A strong linear association existed between the 2 methods, according to the regression coefficient (b=0.75; 95% C.I.=0.70-0.80) and correlation coefficient (r=0.96; P<0.001). The mean difference between the nephelometric and turbidimetric CRP was 0.02 ± 0.91 mg/dL, and 100% agreement between the methods in the detection of high CRP was observed. CONCLUSION: In patients with non-ST elevation ACS, CRP values obtained by turbidimetry show a strong linear association with the method of nephelometry and perfect agreement in the detection of high CRP.

Analysis of parity between protein-based electrophoretic methods for the characterization of oral Candida species

Electrophoretic studies of multilocus-enzymes (MLEE) and whole-cell protein (SDS-PAGE) were carried out in order to evaluate the parity between different methods for the characterization of five Candida species commonly isolated from oral cavity of humans by numerical taxonomy methods. The obtained data revealed that sodium dodecyl sulfate polyacrylamide gel electrophoresis is more efficient in grouping strains in their respective species while MLEE has much limited resolution in organizing all strains in their respective species-specific clusters. MLEE technique must be regarded for surveys in which just one species of Candida is involved.

Comparison of two methods of tear sampling for protein quantification by Bradford method

The aim of this study was to compare two methods of tear sampling for protein quantification. Tear samples were collected from 29 healthy dogs (58 eyes) using Schirmer tear test (STT) strip and microcapillary tubes. The samples were frozen at -80ºC and analyzed by the Bradford method. Results were analyzed by Student's t test. The average protein concentration and standard deviation from tears collected with microcapillary tube were 4.45mg/mL ±0.35 and 4,52mg/mL ±0.29 for right and left eyes respectively. The average protein concentration and standard deviation from tears collected with Schirmer Tear Test (STT) strip were and 54.5mg/mL ±0.63 and 54.15mg/mL ±0.65 to right and left eyes respectively. Statistically significant differences (p<0.001) were found between the methods. In the conditions in which this study was conducted, the average protein concentration obtained with the Bradford test from tear samples obtained by Schirmer Tear Test (STT) strip showed values higher than those obtained with microcapillary tube. It is important that concentration of tear protein pattern values should be analyzed according the method used to collect tear samples.

Downscaling from GCM precipitation: a benchmark for dynamical and statistical downscaling methods

A precipitation downscaling method is presented using precipitation from a general circulation model (GCM) as predictor. The method extends a previous method from monthly to daily temporal resolution. The simplest form of the method corrects for biases in wet-day frequency and intensity. A more sophisticated variant also takes account of flow-dependent biases in the GCM. The method is flexible and simple to implement. It is proposed here as a correction of GCM output for applications where sophisticated methods are not available, or as a benchmark for the evaluation of other downscaling methods. Applied to output from reanalyses (ECMWF, NCEP) in the region of the European Alps, the method is capable of reducing large biases in the precipitation frequency distribution, even for high quantiles. The two variants exhibit similar performances, but the ideal choice of method can depend on the GCM/reanalysis and it is recommended to test the methods in each case. Limitations of the method are found in small areas with unresolved topographic detail that influence higher-order statistics (e.g. high quantiles). When used as benchmark for three regional climate models (RCMs), the corrected reanalysis and the RCMs perform similarly in many regions, but the added value of the latter is evident for high quantiles in some small regions.

Disorder prediction methods, their applicability to different protein targets and their usefulness for guiding experimental studies

The role and function of a given protein is dependent on its structure. In recent years, however, numerous studies have highlighted the importance of unstructured, or disordered regions in governing a protein’s function. Disordered proteins have been found to play important roles in pivotal cellular functions, such as DNA binding and signalling cascades. Studying proteins with extended disordered regions is often problematic as they can be challenging to express, purify and crystallise. This means that interpretable experimental data on protein disorder is hard to generate. As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein. Currently, over 60 prediction servers exist, utilizing different methods for classifying disorder and different training sets. Here we review several good performing, publicly available prediction methods, comparing their application and discussing how disorder prediction servers can be used to aid the experimental solution of protein structure. The use of disorder prediction methods allows us to adopt a more targeted approach to experimental studies by accurately identifying the boundaries of ordered protein domains so that they may be investigated separately, thereby increasing the likelihood of their successful experimental solution.

Computational aspects of harmonic wavelet Galerkin methods and an application to a precipitation front propagation model

This article is dedicated to harmonic wavelet Galerkin methods for the solution of partial differential equations. Several variants of the method are proposed and analyzed, using the Burgers equation as a test model. The computational complexity can be reduced when the localization properties of the wavelets and restricted interactions between different scales are exploited. The resulting variants of the method have computational complexities ranging from O(N(3)) to O(N) (N being the space dimension) per time step. A pseudo-spectral wavelet scheme is also described and compared to the methods based on connection coefficients. The harmonic wavelet Galerkin scheme is applied to a nonlinear model for the propagation of precipitation fronts, with the front locations being exposed in the sizes of the localized wavelet coefficients. (C) 2011 Elsevier Ltd. All rights reserved.