Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of nucleosides and deoxynucleosides, generating ribose 1-phosphate and the purine base, which is an important step of purine catabolism pathway. The lack of such an activity in humans, owing to a genetic disorder, causes T-cell impairment, and drugs that inhibit this enzyme may have the potential of being utilized as modulators of the immunological system to treat leukemia, autoimmune diseases, and rejection in organ transplantation. Here, we describe kinetics and crystal structure of human PNP in complex with 7-methyl-6-thio-guanosine, a synthetic substrate, which is largely used in activity assays. Analysis of the structure identifies different protein conformational changes upon ligand binding, and comparison of kinetic and structural data permits an understanding of the effects of atomic substitution on key positions of the synthetic substrate and their consequences to enzyme binding and catalysis. Such knowledge may be helpful in designing new PNP inhibitors. © 2005 Elsevier Inc. All rights reserved.

Determination of 2-methylimidazole and 4-methylimidazole in caramel colors by capillary electrophoresis

The use of chemical preservative compounds is common in the food products industry. Caramel color is the most usual additive used in beverages, desserts, and breads worldwide. During its fabrication process, 2- and 4-methylimidazole (MeI), highly carcinogenic compounds, are generated. In these cases, the development of reliable analytical methods for the monitoring of undesirable compounds is necessary. The primary procedure for the analysis of 2- and 4-MeI is using LC- or GC-MS techniques. These procedures are time-consuming and require large amounts of organic solvents and several pretreatment steps. This prevents the routine use of this procedure. This paper describes a rapid, efficient, and simple method using capillary electrophoresis (CE) for the separation and determination of 2- and 4-MeI in caramel colors. The analyses were performed using a 75 μm i.d. uncoated fused-silica capillary with an effective length of 40 cm and a running electrolyte consisting of 160 mmol L-1 phosphate plus 30% acetonitrile. The pH was adjusted to 2.5 with triethylamine. The analytes were separated within 6 min at a voltage of 20 kV. Method validation revealed good repeatability of both migration time (<0.8% RSD) and peak area (<2% RSD). Analytical curves for 2- and 4-MeI were linear in the 0.4-40 mg L-1 concentration interval. Detection limits were 0.16 mg L-1 for 4-MeI and 0.22 mg L-1 for 2-MeI. The extraction recoveries were satisfactory. The developed method showed many advantages when compared to the previously used method. © 2013 American Chemical Society.

Biomimetic sensor based on 5,10,15,20-tetrakis(pentafluorophenyl)-21H,23H- porphyrin iron (III) chloride and MWCNT for selective detection of 2,4-D

Exploitation of the electronic properties of carbon nanotubes for the development of voltammetric and amperometric sensors to monitor analytes of environmental relevance has increased in recent years. This work reports the development of a biomimetic sensor based on a carbon paste modified with 5,10,15,20-tetrakis(pentafluorophenyl)-21H,23H-porphyrin iron (III) chloride (a biomimetic catalyst of the P450 enzyme) and multi-wall carbon nanotubes (MWCNT), for the sensitive and selective detection of the herbicide 2,4- dichlorophenoxyacetic acid (2,4-D). The sensor was evaluated using cyclic voltammetry and amperometry, for electrochemical characterization and quantification purposes, respectively. Amperometric analyses were carried out at -100 mV vs. Ag/AgCl(KClsat), using a 0.1 mol L-1 phosphate buffer solution at pH 6.0 as the support electrolyte. Under these optimized analytical conditions, the sensor showed a linear response between 9.9 × 10-6 and 1.4 × 10-4 mol L-1, a sensitivity of 1.8 × 104 (±429) μA L mol -1, and limits of detection and quantification of 2.1 × 10 -6 and 6.8 × 10-6 mol L-1, respectively. The incorporation of functionalized MWCNT in the carbon paste resulted in a 10-fold increase in the response, compared to that of the biomimetic sensor without MWCNT. In addition, the low applied potential (-100 mV) used to obtain high sensitivity also contributed to the excellent selectivity of the proposed sensor. The viability of the application of this sensor for analysis of soil samples was confirmed by satisfactory recovery values, with a mean of 96% and RSD of 2.1% (n = 3). © 2013 Elsevier B.V.

Estrutura cristalográfica da Purina nucleosídeo foslorilase do Mycobacterium tuberculosis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Monitoring of diclofenac with biomimetic sensor in batch and FIA systems

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

Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D from Loxosceles gaucho venom

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Development and application of a screen-printed electrode modified with MWCNT for the electrocatalytic detection of thiram

Interest in the electronic properties of carbon nanotubes has increased in recent years. These materials can be used in the development of electrochemical sensors for the measurement and monitoring of analytes of environmental interest, such as pharmaceuticals, dyes, and pesticides. This work describes the use of homemade screen-printed electrodes modified with multi-walled carbon nanotubes (MWCNT) for the electrochemical detection of the fungicide thiram. The electrochemical characteristics of the proposed system were evaluated using cyclic voltammetry, with investigation of the electrochemical behavior of the sensor in the presence of the analyte, and estimation of electrochemical parameters including the diffusion coefficient, electron transfer coefficient (α), and number of electrons transferred in the catalytic electro-oxidation. The sensor response was optimized using amperometry. The best sensor performance was obtained in 0.1 mol L-1 phosphate buffer solution at pH 8.0, where a detection limit of 7.9 x 10-6 mol L-1 was achieved. Finally, in order to improve the sensitivity of the sensor, square wave voltammetry (SWV) was used for thiram quantification, instead of amperometry. Using SWV, a response range for thiram from 9.9 x 10-6 to 9.1 x 10-5 mol L-1 was obtained, with a sensitivity of 30948 µA mol L-1, and limits of detection and quantification of 1.6 x 10-6 and 5.4 x 10-6 mol L-1, respectively. The applicability of this efficient new alternative methodology for thiram detection was demonstrated using analyses of enriched soil samples.

Determination of salicylate in blood serum using an amperometric biosensor based on salicylate hydroxylase immobilized in a polypyrrole-glutaraldehyde matrix

The use of an amperometric biosensor for the salicylate determination in blood serum is described. The biosensor is based on salicylate hydroxylase (EC 1.14.13.1) electropolymerized onto a glassy carbon-working electrode with polypyrrole and glutaraldehyde, to improve the biosensor lifetime. The hexacyanoferrate (II) was also incorporated to work as a redox mediator to minimize possible interferences. The salicylate is enzymatically converted to catechol, which is monitored amperometrically by its electrooxidation at +0.170 V versus SCE (saturated calomel electrode). Salicylate determination was carried out maintaining the ratio between β-NADH and salicylate at 4:1 (30°C). The amperometric response of the biosensor was linearly proportional to the salicylate concentration between 2.3 x 10-6 and 1.4 x 10-5 mol l- 1, in 0.1 mol l-1 phosphate buffer (pH 7.8), containing 0.1 mol l-1 KCl and 5.0 x 10-4 mol l-1 Na2H2EDTA, as supporting electrolyte. The recovery studies, in the presence of several interfering compounds, showed recoveries between 96.4 and 104.8%. The useful lifetime of the biosensor in the concentration range evaluated was at least 40 days, in continuous use. Blood serum samples analyzed by this biosensor showed a good correlation compared to the spectrophotometric method (Trinder) used as reference, presenting relative deviations lower than 7.0%. (C) 2000 Elsevier Science B.V.

Structural insights into substrate binding of brown spider venom class II phospholipases D

Phospholipases D (PLDs), the major dermonecrotic factors from brown spider venoms, trigger a range of biological reactions both in vitro and in vivo. Despite their clinical relevance in loxoscelism, structural data is restricted to the apo-form of these enzymes, which has been instrumental in understanding the functional differences between the class I and II spider PLDs. The crystal structures of the native class II PLD from Loxosceles intermedia complexed with myo-inositol 1-phosphate and the inactive mutant H12A complexed with fatty acids indicate the existence of a strong ligand-dependent conformation change of the highly conserved aromatic residues, Tyr 223 and Trp225 indicating their roles in substrate binding. These results provided insights into the structural determinants for substrate recognition and binding by class II PLDs.

Estudos computacionais de esfingomielinases D: docking, dinâmica molecular e métodos híbridos QM/MM

Pós-graduação em Biofísica Molecular - IBILCE

Dynamics of glyphosate-induced conformational changes of Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) determined by hydrogen-deuterium exchange and electrospray mass spectrometry

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the reaction between shikimate 3-phosphate and phosphoenolpyruvate to form 5-enolpyruvylshikimate 3-phosphate, an intermediate in the shikimate pathway, which leads to the biosynthesis of aromatic amino acids. EPSPS exists in an open conformation in the absence of substrates and/or inhibitors and in a closed conformation when bound to the substrate and/or inhibitor. In the present report, the H/D exchange properties of EPSPS from Mycobacterium tuberculosis (Mt) were investigated for both enzyme conformations using ESI mass spectrometry and circular dichroism (CD). When the conformational changes identified by H/D exchanges were mapped on the 3-D structure, it was observed that the apoenzyme underwent extensive conformational changes due to glyphosate complexation, characterized by an increase in the content of alpha-helices from 40% to 57%, while the beta-sheet content decreased from 30% to 23%. These results indicate that the enzyme underwent a series of rearrangements of its secondary structure that were accompanied by a large decrease in solvent access to many different regions of the protein. This was attributed to the compaction of 71% of alpha-helices and 57% of beta-sheets as a consequence of glyphosate binding to the enzyme. Apparently, MtEPSPS undergoes a series of inhibitor-induced conformational changes, which seem to have caused synergistic effects in preventing solvent access to the core of molecule, especially in the cleft region. This may be part of the mechanism of inhibition of the enzyme, which is required to prevent the hydration of the substrate binding site and also to induce the cleft closure to avoid entrance of the substrates.

Hydrogen/deuterium exchange mass spectrometry for characterizing phosphoenolpyruvate-induced structural transitions in Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.1)

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

Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution

Background: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldose-ketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. Results: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 Å resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. Conclusions: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger.

The status of soil phosphate fractions and the ability of fungi to dissolve hardly soluble phosphates

Brazilian soils predominantly consist of iron and aluminum oxides and have a low phosphorus content. The present study was carried out in order to assess the status of phosphate fractions in pasture, forest and agricultural soils and the ability of soil fungi to solubilize iron and aluminum phosphates. The abundance of P fractions in the soils studied occurred in the following order: Fe-P > reductant-soluble Fe-P > occluded Fe-P > occluded Al-P > Al-P > Ca-P. of the 481 fungi isolated, 33 showed the ability to solubilize the inorganic phosphates in culture. of these, 14 were considered to be high or very high solubilizers based on a solubilization capacity > 1000 mu g PO43- ml(-1). Isolate F-111 was the only one that dissolved all the insoluble phosphates used. Nine isolates solubilized both Al-P and Ca-P, and four other isolates only solubilized Ca-P. The highest number of isolates with high solubilization capacity were detected in pasture soil, followed by tropical rain forest and forest patch soils. Pasture soil presented both the largest contents of insoluble phosphates and the largest number of fungal isolates with phosphate-solubilizing ability. The range and size of P fractions influenced the number of fungi and their ability to solubilize hardly soluble phosphates. (c) 2004 Elsevier B.V. All rights reserved.

Effectiveness of fused magnesium potassium phosphate for marandu grass

O alto custo atual do KCl e a grande dependência de sua importação para suprir a demanda nacional sugerem a necessidade de estudos que procurem avaliar a eficiência de outras fontes de K, principalmente aquelas baseadas em matéria-prima nacional. Nesse sentido, foi conduzido um experimento em casa de vegetação com amostras de um Latossolo Vermelho distrófico textura média, adotando-se o delineamento inteiramente casualizado em esquema fatorial 4 x 3 x 2, sendo quatro doses de K (0, 60, 120 e 180 mg kg-1 de K), três fontes [(cloreto de potássio (KCl)], termofosfato magnesiano potássico (FMPP) e a mistura de 70 % FMPP + 30 % KCl) e duas granulometrias (100 e 60 mesh), com três repetições. Verificou-se que a adubação potássica promoveu incrementos significativos na produção de matéria seca (parte aérea) e nos teores de K no solo e na planta, não havendo diferenças entre as fontes e suas granulometrias. Os níveis críticos de K no solo e na parte aérea das plantas foram de 1,53 mmol c dm-3 e 19,1 g kg-1, respectivamente.