Malachite Green and Crystal Violet Decolorization by Ganoderma lucidum and Pleurotus ostreatus Supernatant and by rGlLCC1 and rPOXA 1B Concentrates: Molecular Docking Analysis.

Laccases catalyze the oxidation of various aromatic organic compounds concomitantly with molecular oxygen reduction to water. Triphenylmethane dyes are synthetic compounds widely used in diverse industries. Their removal from effluents is difficult, due to their high degree of structural complexity; hence, their high concentration in effluents cause a negative impact on the environment. In the present work, molecular docking was used to evaluate interactions between rGlLCC1 or rPOXA 1B enzymes with Crystal Violet (CV) or Malachite Green (MG) dyes. In addition, removal tests of the two dyes were performed. Van der Waals interactions were obtained for only the CV dye for both GlLCC1 and POXA 1B enzymes. Nevertheless, in the GlLCC1 model, two π-π interactions were observed. For the MG dye only, Van der Waals interactions were obtained. Moreover, amino acid composition interacting in each model with each dye was similar. It is important to highlight that by molecular docking, none of the estimated ligand configurations generated hydrogen bonds. Thus, explaining the difficulty to degrade CV and MG. Regarding CV, maximum decolorization percentage was 23.6 ± 1.0% using Ganoderma lucidum supernatant and 5.0 ± 0.5% with Pleurotus ostreatus supernatant. When using recombinant laccase enzyme concentrates, decolorization percentages were 9.9 ± 0.1 and 7.5 ± 1.0% for rGlLCC1 and rPOXA 1B, respectively. On the other hand, for the MG dye, maximum decolorization percentages were 52.1 ± 5.1 and 2.3 ± 0.2% using G. lucidum and P. ostreatus concentrates, respectively. Whereas with recombinant laccase enzymatic concentrates, values of 9.4 ± 0.8% were obtained, with rGlLCC1, and 2.1 ± 0.1% when using rPOXA 1B. These findings represent an important step in bioremediation processes improvement and efficiency of industry-generated products, using environmentally friendly alternatives.

Correction to: Malachite Green and Crystal Violet Decolorization by Ganoderma lucidum and Pleurotus ostreatus Supernatant and by rGlLCC1 and rPOXA 1B Concentrates: Molecular Docking Analysis.

The original version of this article unfortunately contained a mistake. The replacement image of Fig. 4 provided by the first corresponding author, Aura M. Pedroza-Rodríguez, is incorrect and that the originally submitted Fig. 4 should have been retained. The original article has been corrected.

Antagonistic action on NMDA/GluN2B mediated currents of two peptides that were conantokin-G structure-based designed.

BACKGROUND: The GluN2B subunit of the N-methyl-D-aspartate receptor (NMDAr) modulates many physiological processes including learning, memory, and pain. Excessive increase in NMDAr/GluN2B activity has been associated with various disorders such neuropathic pain and neuronal death following hypoxia. Thus there is an interest in identifying NMDAr antagonists that interact specifically with the GluN2B subunit. Recently based on structural analysis between the GluN2B subunit and conantokin-G, a toxin that interacts selectively with the GluN2B subunit, we designed various peptides that are predicted to act as NMDAr antagonists by interacting with the GluN2B subunit. In this study we tested this prediction for two of these peptides EAR16 and EAR18. RESULTS: The effects of EAR16 and EAR18 in NMDA-evoked currents were measured in cultured rat embryonic hippocampal neurons and in HEK-293 cells expressing recombinant NMDAr comprised of GluN1a-GluN2A or GluN1a-GluN2B subunits. In hippocampal neurons, EAR16 and EAR18 reduced the NMDA-evoked calcium currents in a dose-dependent and reversible manner with comparable IC50 (half maximal inhibitory concentration) values of 241 and 176 µM, respectively. At 500 µM, EAR16 blocked more strongly the NMDA-evoked currents mediated by the GluN1a-GluN2B (84%) than those mediated by the GluN1a-GluN2A (50%) subunits. At 500 µM, EAR18 blocked to a similar extent the NMDA-evoked currents mediated by the GluN1a-GluN2B (62%) and the GluN1a-GluN2A (55%) subunits. CONCLUSIONS: The newly designed EAR16 and EAR18 peptides were shown to block in reversible manner NMDA-evoked currents, and EAR16 showed a stronger selectivity for GluN2B than for GluN2A.

"In Silico" Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger.

Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of -0,304 and -0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.

PRODUCTION AND PURIFICATION OF IgY ANTIBODIES AS A NOVEL TOOL TO PURIFY THE NR1 SUBUNIT OF NMDA RECEPTOR / PRODUCCIÓN Y PURIFICACIÓN DE ANTICUERPOS IgY COMO UNA HERRAMIENTA NOVEDOSA PARA PURIFICAR LA SUBUNIDAD NR1 DEL RECEPTOR NMDA / PRODUÇÂO E PURIFICAÇÂO DE ANTICORPOS IgY COMO UMA FERRAMENTA INOVADORA PARA PURIFICAR O RECEPTOR NMDA SUBUNIDADE NR1

Producing polyclonal antibodies (IgY) in chickens has advantages over those obtained in other animal models, since they have been used as a tool for studying different proteins (NMDA glutamate receptor in our case, specifically the NR1 subunit). We produced specific antibodies against expression products by the alternative splicing of the gene encoding NMDA receptor NR1 subunit in adult rat brain. Three peptides corresponding to the splicing sites (N1, C1 and C2' cassettes) were designed, synthesised and used individually as antigens in hens. Specific immunoglobulins were purified from yolks. The antibodies were then used for purifying the NMDA receptor NR1 subunit using affinity chromatography coupling the three antibodies to the support.

La producción de anticuerpos policlonales en gallinas (IgY) tiene ventajas sobre anticuerpos obtenidos en otros modelos animales y se han empleado como una nueva herramienta para estudiar diferentes proteínas (el receptor de glutamate tipo NMDA en nuestro caso, específicamente la subunidad NR1). Produjimos anticuerpos específicos contra productos de expresión por splicing alternativo del gen que codifica la subunidad NR1 del receptor tipo NMDA en el cerebro de rata adulta. Se diseñaron 3 péptidos correspondientes a los sitios de splicing del gen (conocidos como casetes N1, C1 y C2'), se sintetizaron y se usaron individualmente como antígenos en gallinas. Inmunoglobulinas específicas se purificaron de las yemas. Los anticuerpos se usaron para purificar la subunidad NR1 del receptor tipo NMDA usando cromatografía de afinidad, a través del acople de los tres anticuerpos al soporte.

A produção de anticorpos policlonais (IgY) em galinhas tem vantagens sobre os obtidos em outros modelos animais e eles têm sido usados como uma ferramenta para o estudo de proteínas diferentes (NMDA receptor de glutamato no nosso caso, especificamente a subunidade NR1). Nós produzimos anticorpos específicos contra produtos de expressão pela splicing alternativo do gene que codifica receptor NMDA subunidade NR1 no cérebro de ratos adultos. Três peptídeos correspondentes aos locais de splicing (N1, C1 e C2' cassetes) foram concebidos, sintetizados e utilizados individualmente como antígenos em galinhas. Imunoglobulinas específicas foram purificadas a partir de gemas. Os anticorpos foram então usados para purificar o receptor NMDA subunidade NR1 utilizando cromatografia de afinidade, por meio da junção dos três anticorpos ao suporte.

Aproximación in silico a la evolución de la familia de genes que conforman el receptor ionotrópico de glutamato en cuatro especies de primates / In silico approach to the evolution of ionotropic glutamate receptor gene family in four primate species / Aproximação In silico á evolução da família de genes que compõem o receptor ionotrópico de Glutamato em quatro espécies de primatas

El hombre como especie posee un cerebro único en capacidades de análisis por su estructura y patrones de organización que presumiblemente son la base de la inteligencia y la habilidad de manipular el entorno. Adicionalmente, el desarrollo y la evolución del cerebro responden los procesos genéticos subyacentes. Objetivo. Presentar una aproximación al proceso evolutivo de los iGluR con el método filogenético de máxima verosimilitud (ML) y bayesiano (By). Materiales y métodos. Para lo cual se emplean métodos in silico que permiten plantear un modelo de evolución molecular y el reconocimiento cualitativo de los bloques de sintenia, para estos genes en las especies de primates (chimpancé, orangután, mono rhesus y hombre). Resultados. El Glutamato es el principal neurotransmisor y juega un papel importante en la plasticidad neuronal y la neurotoxicidad. La neurotransmisión vía glutamato es mediada por los receptores ionotrópicos de Glutamato (iGluR) tipo NMDA y no-NMDA (AMPA y KA). Se tiene que por cada inferencia filogenética obtenida, se confirma que los iGluR de los mamíferos podrían haber evolucionado a partir de un mecanismo más primitivo de señalización, por lo cual se presentan agrupaciones similares entre algunas especies de primates con roedores. Conclusión: Las secuencias de NR-2 han permanecido en una selección purificadora, y que la escala de divergencia neutral es más rápida en los primates que en los roedores; sin embargo es necesario aplicar otros estudios para confirman estas teorías de evolución.

Man as a species has a brain unique in analysis capabilities due to its structure and organizational patterns that are presumably the basis of intelligence and the ability to manipulate the environment. Additionally, the development and evolution of the brain respond underlying genetic processes. Objective. To present an approach to the evolutionary process of the iGluR with the maximum likelihood (ML) and Bayesian (By) phylogenetic analysis methods. Materials and methods. we used in silico methods to propose a model of molecular evolution and to do a qualitative recognition of synteny blocks for these genes in different species of primates (chimpanzee, orangutan, rhesus monkey and man). Results. Glutamate is the main neurotransmitter and plays an important role in neuronal plasticity and neurotoxicity. Neurotransmission via glutamate is mediated by ionotropic glutamate receptors (iGluR) NMDA type and non-NMDA type (AMPA and KA). For every phylogenetic inference, we confirmed that the iGluRs of mammals could have evolved from a primitive signaling mechanism, thus explaining similar clusters between some species of primates and rodents. Conclusion. The NR-2 sequences have been exposed to a purifying selection, and the neutral level of divergence is faster in primates than in rodents, however further studies are needed to confirm these theories of evolution.

O homem como espécie tem um cérebro único em capacidades de análise por sua estrutura e padrões de organização que, presumivelmente, são a base da inteligência e da capacidade de manipular o meio ambiente. Além ao desenvolvimento e a evolução do cérebro, respondem os processos genéticos subjacentes. Objetivo. Apresentar uma aproximação ao processo evolutivo dos iGluR com o método filogenético de máxima verossimilhança (ML) e bayesiano (By.) Materiais e métodos. Foram empregados métodos in silico que permitem apresentar um modelo de evolução molecular e o reconhecimento qualitativo dos blocos de sintenia, para estes genes das espécies de primatas (chimpanzé, orangotango, o macaco rhesus e o homem). Resultados. O Glutamato é o principal neurotransmissor e desempenha um importante papel na plasticidade neuronal e na neurotoxicidade. A neurotransmissão via Glutamato é mediada pelos receptores ionotrópicos de Glutamato (iGluR) do tipo NMDA e no-NMDA (AMPA e KA). Foi observado que por cada inferência filogenética obtida, confirmase que os iGluR dos mamíferos poderiam ter evoluído a partir de um mecanismo mais primitivo de sinalização, pelo qual se apresentam agrupações semelhantes entre algumas espécies de primatas com roedores. Conclusão. As seqüências de NR-2 têm permanecido numa seleção purificadora, e que a escala de divergência neutral é mais rápida em primatas do que em roedores; embora, é necessario realizar outras pesquisas para confirmar estas teorias da evolução.