Molecular evolution of B<Subscript>6</Subscript> enzymes: Binding of pyridoxal-5'-phosphate and Lys41Arg substitution turn ribonuclease A into a model B<Subscript>6</Subscript> protoenzyme

Background  

The pyridoxal-5'-phosphate (PLP)-dependent or vitamin B₆-dependent enzymes that catalyze manifold reactions in the metabolism of amino acids belong to no fewer than four evolutionarily independent protein families. The multiple evolutionary origin and the essential mechanistic role of PLP in these enzymes argue for the cofactor having arrived on the evolutionary scene before the emergence of the respective apoenzymes and having played a dominant role in the molecular evolution of the B₆ enzyme families. Here we report on an attempt to re-enact the emergence of a PLP-dependent protoenzyme. The starting protein was pancreatic ribonuclease A (RNase), in which active-site Lys41 or Lys7 readily form a covalent adduct with PLP.     

Microwave-assisted and scandium triflate catalyzed synthesis of tetrahydrobenzo[<Emphasis Type="Italic">a</Emphasis>]xanthen-11-ones

Abstract  

Synthesis of 12-aryl-8,9,10,12-tetrahydro-benzo[a]xanthen-11-ones was achieved by one-pot condensation of β-naphthol, substituted benzaldehydes, and 1,3-dicarbonyl compounds catalyzed by Sc(OTf)₃ under microwave irradiation in excellent isolated yields. The catalyst was recycled up to four cycles with no appreciable loss in catalytic activity. The compounds were evaluated for Src kinase activity and anticancer activity.     

Exploring laccase-like multicopper oxidase genes from the ascomycete <Emphasis Type="Italic">Trichoderma reesei</Emphasis>: a functional,phylogenetic and evolutionary study

Background  

The diversity and function of ligninolytic genes in soil-inhabiting ascomycetes has not yet been elucidated, despite their possible role in plant litter decay processes. Among ascomycetes, Trichoderma reesei is a model organism of cellulose and hemicellulose degradation, used for its unique secretion ability especially for cellulase production. T. reesei has only been reported as a cellulolytic and hemicellulolytic organism although genome annotation revealed 6 laccase-like multicopper oxidase (LMCO) genes. The purpose of this work was i) to validate the function of a candidate LMCO gene from T. reesei, and ii) to reconstruct LMCO phylogeny and perform evolutionary analysis testing for positive selection.     

Studies of the intermediary metabolism in cultured cells of the insect <Emphasis Type="Italic">Spodoptera frugiperda</Emphasis> using <Superscript>13</Superscript>C- or <Superscript>15</Superscript>N-labelled tracers

Background  

Insect cells can serve as host systems for the recombinant expression of eukaryotic proteins. Using this platform, the controlled expression of ¹⁵N/¹³C labelled proteins requires the analysis of incorporation paths and rates of isotope-labelled precursors present in the medium into amino acids. For this purpose, Spodoptera frugiperda cells were grown in a complex medium containing [U-¹³C₆]glucose. In a second experiment, cultures of S. frugiperda were grown in the presence of ¹⁵N-phenylalanine.     

Supramolecular assembled of hexameric water clusters into a 1D chain containing (H<Subscript>2</Subscript>O)<Subscript>6</Subscript> and [(H<Subscript>2</Subscript>O)<Subscript>4</Subscript>O<Subscript>2</Subscript>] stabilized by hydrogen bonding in a copper complex

Background  

Various water clusters including hexamers, heptamers, octamers, decamers and 1D or 2D infinite water chains in a number of organic and inorganic-organic hybrid hosts, have been reported.     

Development of ERK Activity Sensor,an <Emphasis Type="Italic">in vitro</Emphasis>, FRET-based sensor of Extracellular Regulated Kinase activity

Background  

Study of ERK activation has thus far relied on biochemical assays that are limited to the use of phospho-specific antibodies and radioactivity in vitro, and analysis of whole cell populations in vivo. As with many systems, fluorescence resonance energy transfer (FRET) can be utilized to make highly sensitive detectors of molecular activity. Here we introduce FRET-based ERK Activity Sensors, which utilize variants of Enhanced Green Fluorescent Protein fused by an ERK-specific peptide linker to detect ERK2 activity.     

Identification and molecular characterization of a novel flavin-free NADPH preferred azoreductase encoded by <Emphasis Type="Italic">azoB</Emphasis> in <Emphasis Type="Italic">Pigmentiphaga kullae</Emphasis> K24

Background  

Microbial degradation of azo dyes is commonly initiated by the reduction of the azo bond(s) by a group of NADH or NADPH dependant azoreductases with many requiring flavin as a cofactor. In this study, we report the identification of a novel flavin-free NADPH preferred azoreductase encoded by azoB in Pigmentiphaga kullae K24.     

EAAC1 is expressed in rat and human prostate epithelial cells; functions as a high-affinity L-aspartate transporter; and is regulated by prolactin and testosterone

Background  

Prostate epithelial cells accumulate a high level of aspartate that is utilized as a substrate for their unique function of production and secretion of enormously high levels of citrate. In most mammalian cells aspartate is synthesized; and, therefore is a non-essential amino acid. In contrast, in citrate-producing prostate cells, aspartate is an essential amino acid that must be derived from circulation. The prostate intracellular/extracellular conditions present a 40:1 concentration gradient. Therefore, these cells must possess a plasma membrane-associated aspartate uptake transport process to achieve their functional activity. In earlier kinetic studies we identified the existence of a unique Na+-dependent high-affinity L-aspartate transport process in rat prostate secretory epithelial cells. The present report is concerned with the identification of this putative L-aspartate transporter in rat and human prostate cells.     

High‐precision determination of lithium and magnesium isotopes utilising single column separation and multi‐collector inductively coupled plasma mass spectrometry

Rationale

Li and Mg isotopes are increasingly used as a combined tool within the geosciences. However, established methods require separate sample purification protocols utilising several column separation procedures. This study presents a single‐step cation‐exchange method for quantitative separation of trace levels of Li and Mg from multiple sample matrices.

Methods

The column method utilises the macro‐porous AGMP‐50 resin and a high‐aspect ratio column, allowing quantitative separation of Li and Mg from natural waters, sediments, rocks and carbonate matrices following the same elution protocol. High‐precision isotope determination was conducted by multi‐collector inductively coupled plasma mass spectrometry (MC‐ICPMS) on the Thermo Scientific™ NEPTUNE Plus™ fitted with 10¹³ Ω amplifiers which allow accurate and precise measurements at ion beams ≤0.51 V.

Results

Sub‐nanogram Li samples (0.3–0.5 ng) were regularly separated (yielding Mg masses of 1–70 μg) using the presented column method. The total sample consumption during isotopic analysis is <0.5 ng Li and <115 ng Mg with long‐term external 2σ precisions of ±0.39‰ for δ⁷Li and ±0.07‰ for δ²⁶Mg. The results for geological reference standards and seawater analysed by our method are in excellent agreement with published values despite the order of magnitude lower sample consumption.

Conclusions

The possibility of eluting small sample masses and the low analytical sample consumption make this method ideal for samples of limited mass or low Li concentration, such as foraminifera, mineral separates or dilute river waters.

     

Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2

Background  

The LGI2 (leucine-rich, glioma inactivated 2) gene, a prime candidate for partial epilepsy with pericentral spikes, belongs to a family encoding secreted, beta-propeller domain proteins with EPTP/EAR epilepsy-associated repeats. In another family member, LGI1 (leucine-rich, glioma inactivated 1) mutations are responsible for autosomal dominant lateral temporal epilepsy (ADLTE). Because a few LGI1 disease mutations described in the literature cause secretion failure, we experimentally analyzed the secretion efficiency and subcellular localization of several LGI1 and LGI2 mutant proteins corresponding to observed non-synonymous single nucleotide polymorphisms (nsSNPs) affecting the signal peptide, the leucine-rich repeats and the EAR propeller.     

A novel synthetic approach towards pyrazole-4-carboxamides using N-(3-(dimethylamino)-2-formylacryloyl)formamide

Abstract  

A novel synthesis of pyrazole-4-carboxamides is reported. The reaction of N-(3-(dimethylamino)-2-formylacryloyl)formamide, an intermediate obtained by Vilsmeier–Haack formylation of acetonitrile, with hydrazine hydrate or monosubstituted hydrazines provides such compounds in good yields. This method has advantages over other methods for construction of such ring systems previously described in the literature.     

Kinetic characterisation of arylamine <Emphasis Type="Italic">N</Emphasis>-acetyltransferase from <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis>

Background  

Arylamine N-acetyltransferases (NATs) are important drug- and carcinogen-metabolising enzymes that catalyse the transfer of an acetyl group from a donor, such as acetyl coenzyme A, to an aromatic or heterocyclic amine, hydrazine, hydrazide or N-hydroxylamine acceptor substrate. NATs are found in eukaryotes and prokaryotes, and they may also have an endogenous function in addition to drug metabolism. For example, NAT from Mycobacterium tuberculosis has been proposed to have a role in cell wall lipid biosynthesis, and is therefore of interest as a potential drug target. To date there have been no studies investigating the kinetic mechanism of a bacterial NAT enzyme.     

Local and global modes of drug action in biochemical networks

Background  

It is becoming increasingly accepted that a shift is needed from the traditional target-based approach of drug development towards an integrated perspective of drug action in biochemical systems. To make this change possible, the interaction networks connecting drug targets to all components of biological systems must be identified and characterized.     

Automated extraction of chemical structure information from digital raster images

Background  

To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated.     

Glyceraldehyde-3-phosphate dehydrogenase is largely unresponsive to low regulatory levels of hydrogen peroxide in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Background  

The reversible oxidation of protein SH groups has been considered to be the basis of redox regulation by which changes in hydrogen peroxide (H₂O₂) concentrations may control protein function. Several proteins become S-glutathionylated following exposure to H₂O₂ in a variety of cellular systems. In yeast, when using a high initial H₂O₂ dose, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified as the major target of S-glutathionylation which leads to reversible inactivation of the enzyme. GAPDH inactivation by H₂O₂ functions to reroute carbohydrate flux to produce NADPH. Here we report the effect of low regulatory H₂O₂ doses on GAPDH activity and expression in Saccharomyces cerevisiae.     

Characterization of tetracycline modifying enzymes using a sensitive <Emphasis Type="Italic">in vivo</Emphasis> reporter system

Background  

Increasing our understanding of antibiotic resistance mechanisms is critical. To enable progress in this area, methods to rapidly identify and characterize antibiotic resistance conferring enzymes are required.     

Osmotic stress-dependent serine phosphorylation of the histidine kinase homologue DokA

Background  

Two-component systems consisting of histidine kinases and their corresponding receivers are widespread in bacterial signal transduction. In the past few years, genes coding for homologues of two-component systems were also discovered in eukaryotic organisms. DokA, a homologue of bacterial histidine kinases, is an element of the osmoregulatory pathway in the amoeba Dictyostelium. The work described here addresses the question whether DokA is phosphorylated in vivo in response to osmotic stress.     

Development of a sensitive non-radioactive protein kinase assay and its application for detecting DYRK activity in <Emphasis Type="Italic">Xenopus laevis</Emphasis> oocytes

Background  

Although numerous non-radioactive methods are in use to measure the catalytic activity of protein kinases, most require specialized equipment and reagents and are not sufficiently sensitive for the detection of endogenous kinase activity in biological samples. Kinases of the DYRK family have important functions in developmental and pathophysiological processes in eukaryotic organisms including mammals. We aimed to develop a highly sensitive, low-tech assay suitable to determine the activity of DYRK family kinases in tissues or cells from diverse sources.     

An <Emphasis Type="Italic">ab initio</Emphasis>and AIM investigation into the hydration of 2-thioxanthine

Background  

Hydration is a universal phenomenon in nature. The interactions between biomolecules and water of hydration play a pivotal role in molecular biology. 2-Thioxanthine (2TX), a thio-modified nucleic acid base, is of significant interest as a DNA inhibitor yet its interactions with hydration water have not been investigated either computationally or experimentally. Here in, we reported an ab initio study of the hydration of 2TX, revealing water can form seven hydrated complexes.     

A highly efficient and recyclable fluorous palladium catalyst for Heck reactions in water

Abstract  

A fluorous nano-palladium catalyst has been synthesized and characterized. The catalyst is highly active for the Heck reaction of aryl halides with substituted styrenes in water under air. The corresponding Heck products were obtained in high yields with good stereoselectivity (E/Z up to 98:2). In addition, the catalyst could be recovered by fluorous liquid–liquid separation and reused four times without significant loss of activity or stereoselectivity.