Thermodynamic and structural analysis of interactions between peptide ligands and SEB

Staphylococcal enterotoxin B (SEB) is an exotoxin produced by Staphylococcus aureus and commonly associated with food poisoning. In this study, SEB‐binding peptides were identified by screening a phage displayed peptide library. The binding of peptides to SEB was tested with isothermal titration calorimetry (ITC) and of the five selected peptides, three showed affinity to SEB, with one measured to have the highest affinity constant (10⁵ M^?1). ITC revealed that the interaction of peptide ligands with SEB was driven entropically and the binding was dominated by hydrophobic interactions. Circular dichroism (CD) measurements and molecular dynamics (MD) simulations, together, give a structural insight into the interaction of peptides with SEB. While SEB binding peptides showed random coil structure before binding, after complex formation they had more ordered structures. The peptide with highest affinity to SEB showed stable conformation during MD simulation. Taken together, our approach about thermodynamic and structural characterization of peptide ligands can be used to develop aptamers, with high affinity and selectivity, for biosensor applications. Copyright © 2009 John Wiley & Sons, Ltd.     

The effect of salt stress on lipid peroxidation, antioxidative enzymes and proline content of sesame cultivars

The effect of increasing NaCl concentrations was studied on two different cultivars (cv. Orhangazi and cv. Cumhuriyet) of Sesamum indicum. Seedlings were grown for 40 days in half strength Hoagland solution and after 40 days treated with different NaCl concentrations (0, 50 and 100 mM) for 21 days. Differences in growth parameters, lipid peroxidation, antioxidative enzyme activities and proline accumulation were tested in order to put forward the relative tolerance or sensitivity of the cultivars. Results indicated that both parameters differ according to the cultivar's ability in coping oxidative stress caused by salinity. Constitutive levels of antioxidative enzyme activities were almost the same between the cultivars; however, cv. Cumhuriyet was able to induce antioxidative enzyme activities more efficiently when subjected to salt stress. Growth parameters, lipid peroxidation and proline accumulation results are also in good correlation with supporting this cultivar's being relatively tolerant.     

3-Pyridinylboronic Acid Ameliorates Rotenone-Induced Oxidative Stress Through Nrf2 Target Genes in Zebrafish Embryos

Neurochemical Research - Parkinson’s disease (PD) is one of the most common forms of neurodegenerative diseases and research on potential therapeutic agents for PD continues. Rotenone is a...     

A selective molecularly imprinted polymer for immobilization of acetylcholinesterase (AChE): an active enzyme targeted and efficient method

In the present study, we immobilized acetylcholinesterase (AChE) enzyme onto acetylcholine removed imprinted polymer and acetylcholine containing polymer. First, the polymers were produced with acetylcholine, substrate of AChE, by dispersion polymerization. Then, the enzyme was immobilized onto the polymers by using two different methods: In the first method (method A), acetylcholine was removed from the polymer, and then AChE was immobilized onto this polymer (acetylcholine removed imprinted polymer). In the second method (method B), AChE was immobilized onto acetylcholine containing polymer by affinity. In method A, enzyme‐specific species (binding sites) occurred by removing acetylcholine from the polymer. The immobilized AChE reached 240% relative specific activity comparison with free AChE because the active enzyme molecules bounded onto the polymer. Transmission electron microscopy results were taken before and after immobilization of AChE for the assessment of morphological structure of polymer. Also, the experiments, which include optimum temperature (25–65°C), optimum pH (3–10), thermal stability (4–70°C), kinetic parameters, operational stability and reusability, were performed to determine the characteristic of the immobilized AChE. Copyright © 2015 John Wiley & Sons, Ltd.     

Kinetic and docking studies of phenol-based inhibitors of carbonic anhydrase isoforms I, II, IX and XII evidence a new binding mode within the enzyme active site

Carbonic anhydrases (CAs, EC 4.2.1.1) are inhibited by sulfonamides, inorganic anions, phenols, coumarins (acting as prodrugs) and polyamines. A novel class of CA inhibitors (CAIs), interacting with the CA isozymes I, II (cytosolic) and IX, XII (transmembrane, tumor-associated) in a different manner, is reported here. Kinetic measurements allowed us to identify hydroxy-/methoxy-substituted benzoic acids as well as di-/tri-methoxy benzenes as submicromolar-low micromolar inhibitors of the four CA isozymes. Molecular docking studies of a set of such inhibitors within CA I and II allowed us to understand the inhibition mechanism. This new class of inhibitors binds differently compared to all other classes of inhibitors known to date: they were found between the phenol-binding site and the coumarin-binding site, filling thus the middle of the enzyme cavity. They exploit different interactions with amino acid residues and water molecules from the CA active site compared to other classes of inhibitors, offering the possibility to design CAIs with an interesting inhibition profile compared to the clinically used sulfonamides/sulfamates.     

Biological control of the citrus red mite <Emphasis Type="Italic">Panonychus</Emphasis><Emphasis Type="Italic">citri</Emphasis> by the predator mite <Emphasis Type="Italic">Typhlodromus athiasae</Emphasis> on two citrus cultivars under greenhouse conditions

This study examined the efficacy of the predatory mite Typhlodromus athiasae Porath and Swirski (Acari: Phytoseiidae) as a biological control agent of the citrus red mite Panonychus citri (McGregor) (Acari: Tetranychidae) on seedlings of Washington and Valencia citrus cultivars at 1:10, 1:20 and 1:40 predator:prey release ratios under greenhouse conditions. At predator:prey ratios of 1:10, significant reductions on P. citri populations were observed one week after release of T. athiasae, and populations remained at low levels thereafter. The highest mean numbers of P. citri were found in the third week on the Washington cultivar and in the fourth week on Valencia, in a control group with no predators. This study demonstrates the potential of T. athiasae to effectively control P. citri on Washington and Valencia cultivars under greenhouse conditions at predator:prey ratios of 1:10. However, T. athiasae was unable to control the citrus red mite populations when the predator:prey ratio was reduced to 1:40. We therefore recommend a release ratio of 1:10 for effective control of P. citri in greenhouses on seedlings of Washington and Valencia citrus.     

Genetic relationships among NE Turkish Lilium L. (Liliaceae) species based on a random amplified polymorphic DNA analysis

Random amplified polymorphic DNA (RAPD) fingerprinting was used to study species boundaries in six closely related NE Turkish Lilium (Liliaceae) taxa of the section Liriotypus. The investigated taxa were L. ciliatum, L. akkusianum, L. ponticum, L. kesselringianum, L. armenum, and L. szovitsianum. Of the 108 primers screened, 11 provided polymorphic and reproducible bands. A total of 93 polymorphic bands were scored for 122 individuals from 18 populations of the six Lilium taxa and principle coordinate analysis and neighbour-joining cluster analysis based on these RAPD profiles were performed. The results demonstrate a clear distinction between the two species L. ciliatum and L. akkusianum, and the other four species. While populations of the two species groups are found to be allopatrically distributed, the two species groups overlap in their geographical ranges. Analysis of molecular variance (AMOVA) indicated that nearly half of the total molecular variance is found within the individual populations and that the molecular variance among species is as high as the variance within the individual species, indicating that genetic differentiation of the species is rather weak.     

Effects of shock waves on oxidative stress and some trace element levels of rat liver and diaphragm muscles

This study was designed to investigate whether the short-term extracorporeal shockwave lithotripsy (ESWL) exposure to kidney produces an oxidative stress and a change in some trace element levels in liver and diaphragm muscles of rats. Twelve male Wistar albino rats were divided randomly into two groups, each consisting of six rats. The animals in the first group did not receive any treatment and served as control group. The right-side kidneys of animals in group 2 were treated with two-thousand 18 kV shock waves while anesthetized with 50 mg kg(-1) ketamine. The localization of the right kidney was achieved after contrast medium injection through a tail vein under fluoroscopy control. The animals were killed 72 h after the ESWL treatment, and liver and diaphragm muscles were harvested for the determination of tissue oxidative stress and trace element levels. Although the malondialdehyde level increased, superoxide dismutase and glutathione peroxidase enzyme activities decreased in the livers and diaphragm muscles of ESWL-treated rats. Although glutathione level increased in liver, it decreased in diaphragm muscles of ESWL-treated animals. Fe, Mg and Mn levels decreased, and Cu and Pb levels increased in the livers of ESWL-treated animals. Fe and Cu levels increased, and Mg, Pb, Mn and Zn levels decreased in the diaphragm muscles of ESWL-treated animals. It also causes a decrease or increase in many mineral levels in liver and diaphragm muscles, which is an undesirable condition for the normal physiological function of tissues.