Substrate binding mode and its implication on drug design for botulinum neurotoxin A

The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins, the causative agents of botulism, block the neurotransmitter release by specifically cleaving one of the three SNARE proteins and induce flaccid paralysis. The Centers for Disease Control and Prevention (CDC) has declared them as Category A biowarfare agents. The most potent among them, botulinum neurotoxin type A (BoNT/A), cleaves its substrate synaptosome-associated protein of 25 kDa (SNAP-25). An efficient drug for botulism can be developed only with the knowledge of interactions between the substrate and enzyme at the active site. Here, we report the crystal structures of the catalytic domain of BoNT/A with its uncleavable SNAP-25 peptide (197)QRATKM(202) and its variant (197)RRATKM(202) to 1.5 A and 1.6 A, respectively. This is the first time the structure of an uncleavable substrate bound to an active botulinum neurotoxin is reported and it has helped in unequivocally defining S1 to S5' sites. These substrate peptides make interactions with the enzyme predominantly by the residues from 160, 200, 250 and 370 loops. Most notably, the amino nitrogen and carbonyl oxygen of P1 residue (Gln197) chelate the zinc ion and replace the nucleophilic water. The P1'-Arg198, occupies the S1' site formed by Arg363, Thr220, Asp370, Thr215, Ile161, Phe163 and Phe194. The S2' subsite is formed by Arg363, Asn368 and Asp370, while S3' subsite is formed by Tyr251, Leu256, Val258, Tyr366, Phe369 and Asn388. P4'-Lys201 makes hydrogen bond with Gln162. P5'-Met202 binds in the hydrophobic pocket formed by the residues from the 250 and 200 loop. Knowledge of interactions between the enzyme and substrate peptide from these complex structures should form the basis for design of potent inhibitors for this neurotoxin.     

Synthesis of novel inhibitors of β-glucuronidase based on benzothiazole skeleton and study of their binding affinity by molecular docking

Benzothiazole derivatives 1-26 have been synthesized and their in vitro β-glucuronidase potential has been evaluated. Compounds 4 (IC(50)=8.9 ± 0.25 μM), 5 (IC(50)=36.1 ± 1.80 μM), 8 (IC(50)=8.9 ± 0.38 μM), 13 (IC(50)=19.4 ± 1.00 μM), 16 (IC(50)=4.23 ± 0.054 μM), and 18 (IC(50)=2.26 ± 0.06 μM) showed β-glucuronidase activity potent than the standard (d-saccharic acid 1,4-lactone, IC(50)=48.4 ± 1.25 μM). Compound 9 (IC(50)=94.0 ± 4.16 μM) is found to be the least active among the series. All active analogs were also evaluated for cytotoxicity and none of the compounds showed any cytotoxic effect. Furthermore, molecular docking studies were performed using the gold 3.0 program to investigate the binding mode of benzothiazole derivatives. This study identifies a novel class of β-glucuronidase inhibitors.     

Epibrassinolide Application Regulates Some Key Physio-biochemical Attributes As Well As Oxidative Defense System in Maize Plants Grown Under Saline Stress

It was aimed to investigate the ameliorative effect of exogenously applied 24-epibrassinolide (EBR) on some key growth parameters and mineral elements in two salt-stressed maize (PR 32T83 and PR 34N24) cultivars. A factorial experiment was designed with two electrical permeability (EC) levels (1.1 and 8.0 dS/m) and two levels (1.5 and 2.0 µM) of EBR supplied as a seed treatment, foliar spray, or both in combination. The foliar application of EBR was done once a week during the experiment. After 42 days of these treatments, the plants were harvested to assess growth, water relations, and oxidative and antioxidative systems. Salt stress markedly reduced plant fresh and dry weights, maximum fluorescence yield of PS-II, chlorophyll contents, leaf water potential, and leaf K and Ca, but it increased membrane permeability, the activities of superoxide dismutase (SOD; EC 1.15.1.1), peroxidase (POD; EC. 1.11.1.7), and catalase (CAT; EC. 1.11.1.6) enzymes, and the contents of proline and glycine betaine, leaf sap osmotic pressure, lipid peroxidation, hydrogen peroxide, and leaf Na and Cl. However, both seed treatment and foliar application of EBR to the maize plants exposed to saline conditions enhanced key growth attributes, water relations, and the activities of various antioxidant enzymes as well as the levels of proline, but they reduced electrolyte leakage, and H₂O₂ and MDA contents. Saline stress reduced leaf N, Ca²⁺, K⁺, and P contents as compared to those in the non-stressed plants. Both seed treatment and foliar application of EBR reduced Na⁺ and Cl^? concentrations, but increased those of N, Ca²⁺, K⁺, and P. Foliar application of EBR was more effective in increasing nutrient levels of plants grown at the high saline regime compared to the seed treatment of EBR. The study clearly indicates that both seed treatment and foliar application of EBR at the rate of 2.0 µM can overcome the detrimental effect of salinity stress on maize growth, which was found to be significantly linked to reduced concentrations of Na, Cl, MDA, and H₂O₂ as well as EL and increased activities of key antioxidant enzymes in the maize plants.     

The abundance of herbivorous fish on an inshore Red Sea reef following a mass coral bleaching event

A healthy herbivore community is critical for the ability of a reef to resist and recover from severe disturbances and to regain lost coral cover (i.e., resilience). The densities of the two major herbivorous fish groups (the family Acanthuridae and scarine labrids) were comparatively studied for an inshore reef that was severely impacted by a mass coral bleaching event in 2010 and an unaffected reef within the same region. Densities were found to be significantly higher on the affected reef, most likely due to the high algal densities on that reef. However, densities of herbivores on both reefs were found to be on average about 1–2 orders of magnitude lower than previously published reports from some Pacific reefs and from Red Sea reefs in the Gulf of Aqaba and only slightly higher than Caribbean reefs. Thus, it is predicted that recovery for this reef and similarly affected reefs may be very slow. The protection of herbivores from overfishing and the introduction of other management strategies that maximize reef resilience in Saudi Arabian waters are highly recommended.     

The recognition of multi-class protein folds by adding average chemical shifts of secondary structure elements

The recognition of protein folds is an important step in the prediction of protein structure and function. Recently, an increasing number of researchers have sought to improve the methods for protein fold recognition. Following the construction of a dataset consisting of 27 protein fold classes by Ding and Dubchak in 2001, prediction algorithms, parameters and the construction of new datasets have improved for the prediction of protein folds. In this study, we reorganized a dataset consisting of 76-fold classes constructed by Liu et al. and used the values of the increment of diversity, average chemical shifts of secondary structure elements and secondary structure motifs as feature parameters in the recognition of multi-class protein folds. With the combined feature vector as the input parameter for the Random Forests algorithm and ensemble classification strategy, we propose a novel method to identify the 76 protein fold classes. The overall accuracy of the test dataset using an independent test was 66.69%; when the training and test sets were combined, with 5-fold cross-validation, the overall accuracy was 73.43%. This method was further used to predict the test dataset and the corresponding structural classification of the first 27-protein fold class dataset, resulting in overall accuracies of 79.66% and 93.40%, respectively. Moreover, when the training set and test sets were combined, the accuracy using 5-fold cross-validation was 81.21%. Additionally, this approach resulted in improved prediction results using the 27-protein fold class dataset constructed by Ding and Dubchak.     

The effect and action mechanism of resveratrol on the vascular endothelial cell by high glucose treatment

To investigate the effect and action mechanism of resveratrol on the vascular endothelial cell by high glucose treatment. Primarily cultured human umbilical vein endothelial cells (HUVECs) were pretreated by resveratrol (0.2 μmol/L) and holding for 6 h, and then cultured in Dulbecco Modified Eagle Medium (DMEM) within 0.45 mmol/L of palmimte acid and 32.8 mmol/L of glucose, which is holding for 12 h. The cells were collected to analyze the expression of E-selected element. Supernatant of cultured cells, induced by 100 nmol/L insulin for 30 min, was used to analyze the nitric oxide content. Compared with normal control cells, the secretion of nitric oxide is stimulated by insulin decrease, however, the expression of E-selected element increased in HUVEC. Resveratrol treatment increased the secretion of nitric oxide stimulated by insulin and decreased the expression of E-selected element and partly counteracts the impairment of high glucose and palmitate acid on the function of endothelial cells. Resveratrol can improve and protect the function of high glucose and fatty acid cultured endothelial cell, and therefore may be a promising medicine in the prevention or therapy of diabetic macrovascular diseases.     

Effect of water temperature,feeding frequency,and protein percent in the diet on water quality,growth and behavior of Nile tilapia Oreochromis niloticus (Linnaeus, 1758)

This study evaluated how water temperature (26, 28, and 30°C), number of meals per day (one or two meals), and protein percent in diet (20, 25 and 30%) impact growth performance, biometric indices, and feeding behavior of Nile tilapia, Oreochromis niloticus. Fish were randomly allocated into 18 equal replicate groups. Higher final body weight was observed in fish reared at 30°C and fed one meal per day containing 30% crude protein. Better weight gain, weight gain %, feed conversion ratio, specific growth rate, and condition factor were recorded in fish reared at 26°C and fed one meal per day containing 30% protein. The best length weight relationship was obtained in fish reared at 26°C and fed one meal per day containing 30% crude protein. Shorter feeding duration and duration of appetite inhibition latency were recorded in fish reared at 30°C, fed one meal per day, and given a diet containing 30% protein. The highest proactivity was recorded in fish reared at 30°C, received one meal per day, and with 25% crude protein in their diet. Conclusively, rearing Nile tilapia at 26–30°C with a lower feeding frequency (one meal/day) and a 30% crude protein diet achieved better performance and feeding behavior.     

Computational analysis of bovine alpha-1 collagen sequences

Bovine collagen alpha-1 is a naturally occurring extracellular matrix protein found in tendons and other connective tissues. It playsa vital role in cell growth, differentiation, attachment, and migration. Recent findings have established that collagen alpha-1 isinvolved in osteogenesis imperfecta phenotype in cattle but deep information about other members of this large family is notavailable so far. So with a view to finding a new edge and attempt to figure out a correlation among the well attributed Bovinealpha-1 collagen sequences are executed and analyzed. To do so, comparative analysis among the 28 members of collagen familyhas been carried out using Computational tools. Consequently, based on the physico-chemical, secondary structural, functionaland phylogenetic classifications, we have selected collagen 12, 14 and 20 as targets for pathological conditions. These proteinsbelong to the FACIT family and significantly showed low glycine and proline content, high instability and aliphatic index.Moreover, FACIT family collagens contain multiple triple helical domains and being members of the FACIT family, bovinecollagen 12, 14, 20 do not form fibrils by themselves but they are associated to collagen 1 associated fibrils. These collagenmolecules might be crucial candidates to detect and understand the process of matrix remodeling in diseases especially in the arenaof cellular compartments.     

A chick model of retinal detachment: cone rich and novel

Background

Development of retinal detachment models in small animals can be difficult and expensive. Here we create and characterize a novel, cone-rich retinal detachment (RD) model in the chick.

Methodology/Principal Findings

Retinal detachments were created in chicks between postnatal days 7 and 21 by subretinal injections of either saline (SA) or hyaluronic acid (HA). Injections were performed through a dilated pupil with observation via surgical microscope, using the fellow eye as a control. Immunohistochemical analyses were performed at days 1, 3, 7, 10 and 14 after retinal detachment to evaluate the cellular responses of photoreceptors, Müller glia, microglia and nonastrocytic inner retinal glia (NIRG). Cell proliferation was detected with bromodeoxyuridine (BrdU)-incorporation and by the expression of proliferating cell nuclear antigen (PCNA). Cell death was detected with terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL). As in mammalian models of RD, there is shortening of photoreceptor outer segments and mis-trafficking of photoreceptor opsins in areas of RD. Photoreceptor cell death was maximal 1 day after RD, but continued until 14 days after RD. Müller glia up-regulated glial fibriliary acidic protein (GFAP), proliferated, showed interkinetic nuclear migration, and migrated to the subretinal space in areas of detachment. Microglia became reactive; they up-regulated CD45, acquired amoeboid morphology, and migrated toward outer retina in areas of RD. Reactive NIRG cells accumulated in detached areas.

Conclusions/Significance

Subretinal injections of SA or HA in the chick eye successfully produced retinal detachments and cellular responses similar to those seen in standard mammalian models. Given the relatively large eye size, and considering the low cost, the chick model of RD offers advantages for high-throughput studies.