Enumerating Pathways of Proton Abstraction Based on a Spatial and Electrostatic Analysis of Residues in the Catalytic Site

The pathways of proton abstraction (PA), a key aspect of most catalytic reactions, is often controversial and highly debated. Ultrahigh-resolution diffraction studies, molecular dynamics, quantum mechanics and molecular mechanic simulations are often adopted to gain insights in the PA mechanisms in enzymes. These methods require expertise and effort to setup and can be computationally intensive. We present a push button methodology – Proton abstraction Simulation (PRISM) – to enumerate the possible pathways of PA in a protein with known 3D structure based on the spatial and electrostatic properties of residues in the proximity of a given nucleophilic residue. Proton movements are evaluated in the vicinity of this nucleophilic residue based on distances, potential differences, spatial channels and characteristics of the individual residues (polarity, acidic, basic, etc). Modulating these parameters eliminates their empirical nature and also might reveal pathways that originate from conformational changes. We have validated our method using serine proteases and concurred with the dichotomy in PA in Class A β-lactamases, both of which are hydrolases. The PA mechanism in a transferase has also been corroborated. The source code is made available at www.sanchak.com/prism

The Effect of Aeration for 6-Pentyl-alpha-pyrone, Conidia and Lytic Enzymes Production by Trichoderma asperellum Strains Grown in Solid-State Fermentation

International audienceIn recent years, the production of biopesticides has gained great attention in the scientific word because it is an important alternative to replace the much debated chemical pesticides used on the field crops. Fungal lytic enzymes, conidia and secondary metabolites like 6 pentyl-alpha-pyrone (6-PP) play a very important role in the biological control of pests. On the present study, the influence of application of air through a solid-state fermentation using three Trichoderma asperellum strains to produce conidia, 6-PP and essential enzymes were evaluated. A mix of vine shoots, potatoes flour, jatropha, olive pomace and olive oil as substrates was used. T. asperellum TV104 showed the best 6-PP production (3.06 ± 0.15 mg g DM−1), cellulases activities (34.3 ± 0.4 U g−1), and amylase activity (46.3 ± 0.6 U g−1) however, T. asperellum TF1 produced the higher levels of lipase (30.6 ± 0.3 U g−1), under air conditions. The production of these same enzymes was less efficient without the application of forced aeration. The forced aeration increased the conidia production, the best value was observed with T. asperellum TF1 (2.23 ± 0.07 × 109 g DM−1)

Sweet Peppers

Sweet pepper is an important greenhouse vegetable crop and highly attractive to multiple pest and pathogen species. The main pests and diseases detrimental to pepper crops in various parts of the globe are reported here, along with the most effective or sustainable control strategies currently applied to manage them. Biological control of the main pest species, such as thrips, whiteflies and spider mites, is in general very successful with generalist predators, because of their ability to establish populations prior to pest invasions by using the plant-provided pollen as an alternative food source. However, other pest species, such as aphids, stink bugs and the pepper weevil, are still hard to control without pesticides and require new tools for management that do not disrupt the robust system of biological control. Most diseases can be controlled well by managing the climate, soil solarization, growing out of soil or by applying bacterial or fungal antagonists. All these tools together offer the opportunity to manage most pest and diseases with a minimal use of pesticides