Prediction of contact maps with neural networks and correlated mutations

Contact maps of proteins are predicted with neural network-basedmethods, using as input codings of increasing complexity includingevolutionary information, sequence conservation, correlatedmutations and predicted secondary structures. Neural networksare trained on a data set comprising the contact maps of 173non-homologous proteins as computed from their well resolvedthree-dimensional structures. Proteins are selected from theProtein Data Bank database provided that they align with atleast 15 similar sequences in the corresponding families. Thepredictors are trained to learn the association rules betweenthe covalent structure of each protein and its contact map witha standard back propagation algorithm and tested on the sameprotein set with a cross-validation procedure. Our results indicatethat the method can assign protein contacts with an averageaccuracy of 0.21 and with an improvement over a random predictorof a factor >6, which is higher than that previously obtainedwith methods only based either on neural networks or on correlatedmutations. Furthermore, filtering the network outputs with aprocedure based on the residue coordination numbers, the accuracyof predictions increases up to 0.25 for all the proteins, withan 8-fold deviation from a random predictor. These scores arethe highest reported so far for predicting protein contact maps.     

Influence of the chemical structure of additives poly(ethylene-co-vinyl acetate)-based on the pour point of crude oils

One of the methods to prevent wax precipitation, during petroleum production, transport, and refining, is the use of polymer additives that can reduce the oil pour point. However, no single additive work for all types of crude oil and this relation is not yet well known. In this study, a family of polymers based on poly(ethylene-co-vinyl acetate), containing hydroxyl groups and long pendant hydrocarbon chains (from C6 to C18), were synthesized and characterized by H¹ nuclear magnetic resonance and solubility test. Four crude oil samples containing different amounts and size distribution of the wax were used. The additive's action is favored by higher contents of iso + cycloalkanes and lower contents of n-paraffins with larger chain sizes. The presence of the CH₃COO group in the copolymers promoted the lowering of the pour point, supported by a low OH concentration and the presence of a long pendant hydrocarbon chain: the best results were obtained with C10 and C12 chain lengths. © 2020 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020 , 137, 48969.     

Substrate Flexibility of the Flavin-Dependent Dihydropyrrole Oxidases PigB and HapB Involved in Antibiotic Prodigiosin Biosynthesis

In the biosynthesis of the tripyrrolic pigment prodigiosin, PigB is a predicted flavin-dependent oxidase responsible for the formation of 2-methyl-3-amylpyrrole (MAP) from a dihydropyrrole. To prove which dihydropyrrole is the true intermediate, both possibilities, 5-methyl-4-pentyl-3,4-dihydro-2H-pyrrole ( 5 a , resulting from transamination of the aldehyde of 3-acetyloctanal) and 2-methyl-3-pentyl-3,4-dihydro-2H-pyrrole ( 6 , resulting from transamination of the ketone), were synthesised. Only 5 a restored pigment production in a strain of Serratia sp. ATCC 39006 blocked earlier in MAP biosynthesis. PigB is membrane-associated and inactive when its transmembrane domain was deleted, but HapB, its homologue in Hahella chejuensis, lacks the transmembrane domain and is active in solution. Two colourimetric assays for PigB and HapB were developed, and the HapB-catalysed reaction was kinetically characterised. Ten analogues of 5 a were synthesised, varying in the C2 and C3 side chains, and tested as substrates of HapB in vitro and for restoration of pigment production in Serratia ΔpigD in vivo. All lengths of side chain tested at C3 were accepted, but only short side chains at C2 were accepted. The knowledge that 5 a is an intermediate in prodigiosin biosynthesis and the ease of synthesis of analogues of 5 a makes a range of prodigiosin analogues readily available by mutasynthesis.     

Extracellular Vesicles in CNS Developmental Disorders

The central nervous system (CNS) is the most complex structure in the body, consisting of multiple cell types with distinct morphology and function. Development of the neuronal circuit and its function rely on a continuous crosstalk between neurons and non-neural cells. It has been widely accepted that extracellular vesicles (EVs), mainly exosomes, are effective entities responsible for intercellular CNS communication. They contain membrane and cytoplasmic proteins, lipids, non-coding RNAs, microRNAs and mRNAs. Their cargo modulates gene and protein expression in recipient cells. Several lines of evidence indicate that EVs play a role in modifying signal transduction with subsequent physiological changes in neurogenesis, gliogenesis, synaptogenesis and network circuit formation and activity, as well as synaptic pruning and myelination. Several studies demonstrate that neural and non-neural EVs play an important role in physiological and pathological neurodevelopment. The present review discusses the role of EVs in various neurodevelopmental disorders and the prospects of using EVs as disease biomarkers and therapeutics.     

Kuwanon‐L as a New Allosteric HIV‐1 Integrase Inhibitor: Molecular Modeling and Biological Evaluation

HIV‐1 integrase (IN) active site inhibitors are the latest class of drugs approved for HIV treatment. The selection of IN strand‐transfer drug‐resistant HIV strains in patients supports the development of new agents that are active as allosteric IN inhibitors. Here, a docking‐based virtual screening has been applied to a small library of natural ligands to identify new allosteric IN inhibitors that target the sucrose binding pocket. From theoretical studies, kuwanon‐L emerged as the most promising binder and was thus selected for biological studies. Biochemical studies showed that kuwanon‐L is able to inhibit the HIV‐1 IN catalytic activity in the absence and in the presence of LEDGF/p75 protein, the IN dimerization, and the IN/LEDGF binding. Kuwanon‐L also inhibited HIV‐1 replication in cell cultures. Overall, docking and biochemical results suggest that kuwanon‐L binds to an allosteric binding pocket and can be considered an attractive lead for the development of new allosteric IN antiviral agents.     

Hybrid sol–gel coatings for corrosion protection of galvanized steel in simulated concrete pore solution

The aim of this experimental research was to study the electrochemical behavior of organic–inorganic hybrid (OIH) coatings for corrosion protection of hot-dip galvanized steel (HDGS) in the first instants of immersion in simulated concrete pore solution (SCPS) (pH > 12.5). The electrochemical performance of the OIH coatings was assessed by electrochemical impedance spectroscopy, potentiodynamic polarization curves, macrocell current density, and polarization resistance. The OIH coatings were prepared via the sol–gel method and were deposited on HDGS surfaces by dip-coating using one or three dip steps. The electrochemical results obtained for HDGS samples coated with OIH matrices in SCPS showed higher corrosion resistance than bare HDGS; as the molecular weight (MW) of Jeffamine^® increased the barrier protection of the coating decreased. The lowest protection efficiency was found for HDGS samples synthesized with oligopolymers with an MW of 2000. Coatings produced with an oligopolymer of 230 MW conferred the highest protection. The surface morphology of the OIH coatings deposited on HDGS surfaces was studied by atomic force microscopy. The results show that the roughness of the OIH films depends on the MW of Jeffamine^® and on the number of dip-coating steps used. Thermogravimetry results show that the Jeffamine^® MW affected the thermal properties of the prepared OIH samples. The prepared OIH materials are thermally stable within the range of 20–80°C.     

Natural Polyphenols Selectively Inhibit β‐Carbonic Anhydrase from the Dandruff‐Producing Fungus Malassezia globosa: Activity and Modeling Studies

Around 50 % of the worldwide population is affected by dandruff, which is triggered by a variety of factors. The yeast Malassezia globosa has been labeled as the most probable causative agent for the onset of dandruff. The β‐carbonic anhydrase (CA) of MgCA was recently validated as an anti‐dandruff target, with its inhibition being responsible for in vivo growth defects in the fungus. As classical CA inhibitors of the sulfonamide type give rise to permeability problems through biological membranes, finding non‐sulfonamide alternatives for MgCA inhibition is of considerable interest in the cosmetic field. We recently screened a large library of human (h) CA inhibitors for MgCA inhibition, including different chemotypes, such as monothiocarbamates, dithiocarbamates, phenols, and benzoxaboroles. Herein, we expanded the research toward new MgCA inhibitors by considering a set of natural polyphenols (including flavones, flavonols, flavanones, flavanols, isoflavones, and depsides) that exhibited MgCA inhibitory activity in the micromolar range, as well as selectivity for the fungal isozyme over off‐target human isoforms. The binding mode of representative derivatives within the MgCA catalytic cleft was investigated by docking studies using a homology‐built model.     

Catalysts based in cerium oxide for wet oxidation of acrylic acid in the prevention of environmental risks

Acrylic acid is a refractory compound for the non-catalytic wet oxidation (WO) process and can seriously damage the environment when released in industrial effluents. Oxidation of acrylic acid by catalytic wet oxidation (CWO) was studied in slurry conditions in a high-pressure batch reactor at 200 °C and 15 bar of oxygen partial pressure. Several solid cerium-based catalysts prepared in our laboratory were used (Ag/Ce, Co/Ce, Mn/Ce, CeO, MnO) and evaluated in terms of activity, selectivity and stability. Mn/Ce shows the higher activity in 2 h with 97.7% reduction of total organic carbon (TOC) followed by: MnO(95.5%)>Ag/Ce(85.0%)>Co/Ce(65.1%)>CeO(61.2%). Attempts were also carried out to analyze the influence of different Mn/Ce molar ratios. High percentages of Mn lead to practically total organic carbon concentration (TOC) abatements while low ratios lead to the formation of non-oxidizable compounds. Acrylic acid was readily degraded by all the catalysts pointing out the high importance of using a catalytic process. pH was an indicator of the reaction pathway and acetic acid was found as the major reaction intermediate compound; however it is completely oxidized after 2 h with exception for Co/Ce, CeO and MnO. Carbon adsorption and leaching of metals were poorly found for Mn/Ce indicating high stability. The catalyst microstructure after the reaction was analyzed and formation of whiskers of β-MnO₂ (or less probably MnOOH) were observed at the catalyst surface. Therefore, Mn/Ce revealed to be a promising catalyst for the treatment of effluents containing acrylic acid; nevertheless, its commercialization depends on further research.