45,073 research outputs found
The T-knot motif revisited RID A-4573-2009
No full textThe T-knot scaffold, a disulphide-reinforced structural motif shared by several proteins with very different biological functions, has been defined as 'a stretch of the protein chain which comprises two strands of a beta-sheet and three loops, knotted by two disulphides into the shape of the letter T'. In this communication we show that the presence of a central beta-sheet is not a required structural feature for proteins sharing the T-knot topology. Moreover, superposition of the three-dimensional structures of representative members of the T-knot family highlights a common and structurally well-defined core, formed by the two knotted disulphides, substituting for a larger residue-based hydrophobic core. These results suggest that folding and stability of the T-knot scaffold mainly depend on the geometry of the two knotted disulphides and on the loop length, and that the secondary structure elements are not a prerequisite for motif formation. Accordingly, a redefinition of the T-knot motif is proposed
Leech antihemostatic proteins share the T-knot scaffold, a disulfide-reinforced structural motif
No full textThe occcurence of similar topologies among unrelated proteins is an emerging theme in structural biology. Here we report that the T-knot scaffold, a disulfide-reinforced structural motif shared by knottins and EGF-like proteins, is also present in leech antihemostatic proteins. Our finding emphasizes the versatile nature of this small structural motif, representing a compact structural unit suitable for the diverse biological functions performed by knottins, EGF-like proteins and leech antihemostatic proteins
Data from computational analysis of the peptide linkers in the mocr bacterial transcriptional regulators
No full textAbstract Detailed data from statistical analyses of the structural properties of the inter-domain linker peptides of the bacterial regulators of the family MocR are herein reported. MocR regulators are a recently discovered subfamily of bacterial regulators possessing an N-terminal domain, 60 residue long on average, folded as the winged-helix-turn-helix architecture responsible for DNA recognition and binding, and a large C-terminal domain (350 residue on average) that belongs to the fold type-I pyridoxal 5′-phosphate (PLP) dependent enzymes such aspartate aminotransferase. Data show the distribution of several structural characteristics of the linkers taken from bacterial species from five different phyla, namely Actinobacteria, Alpha-, Beta-, Gammaproteobacteria and Firmicutes. Interpretation and discussion of reported data refer to the article “Structural properties of the linkers connecting the N- and C- terminal domains in the MocR bacterial transcriptional regulators” (T. Milano, S. Angelaccio, A. Tramonti, M. L. Di Salvo, R. Contestabile, S. Pascarella, 2016) [1]
Antioxidant efficacy of iridoid and phenylethanoid glycosides from the medicinal plant Teucrium chamaedris in cell-free systems
No full textTwelve glycosides, seven iridoids and five phenylethanoids, have been isolated from leaf and root methanolic extracts of Wall Germander (Teucrium chamaedrys), a Mediterranean species historically used as a medicinal plant. Among them, three iridoid and one phenylethanoid glycosides have been isolated and characterized for the first time. All of the structures have been elucidated on the basis of their spectral data, especially 1D and 2D NMR experiments. The antioxidative properties of pure metabolites, as well as of crude organic extracts of the plant, have been analyzed on the basis of their DPPH radical scavenging capability. The antioxidant capacity in cell-free systems of the isolated metabolites was carried out by measuring their capabilities to inhibit the synthesis of thiobarbituric acid reactive species in assay media using as oxidable substrates a vegetable fat and the pentose sugar 2-deoxyribose and to prevent oxidative damage of the hydrosoluble bovine serum albumin (BSA) protein. Phenylethanoid glycosides resulted efficacious DPPH radical, while iridoid glycosides prevent massively the 2-deoxyribose and BSA oxidations in assay media. © 2009 Elsevier Ltd. All rights reserved
Phytotoxicity evaluation of five pharmaceutical pollutants detected in surface water on germination and growth of cultivated and spontaneous plants
No full textThe phytotoxicity of 5 pharmaceuticals detected in Italian rivers, atorvastatin (7-[2-(4-fluorophenyl)-3-phenyl-4-(phenylcarbamoyl)-5-propan-2-yl- pyrrol-1-yl]-3,5-dihydroxy-heptanoic acid), gemfibrozil (5-(2,5-dimethylphenoxy) -2,2-dimethyl-pentanoic acid), tamoxifene (2-[4-(1,2-diphenylbut-1-enyl)phenoxy] -N,N-dimethyl-ethanamine), ethinyl estradiol (17-ethynyl-13-methyl-7,8,9,11, 12,13,14,15,16,17-decahydro-6H-cyclopenta[a]phenanthrene-3,17-diol) and sildenafil (methyl-9-propyl-2,4,7,8-tetrazabicyclo[4.3.0] nona-3,8,10-trien-5- one), has been assessed in a laboratory model. The treatment system consists of three main successive sections. The first one includes the phytotoxic evaluation of the single compounds on crops, Lactuca sativa (lettuce), Dacus carota subsp. sativa (carrot), and Lycopersicon esculentum (tomato), until the 10-9 M, concentration lower then the environmental amounts. The second section includes the phytotoxicity assessment of all the selected chemicals on wild species, Avena fatua (wild oats), Amaranthus retroflexus (redroot pigweed), Lolium perenne (perennial ryegrass), Taraxacum officinale (common dandelion), and Chenopodium album (lambsquarter), at the same concentration as previously used. The third section of the procedure includes the evaluation of the effects of the five pharmaceuticals, at 1 μM and 1 nM environmental concentrations, on the metabolism of L. sativa. The variation of the composition of the photosynthetic pigments, sugars, lipids, phenols, fatty acids and flavonoids in lettuce seedlings exposed to the pollutants in respect to the blank was evaluated. The results of the phytotoxicity assays showed the possibility of a notable impact on the different vegetal communities and evidenced different sensitivity among cultivated and wild species, probably due to the different plant physiology. Copyright © Taylor & Francis Group, LLC
Settling of finite-size particles in isotropically forced, homogeneous turbulence: interface-resolved simulations
No full textWe have simulated the gravity-induced settling of finite-size particles in a turbulent background flow which is forced in a statistically-stationary fashion. The simulations are accurately resolving the solid-fluid interface with the aid of an immersed boundary technique [1]. The parameters of the simulation are (apart from background turbulence) identical to those of reference [2], where particle clustering was observed at a Galileo number of 178 and a solid volume fraction of 0.005. In the present case, it is found that a relative turbulence intensity of 0.24 leads to the disappearance of the clusters; as a consequence, the increase in average particle settling velocity found in [2] also vanishes. [1] M. Uhlmann. An immersed boundary method with direct forcing for the simulation of particulate flows. J. Comput. Phys., 209(2):448–476, 2005. [2] M. Uhlmann and T. Doychev. Sedimentation of a dilute suspension of rigid spheres at intermediate Galileo numbers: the effect of clustering upon the particle motion. J. Fluid Mech., 752:310–348, 2014
Chemical characterization of new oxylipins from Cestrum parqui, and their effects on seed germination and early seedling growth
No full textIsolation, chemical characterization, and phytotoxicity of five new oxylipins, together with seven already known related compounds, from Cestrum parqui L'HERL. is reported. All the structures were elucidated on the basis of their spectral data, especially 1D- (1H- and 13C-NMR, DEPT) and 2D-NMR (COSY, TOCSY, HSQC, HMBC, and NOESY). The configurations of the stereogenic C-atoms were determined by the Mosher's method. The compounds have been assayed for their phytotoxicity on Lactuca sativa at concentrations ranging between 10-4 and 10-8 m. The results of the phytotoxicity tests on the germination and growth of the test species, obtained by a cluster analysis, showed interesting relationship between the chemical structures of the compounds and their biological effects. © 2008 Verlag Helvetica Chimica Acta AG, Zürich
Mesophilic-hydrothermal-thermophilic (M-H-T) digestion of green corn straw
No full textMesophilic-hydrothermal (80-160 degrees C, 30 min)-thermophilic (M-H-T) digestion and control tests of mesophilic (M), thermophilic (T), hydrothermal-mesophilic (H-M), and mesophilic-thermophilic digestion (M-T) of green corn straw were conducted for a 20-day fermentation period. The results indicate that M-H-T is an efficient method to improve methane production. A maximum methane yield of 371.74 mL/g volatile solid was obtained by the M (3 days)-H (140 degrees C)-T (17 days) process, which was 20.44%, 16.55%, 31.44%, and 14.31% higher than the yields of the M, T, 140-M, and M-T processes. The enhanced methane production was attributed to (1) the improved hemicellulose degradation and lignin disorganization; (2) prevention of the degradation of soluble sugar, easily hydrolyzed hemicellulose and cellulose into furfural and methylfurfural; and (3) lack of formation of Maillard reaction products during initial hydrothermal treatment. (C) 2015 Elsevier Ltd. All rights reserved
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