New acylated bradykinin analogues: effect on rat blood pressure and rat uterus.

It was previously reported that acylation of the N-terminus of several known B(2) antagonists with various types of bulky acyl groups consistently improved their antagonistic potency in the rat blood pressure assay. On the other hand, earlier results seem to suggest that the effects of acylation on the contractility of isolated rat uterus depend substantially on the chemical character of the acyl group, as it was observed that this modification may either change the range of antagonism or even transform it into agonism. Bearing all this in mind, three new analogues of bradykinin were designed by modifying the moderately potent B(2) antagonist, previously synthesized by Stewart's group, D-Arg-Arg-Pro-Hyp-Gly-Thr-Ser-D-Phe-Thi-Arg. New analogues were obtained by acylation of the N-terminus of the above peptide with succinic acid, 12-aminododecanoic acid and 4-aminobenzoic acid in order to confirm whether either the positive or the negative charge on the N-terminal end of the peptide is responsible for the transformation of activity. The activity of analogues was assessed on blood pressure and in uterotonic in vitro tests. The modifications proposed either preserved or increased the antagonistic potency in the rat blood pressure test. On the other hand, the three substituents, depending on their chemical character, differently influenced the interaction with the rat uterine receptors. The results may be of value in the design of new B(2) agonists and antagonists.     

Structural analysis of papain-like NlpC/P60 superfamily enzymes with a circularly permuted topology reveals potential lipid binding sites

NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, "closed" conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.     

Interferon‐γ promotes vascular remodeling in human microvascular endothelial cells by upregulating endothelin (ET)‐1 and transforming growth factor (TGF) β2

Systemic sclerosis (SSc) is a complex disease characterized by vascular alterations, activation of the immune system and tissue fibrosis. Previous studies have implicated activation of the interferon pathways in the pathogenesis of SSc. The goal of this study was to determine whether interferon type I and/or type II could play a pathogenic role in SSc vasculopathy. Human dermal microvascular endothelial cells (HDMVECs) and fibroblasts were obtained from foreskins of healthy newborns. The RT Profiler PCR Array System was utilized to screen for EndoMT genes. Treatment with IFN‐α or IFN‐γ downregulated Fli1 and VE‐cadherin. In contrast, IFN‐α and IFN‐γ exerted opposite effects on the expression of α‐SMA, CTGF, ET‐1, and TGFβ2, with IFN‐α downregulating and IFN‐γ upregulating this set of genes. Blockade of TGFβ signaling normalized IFN‐γ‐mediated changes in Fli1, VE‐cadherin, CTGF, and ET‐1 levels, whereas upregulation of α‐SMA and TGFβ2 was not affected. Bosentan treatment was more effective than TGFβ blockade in reversing the actions of IFN‐γ, including downregulation of α‐SMA and TGFβ2, suggesting that activation of the ET‐1 pathway plays a main role in the IFN‐γ responses in HDMECs. IFN‐γ induced expression of selected genes related to endothelial‐to‐mesenchymal transition (EndoMT), including Snail1, FN1, PAI1, TWIST1, STAT3, RGS2, and components of the WNT pathway. The effect of IFN‐γ on EndoMT was mediated via TGFβ2 and ET‐1 signaling pathways. This study demonstrates distinct effects of IFN‐α and IFN‐γ on the biology of vascular endothelial cells. IFN‐γ may contribute to abnormal vascular remodeling and fibrogenesis in SSc, partially via induction of EndoMT. J. Cell. Physiol. 228: 1774–1783, 2013. © 2013 Wiley Periodicals, Inc.     

Candidate loci for phenology and fruitfulness contributing to the phenotypic variability observed in grapevine

Key message

In this study, we identified several genes, which potentially contribute to phenological variation in the grapevine. This may help to maintain consistent yield and suitability of particular varieties in future climatic conditions.

Abstract

The timing of major developmental events in fruit crops differs with cultivar, weather conditions and ecological site. This plasticity results also in diverse levels of fruitfulness. Identifying the genetic factors responsible for phenology and fertility variation may help to improve these traits to better match future climates. Two Vitis vinifera populations, an F1 progeny of Syrah × Pinot Noir and a phenological core collection composed of 163 cultivars, were evaluated for phenology and fertility subtraits during three to six growing seasons in the same geographical location. The phenotypic variability in the core collection mostly overlapped with that observed in the F1 progeny and several accessions had exceeding values of phenological response. The progeny population was used together with SSR and SNP markers to map quantitative trait loci (QTLs). This allowed us to detect nine QTLs related to budburst, flowering beginning, the onset of ripening (véraison) and total fertility, explaining from 8 to 44 % of phenotypic variation. A genomic region on chromosome 15 was associated with budburst and véraison and two QTLs for fruitfulness were located on chromosomes 3 and 18. Several genes potentially affecting fertility and the timing of fruit development were proposed, based on their position and putative function. Allelic variation at these candidate loci may be explored by sampling accessions from the core collection.     

DISOselect: Disorder predictor selection at the protein level

The intense interest in the intrinsically disordered proteins in the life science community, together with the remarkable advancements in predictive technologies, have given rise to the development of a large number of computational predictors of intrinsic disorder from protein sequence. While the growing number of predictors is a positive trend, we have observed a considerable difference in predictive quality among predictors for individual proteins. Furthermore, variable predictor performance is often inconsistent between predictors for different proteins, and the predictor that shows the best predictive performance depends on the unique properties of each protein sequence. We propose a computational approach, DISOselect, to estimate the predictive performance of 12 selected predictors for individual proteins based on their unique sequence‐derived properties. This estimation informs the users about the expected predictive quality for a selected disorder predictor and can be used to recommend methods that are likely to provide the best quality predictions. Our solution does not depend on the results of any disorder predictor; the estimations are made based solely on the protein sequence. Our solution significantly improves predictive performance, as judged with a test set of 1,000 proteins, when compared to other alternatives. We have empirically shown that by using the recommended methods the overall predictive performance for a given set of proteins can be improved by a statistically significant margin. DISOselect is freely available for non‐commercial users through the webserver at http://biomine.cs.vcu.edu/servers/DISOselect/ .