Modulation of angiogenic factors by ursolic acid

Investigations were carried out to understand the molecular basis of the effect of ursolic acid on angiogenesis by analysing its effects on the expression of modulators of angiogenesis by HUVECs in culture. Treatment with ursolic acid increased the expression of adhesion molecules such as E-selectin, CD-31 and I-CAM, upregulated angiogenic growth factors such as VEGF and FGF-2 and their receptors and caused increase in the ratio of PGE₂ to PGD₂. Reversal of the effect of ursolic acid by inhibition of PI3K-Akt pathway and increase in the level of phospho Akt suggest that the ursolic acid effect is mediated through PI3K-Akt pathway.     

Epigenetic alterations of CDH1 and APC genes: relationship with activation of Wnt/beta-catenin pathway in invasive ductal carcinoma of breast

Activation of canonical Wnt/beta-catenin pathway in Invasive Ductal Carcinoma of Breast (IDCs) was recently reported from our laboratory. Herein, we analyzed promoter methylation status of CDH1 and Adenomatous polyposis coli (APC) genes in 50 IDCs and correlated with expression of E-cadherin (E-CD) and APC proteins and with activation of oncogenic Wnt/beta-catenin signaling pathway components, Dvl, beta-catenin and CyclinD1. Further, Wnt/beta-catenin driven epithelial mesenchymal transition (EMT) was investigated by correlating the expression of Dvl, beta-catenin and CyclinD1 with vimentin expression in these IDCs. Promoter hypermethylation was observed in 25/50 (50%) IDCs for CDH1 and in 11/50 (22%) tumors for APC, associated with loss of expression of E-CD and APC proteins; concordant hypermethylation of these genes was observed in paired patients' sera. Further, 57% of tumors harboring CDH1 methylation and 50% tumors harboring the methylated APC gene showed nuclear localization of beta-catenin, suggesting activation of the canonical Wnt/beta-catenin pathway. Our study demonstrates significant association between vimentin expression and nuclear beta-catenin (p=0.001; Odds ratio (OR)=25.6) and Dvl (p=0.023; OR=8.0), suggesting that EMT may be driven by Wnt/beta-catenin activation in IDCs. In conclusion, we demonstrate correlation of CDH1 and APC promoter methylation with loss of E-CD and APC proteins and with activation of Wnt/beta-catenin signaling pathway. Association of nuclear Dvl and beta-catenin with vimentin expression suggests the importance of Wnt/beta-catenin pathway driven EMT in IDCs. The concordance between CDH1 and APC methylation in IDCs and paired circulating DNA underscores the utility of serum DNA as a non-invasive tool for methylation analysis in IDC patients.     

Sequestration of mutated alpha1-antitrypsin into inclusion bodies is a cell-protective mechanism to maintain endoplasmic reticulum function

A variant alpha1-antitrypsin with E342K mutation has a high tendency to form intracellular polymers, and it is associated with liver disease. In the hepatocytes of individuals carrying the mutation, alpha1-antitrypsin localizes both to the endoplasmic reticulum (ER) and to membrane-surrounded inclusion bodies (IBs). It is unclear whether the IBs contribute to cell toxicity or whether they are protective to the cell. We found that in hepatoma cells, mutated alpha1-antitrypsin exited the ER and accumulated in IBs that were negative for autophagosomal and lysosomal markers, and contained several ER components, but not calnexin. Mutated alpha1-antitrypsin induced IBs also in neuroendocrine cells, showing that formation of these organelles is not cell type specific. In the presence of IBs, ER function was largely maintained. Increased levels of calnexin, but not of protein disulfide isomerase, inhibited formation of IBs and lead to retention of mutated alpha1-antitrypsin in the ER. In hepatoma cells, shift of mutated alpha1-antitrypsin localization to the ER by calnexin overexpression lead to cell shrinkage, ER stress, and impairment of the secretory pathway at the ER level. We conclude that segregation of mutated alpha1-antitrypsin from the ER to the IBs is a protective cell response to maintain a functional secretory pathway.     

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

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Insight to pyrazinamide resistance inMycobacterium tuberculosisby molecular docking

Pyrazinamide (PZA) - an important drug in the anti-tuberculosis therapy, activated by an enzyme Pyrazinamidase (PZase). The basis of PZA resistance in Mycobacterium tuberculosis was owing to mutation in pncA gene coding for PZase. Homology modeling of PZase was performed using software Discovery Studio (DS) 2.0 based on the crystal structure of the PZase from Pyrococcus horikoshii (PDB code 1im5), in this study. The model comprises of one sheet with six parallel strands and seven helices with the amino acids Asp8, Asp49, Trp68, Lys96, Ala134, Thr135 and Cys138 at the active site. Five mutants were generated with Gly at position 8, Thr at position 96, Arg at position 104, Tyr and Ser at position 138. The Wild-type (WT) and five mutant models were docked with PZA. The results indicate that the mutants Lys96Thr, Ser104Arg Asp8Gly and Cys138Tyr may contribute to higher level drug resistance than Cys138Ser. These models provide the first in-silico evidence for the binding interaction of PZA with PZase and form the basis for rationalization of PZA resistance in naturally occurring pncA mutant strains of M. tuberculosis.     

Measurement of Elastic Modulus of Collagen Type I Single Fiber

Collagen fibers are the main components of the extra cellular matrix and the primary contributors to the mechanical properties of tissues. Here we report a novel approach to measure the longitudinal component of the elastic moduli of biological fibers under conditions close to those found in vivo and apply it to type I collagen from rat tail tendon. This approach combines optical tweezers, atomic force microscopy, and exploits Euler-Bernoulli elasticity theory for data analysis. This approach also avoids drying for measurements or visualization, since samples are freshly extracted. Importantly, strains are kept below 0.5%, which appear consistent with the linear elastic regime. We find, surprisingly, that the longitudinal elastic modulus of type I collagen cannot be represented by a single quantity but rather is a distribution that is broader than the uncertainty of our experimental technique. The longitudinal component of the single-fiber elastic modulus is between 100 MPa and 360 MPa for samples extracted from different rats and/or different parts of a single tail. Variations are also observed in the fibril-bundle / fibril diameter with an average of 325±40 nm. Since bending forces depend on the diameter to the fourth power, this variation in diameter is important for estimating the range of elastic moduli. The remaining variations in the modulus may be due to differences in composition of the fibril-bundles, or the extent of the proteoglycans constituting fibril-bundles, or that some single fibrils may be of fibril-bundle size.     

Negative modulation of eNOS by laminin involving post‐translational phosphorylation

Nitric oxide (NO) regulates the vascular tone, and influences survival and apoptosis of endothelial cells (ECs). NO is produced by nitric oxide synthase (NOS) and eNOS is the constitutive enzyme in the endothelium. Though the extracellular matrix (ECM) has been reported to regulate various EC functions, the role of ECM in the regulation of eNOS is not clear. The present study was designed to analyze if laminin‐1 (Ln‐1), the major glycoprotein of the basement membrane, can regulate eNOS. The activity of eNOS was significantly low in ECs maintained on Ln‐1 as compared to those on Col I and polylysine. Reversal of the effect of Ln‐1 on treatment with inhibitor of p38 MAPK and changes in Thr and Ser phosphorylation in purified eNOS suggested that eNOS activity in cells maintained on Ln‐1 is negatively regulated by post‐translational phosphorylation at Ser and Thr residues by recruiting p38 MAPK pathway. Increase in eNOS activity and induction of apoptosis upon inhibition of p38 MAPK and reversal of this on inhibition of NOS by L ‐NAME suggested that increased NO induced apoptosis in ECs maintained on Ln‐1 when p38 MAPK was inhibited. These results suggest that Ln contributes to survival of ECs by negatively modulating eNOS in a p38 MAPK dependent pathway. J. Cell. Physiol. 219: 123–131, 2009. © 2008 Wiley‐Liss, Inc.     

Modeling protein-protein,protein-peptide,and protein-oligosaccharide complexes: CAPRI 7th edition

We present the seventh report on the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions. Performance was evaluated on the basis of 36 114 models of protein complexes submitted by 57 groups—including 13 automatic servers—in prediction rounds held during the years 2016 to 2019 for eight protein-protein, three protein-peptide, and five protein-oligosaccharide targets with different length ligands. Six of the protein-protein targets represented challenging hetero-complexes, due to factors such as availability of distantly related templates for the individual subunits, or for the full complex, inter-domain flexibility, conformational adjustments at the binding region, or the multi-component nature of the complex. The main challenge for the protein-peptide and protein-oligosaccharide complexes was to accurately model the ligand conformation and its interactions at the interface. Encouragingly, models of acceptable quality, or better, were obtained for a total of six protein-protein complexes, which included four of the challenging hetero-complexes and a homo-decamer. But fewer of these targets were predicted with medium or higher accuracy. High accuracy models were obtained for two of the three protein-peptide targets, and for one of the protein-oligosaccharide targets. The remaining protein-sugar targets were predicted with medium accuracy. Our analysis indicates that progress in predicting increasingly challenging and diverse types of targets is due to closer integration of template-based modeling techniques with docking, scoring, and model refinement procedures, and to significant incremental improvements in the underlying methodologies.