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1.  Incorporating Amino Acids Composition and Functional Domains for Identifying Bacterial Toxin Proteins 
BioMed Research International  2014;2014:972692.
Aside from pathogenesis, bacterial toxins also have been used for medical purpose such as drugs for cancer and immune diseases. Correctly identifying bacterial toxins and their types (endotoxins and exotoxins) has great impact on the cell biology study and therapy development. However, experimental methods for bacterial toxins identification are time-consuming and labor-intensive, implying an urgent need for computational prediction. Thus, we are motivated to develop a method for computational identification of bacterial toxins based on amino acid sequences and functional domain information. In this study, a nonredundant dataset of 167 bacterial toxins including 77 exotoxins and 90 endotoxins is adopted to learn the predictive model by using support vector machines (SVMs). The cross-validation evaluation shows that the SVM models trained with amino acids and dipeptides composition could yield an accuracy of 96.07% and 92.50%, respectively. For discriminating endotoxins from exotoxins, the SVM models trained with amino acids and dipeptides composition have achieved an accuracy of 95.71% and 92.86%, respectively. After incorporating functional domain information, the predictive performance is further improved. The proposed method has been demonstrated to be able to more effectively identify and classify bacterial toxins than the other two features on independent dataset, which may aid in bacterial biomedical development.
doi:10.1155/2014/972692
PMCID: PMC4109367  PMID: 25110714
2.  Comparative Proteomic Analysis of Peritoneal Dialysate from Chronic Glomerulonephritis Patients 
BioMed Research International  2013;2013:863860.
Peritoneal dialysis (PD) frequently contributes to peritoneal damage which cannot be easily identified without invasive techniques, implying the urgent need for biomarkers and revealing mechanisms. Chronic glomerulonephritis (CGN) is one of the leading causes of receiving dialysis treatment. Here, we attempted to analyze the peritoneal dialysate collected from CGN patients when they receive continuous ambulatory peritoneal dialysis (CAPD) treatment for the first time and after a year to reveal the protein changes that resulted from PD. Proteins were displayed by two-dimensional gel electrophoresis (2DE). Altered gel spots were digested followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis for protein identification. Eight proteins were found to have differential expression levels between two groups. Their differential expressions were validated by Western blots in other sets of peritoneal dialysates. Proteins identified with higher levels in the first-time dialysate suggested their dominant appearance in CGN patients, while those that showed higher levels in peritoneal dialysate collected after one year may result from initial peritoneal inflammation or changes in the permeability of the peritoneum to middle-sized proteins. All the identified proteins may provide a perceptiveness of peritoneal changes caused by PD and may function as potential biomarkers or drug targets.
doi:10.1155/2013/863860
PMCID: PMC3666394  PMID: 23762862
3.  Phyllanthus urinaria Induces Apoptosis in Human Osteosarcoma 143B Cells via Activation of Fas/FasL- and Mitochondria-Mediated Pathways 
Phyllanthus urinaria (P. urinaria), in this study, was used for the treatment of human osteosarcoma cells, which is one of the tough malignancies with few therapeutic modalities. Herein, we demonstrated that P. urinaria inhibited human osteosarcoma 143B cells growth through an apoptotic extrinsic pathway to activate Fas receptor/ligand expression. Both intracellular and mitochondrial reactive oxygen species were increased to lead to alterations of mitochondrial membrane permeability and Bcl-2 family including upregulation of Bid, tBid, and Bax and downregulation of Bcl-2. P. urinaria triggered an intrinsic pathway and amplified the caspase cascade to induce apoptosis of 143B cells. However, upregulation of both intracellular and mitochondrial reactive oxygen species and the sequential membrane potential change were less pronounced in the mitochondrial respiratory-defective 143Bρ0 cells compared with the 143B cells. This study offers the evidence that mitochondria are essential for the anticancer mechanism induced by P. urinaria through both extrinsic and intrinsic pathways.
doi:10.1155/2012/925824
PMCID: PMC3291129  PMID: 22454688
4.  RegPhos 2.0: an updated resource to explore protein kinase–substrate phosphorylation networks in mammals 
Protein phosphorylation catalyzed by kinases plays crucial roles in regulating a variety of intracellular processes. Owing to an increasing number of in vivo phosphorylation sites that have been identified by mass spectrometry (MS)-based proteomics, the RegPhos, available online at http://csb.cse.yzu.edu.tw/RegPhos2/, was developed to explore protein phosphorylation networks in human. In this update, we not only enhance the data content in human but also investigate kinase–substrate phosphorylation networks in mouse and rat. The experimentally validated phosphorylation sites as well as their catalytic kinases were extracted from public resources, and MS/MS phosphopeptides were manually curated from research articles. RegPhos 2.0 aims to provide a more comprehensive view of intracellular signaling networks by integrating the information of metabolic pathways and protein–protein interactions. A case study shows that analyzing the phosphoproteome profile of time-dependent cell activation obtained from Liquid chromatography-mass spectrometry (LC-MS/MS) analysis, the RegPhos deciphered not only the consistent scheme in B cell receptor (BCR) signaling pathway but also novel regulatory molecules that may involve in it. With an attempt to help users efficiently identify the candidate biomarkers in cancers, 30 microarray experiments, including 39 cancerous versus normal cells, were analyzed for detecting cancer-specific expressed genes coding for kinases and their substrates. Furthermore, this update features an improved web interface to facilitate convenient access to the exploration of phosphorylation networks for a group of genes/proteins.
Database URL: http://csb.cse.yzu.edu.tw/RegPhos2/
doi:10.1093/database/bau034
PMCID: PMC3999940  PMID: 24771658
5.  Crystal structure of tarocystatin–papain complex: implications for the inhibition property of group-2 phytocystatins 
Planta  2011;234(2):243-254.
Tarocystatin (CeCPI) from taro (Colocasia esculenta cv. Kaohsiung no. 1), a group-2 phytocystatin, shares a conserved N-terminal cystatin domain (NtD) with other phytocystatins but contains a C-terminal cystatin-like extension (CtE). The structure of the tarocystatin–papain complex and the domain interaction between NtD and CtE in tarocystatin have not been determined. We resolved the crystal structure of the phytocystatin–papain complex at resolution 2.03 Å. Surprisingly, the structure of the NtD–papain complex in a stoichiometry of 1:1 could be built, with no CtE observed. Only two remnant residues of CtE could be built in the structure of the CtE–papain complex. Therefore, CtE is easily digested by papain. To further characterize the interaction between NtD and CtE, three segments of tarocystatin, including the full-length (FL), NtD and CtE, were used to analyze the domain–domain interaction and the inhibition ability. The results from glutaraldehyde cross-linking and yeast two-hybrid assay indicated the existence of an intrinsic flexibility in the region linking NtD and CtE for most tarocystatin molecules. In the inhibition activity assay, the glutathione-S-transferase (GST)-fused FL showed the highest inhibition ability without residual peptidase activity, and GST-NtD and FL showed almost the same inhibition ability, which was higher than with NtD alone. On the basis of the structures, the linker flexibility and inhibition activity of tarocystatins, we propose that the overhangs from the cystatin domain may enhance the inhibition ability of the cystatin domain against papain.
Electronic supplementary material
The online version of this article (doi:10.1007/s00425-011-1398-8) contains supplementary material, which is available to authorized users.
doi:10.1007/s00425-011-1398-8
PMCID: PMC3144364  PMID: 21416241
CeCPI; Cystatin; Cysteine protease inhibitor; Inhibition activity; Linker flexibility; Phytocystatin
6.  The Suppression of MAD1 by AKT-Mediated Phosphorylation Activates MAD1 Target Genes Transcription 
Molecular carcinogenesis  2009;48(11):1048-1058.
MAX dimerization protein 1 (MAD1) is a transcription suppressor that antagonizes MYC-mediated transcription activation, and the inhibition mechanism occurs mainly through the competition of target genes' promoter MYC binding sites by MAD1. The promoter binding proteins switch between MYC and MAD1 affects cell proliferation and differentiation. However, little is known about MAD1's regulation process in cancer cells. Here, we present evidence that AKT inhibits MAD1-mediated transcription repression by physical interaction with and phosphorylation of MAD1. Phosphorylation reduces the binding affinity between MAD1 and its target genes' promoter and thereby abolishes its transcription suppression function. Mutation of the phosphorylation site from serine to alanine rescues the DNA-binding ability in the presence of activated AKT. In addition, AKT inhibits MAD1 mediated target genes (hTERT and ODC) transcription repression and promotes cell cycle and cell growth. However, mutated S145A MAD1 abrogates the inhibition by AKT. Thus, our results suggest that phosphorylation of MAD1 by AKT inhibits MAD1-mediated transcription suppression and subsequently activates the transcription of MAD1 target genes.
doi:10.1002/mc.20557
PMCID: PMC2783450  PMID: 19526459
AKT; MAD1; hTERT
7.  Utilization of IκB–EGFP Chimeric Gene as an Indicator to Identify Microbial Metabolites with NF-κB Inhibitor Activity 
Biological Procedures Online  2010;12:131-138.
NF-κB regulates several important expressions, such as cytokine release, anti-apoptosis, adhesion molecule expression, and cell cycle processing. Several NF-κB inhibitors have been discovered as an anti-tumor or anti-inflammatory drug. The activity of NF-κB transcription factor is negatively regulated by IκB binding. In this study, IκB assay system was established and IκB–EGFP fusion protein was used as an indicator to monitor the effects of substances on the IκB degradation. The results indicated that the chosen hydroquinone could inhibit the IκB degradation and cause the cell de-attachment from the bottom of culture plate. In addition, this system could also monitor the IκB degradation of microbial metabolite of natural mixtures of propolis. Thus, the IκB assay system may be a good system for drug discovery related to microbial metabolite.
doi:10.1007/s12575-010-9033-9
PMCID: PMC3055915  PMID: 21406073
Microbial metabolite; Antioxidant; IκB; EGFP; Hydroquinone; Propolis

Results 1-7 (7)