Journal of proteomics & bioinformatics最新文献

{"title":"Probing of Phytofungal Proteins for Fungicidal Activity by Molecular Docking","authors":"P. Mishra, M. Eswaran, N. Raman, T. Kaul","doi":"10.35248/0974-276X.19.12.499","DOIUrl":"https://doi.org/10.35248/0974-276X.19.12.499","url":null,"abstract":"Background: Plant fungal diseases are the primary causes of foliage and crop loss eventually affecting the overall economic outcome and yield quality. Hence, various chemical compounds are employed to eradicate the fungi in agriculture. Methods: Virtual screening and molecular docking strategies provide themselves as great alternatives to find lead compounds. Lead compounds for each fungal infection was docked to target protein sequence and assessed for the strongest interaction. Findings: Various molecules were taken under the study, for being the target ligands to bring about a fungicidal reaction in the plant pathogen system. The screening of molecules was done thoroughly to produce the results. Ligands identified through this study allow us to make plant host fight against the fungal pathogen and prevent the occurrence of the disease. The interactions have been thoroughly studied with various softwares like SPDBV and PyMol and through various online databases like STRING, GenePept, PDB, UniProt, PatchDock, Protein structure prediction server -2 and others for the overall evaluation of the drug molecule designed and to study its overall effects for the overall higher efficacy and to prevent the occurrence of the fungal disease and management of the fungal pathogens in agriculture against various economically valuable plants. The lead compounds revealed several hydrophobic and polar contacts were demonstrated by comparing interactions. Applications: The molecular affinity of the fungicidal compound has been tested against the target pathogen as well as the host system components to understand the interaction and to draw out the functioning and the analysis. The compatibility between the molecule and the protein has been studied to decipher the effectiveness of the molecule and its effects in the system. The present results let us establish lead compounds that can be used for the development of antifungal drugs although structural activity relationship studies have to be undertaken.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations.","authors":"Sudhir Srivastava,&nbsp;Michael Merchant,&nbsp;Anil Rai,&nbsp;Shesh N Rai","doi":"10.35248/0974-276x.19.12.496","DOIUrl":"https://doi.org/10.35248/0974-276x.19.12.496","url":null,"abstract":"<p><strong>Introduction: </strong>The quantitative measurements based on liquid chromatography (LC) coupled with mass spectrometry (MS) often suffer from the problem of missing values and data heterogeneity from technical variability. We considered a proteomics data set generated from human kidney biopsy material to investigate the technical effects of sample preparation and the quantitative MS.</p><p><strong>Methods: </strong>We studied the effect of tissue storage methods (TSMs) and tissue extraction methods (TEMs) on data analysis. There are two TSMs: frozen (FR) and FFPE (formalin-fixed paraffin embedded); and three TEMs: MAX, TX followed by MAX and SDS followed by MAX. We assessed the impact of different strategies to analyze the data while considering heterogeneity and MVs. We have used analysis of variance (ANOVA) model to study the effects due to various sources of variability.</p><p><strong>Results and conclusion: </strong>We found that the FFPE TSM is better than the FR TSM. We also found that the one-step TEM (MAX) is better than those of two-steps TEMs. Furthermore, we found the imputation method is a better approach than excluding the proteins with MVs or using unbalanced design.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37716706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review of Computational Prediction of Competing Endogenous RNA","authors":"Sherin K, Achuthsankar S. Nair","doi":"10.4172/0974-276x.1000493","DOIUrl":"https://doi.org/10.4172/0974-276x.1000493","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70907703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Quiescent Metabolic Phenotype of Glioma Stem Cells.","authors":"Elizabeth I Spehalski,&nbsp;Jennifer A Lee,&nbsp;Cord Peters,&nbsp;Philip Tofilon,&nbsp;Kevin Camphausen","doi":"10.35248/0974-276x.19.12.502","DOIUrl":"https://doi.org/10.35248/0974-276x.19.12.502","url":null,"abstract":"<p><strong>Introduction: </strong>Glioblastoma (GBM) is the most common primary malignant brain tumor in humans and, even with aggressive treatment that includes surgical resection, radiation (IR), and chemotherapy administration, prognosis is poor due to tumor recurrence. There is evidence that within GBMs a small number of glioma stem-like cells (GSLCs) exist, which are thought to be therapy resistant and are thus capable of repopulating a tumor after treatment. Like most cancers, GBMs largely employ aerobic glycolysis to create ATP, a phenomenon known as the Warburg Effect. There is no consensus on the metabolic characteristics of cancer stem cells. GSLCs have been shown to rely more heavily on oxidative phosphorylation, but there is also evidence that cancer stem cells can adapt their metabolism by fluctuating between energy pathways or acquiring intermediate metabolic phenotypes. We hypothesized that the metabolism of GSLCs differs from that of differentiated GBM tumor cell lines, and that the steady state metabolism would be differentially altered following radiation treatment.</p><p><strong>Materials and methods: </strong>We evaluated the oxygen consumption rate, extracellular acidification rate, and metabolic enzyme levels of GBM cell lines and GSLCs before and after irradiation using extracellular flux assays. We also measured absolute metabolite levels in these cells via mass spectroscopy with and without radiation treatment.</p><p><strong>Results: </strong>GSLCs were found to be significantly more quiescent in comparison to adherent GBM cell lines, highlighted by lower glycolytic and maximal respiratory capacities as well as lower oxygen consumption and extracellular acidification rates. Analysis of individual metabolite concentrations revealed lower total metabolite concentrations overall but also elevated levels of metabolites in different energy pathways for GSLCs compared to GBM cell lines. Additionally, the metabolism of both GSLCs and GBM cell lines were found to be altered by IR.</p><p><strong>Conclusions: </strong>While there is not one metabolic alteration that distinguishes irradiated GSLC metabolism from that of GBM cell lines, therapies targeting more metabolically quiescent tumor cells and thus the resistant GSLC population may increase a cancer's sensitivity to radiotherapy.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061459/pdf/nihms-1556046.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37721345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Mining of Streptomyces formicae KY5 for Potential Drug like Natural Products Characterizations","authors":"M. Shah, S. Gul, A. Amjad, M. Javed, Batool Fatima, H. Nawaz, Jaweria Ishaq","doi":"10.35248/0974-276x.19.12.505","DOIUrl":"https://doi.org/10.35248/0974-276x.19.12.505","url":null,"abstract":"Genus Streptomyces has been a source of various clinically significant bioactive metabolites. Taxonomically, Streptomyces formicae KY5 is a new and different species. The complete genome sequences of S. formicae KY5 is available in the public DNA sequence databases for different analysis. The accessibility of the genomic sequence presents an excellent opportunity to explore the secondary metabolites potential of this distinct Streptomyces species. In this study, we employed the advance bioinformatics resources to annotate the total genome sequence of S. formicae KY5. Bioinformatics tools are applied to locate all the secondary metabolites hiding beneath their biosynthetic gene clusters (BGCs). The S. formicae KY5 is found to synthesis distinct and various secondary metabolites by undergoing the designated genomic encoding. Predictive analysis conveys that this strain has 34 gene clusters to encode potential secondary metabolites. For structural similarity with other drugs, we scanned the drug bank database, drug target and drug with the highest similarity was retrieved from PDB for molecular docking. Molecular docking analysis was carried out through molecular operating tool to evaluate drug-like potential of the chemical compounds. Three drugs like compounds were predicted from S.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular diversity of the cutaneous proteome and peptidome of the frog Dendropsophus columbianus (Boettger, 1892)","authors":"Sebastien Charneaup","doi":"10.4172/0974-276X-C5-125","DOIUrl":"https://doi.org/10.4172/0974-276X-C5-125","url":null,"abstract":"A skin is a tissue specialized in the production of various molecules such as antimicrobial peptides, immunomodulators, biogenic amines and hormones. These bioactives compounds could be considered of biotechnological interest and new therapeutic alternatives. The aim of the present study was to identify and characterize peptides and proteins present in the cutaneous secretion of the amphibian Dendropsophus columbianus (Boettger, 1892), related to pathogen defense mechanisms. The first approach consisted of the classical fractionation of cutaneous secretion by RP-HPLC. All chromatographic fractions obtained were evaluated for their ability to inhibit bacterial proliferation and analyzed by MALDI-TOF/TOF. A single new antimicrobial neutral peptide was thus isolated and named dendropsophin 1 (Dc 1), with no sequence similarity with annotated peptides. Subsequently, two cationic analogues (Dc 1.1 and Dc 1.2) keeping the amphipathic structure of Dc 1 were designed. Dc 1 and its two analogues exhibited moderate antibacterial activities and no hemolytic and cytotoxic effects in mammalian cells. Dc 1.2 exhibited slightly improved antibacterial properties that could be related to the higher content of α-helix and thermal stability compared to Dc 1 and Dc 1.1 in hydrophobic experimentalw condition. The native peptide Dc 1 could be used as an alternative model to develop new AMPs. In a second modern high-throughput approach, the first comprehensive proteomic and peptidomic study of cutaneous secretion was performed by nanoLCMS/MS using Orbitrap EliteTM mass spectrometer. Data were processed using PEAKS and Blast2GO programs. 1248 proteins present in the cutaneous secretion of D. columbianus were identified, 127 proteins were categorized associated with the defense system and 19 related to the response against microorganisms. Three hydrolases from the total secretion were detected by zymography and subsequently identified, which could be related to the processing of peptides of defense. The peptidome results allowed determining a new group of peptides endogenous to D. columbianus, with high sequence similarity with Dc 1, which were named as dendropsophins. The dendropsophins Dc 2, Dc 7, Dc 13, Dc 17, Dc 18 and Dc 19 showed no activity against bacteria or fungi. However, Dc 2 and Dc 18 are able to activate human neutrophils. This activity could be associated to a modulation of the immune system in D. columbianus. This pathway of defense, highly conserved in vertebrates, opens further perspectives regarding the use of these new molecules in the therapy of infectious diseases.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70916690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"T-patterns and self-similarity from the RNA world to human mass-societies","authors":"pMagnus S Magnussonp","doi":"10.4172/0974-276X-C5-123","DOIUrl":"https://doi.org/10.4172/0974-276X-C5-123","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70916664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Normal modes, what do they tell us about the protein dynamics?","authors":"pLiliane Mouawadp","doi":"10.4172/0974-276X-C4-120","DOIUrl":"https://doi.org/10.4172/0974-276X-C4-120","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70915811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anti-viral value of alien addition lines between oilseed rape (Brassica napus) and Banlangen (Isatis indigotica) as new resource medicine","authors":"pAqeel Ahmad Waheed Akram Shakeel Ahmed Xiaohua Li, Xuebo Hup","doi":"10.4172/0974-276X-C4-122","DOIUrl":"https://doi.org/10.4172/0974-276X-C4-122","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70916729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vitro synthesised functioning reporter mRNA as a method for evaluating the Kozak sequence function directly in the mRNA strand","authors":"pGustavo Torres de Souzap","doi":"10.4172/0974-276X-C4-121","DOIUrl":"https://doi.org/10.4172/0974-276X-C4-121","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70915942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}