Proteomics insights最新文献

{"title":"Phorbol 12-Myristate 13-Acetate-Induced Changes in Chicken Enterocytes.","authors":"Narayan C Rath,&nbsp;Anamika Gupta,&nbsp;Rohana Liyanage,&nbsp;Jackson O Lay","doi":"10.1177/1178641819840369","DOIUrl":"https://doi.org/10.1177/1178641819840369","url":null,"abstract":"<p><p>Increased intestinal epithelial permeability has been linked to many enteric diseases because it allows easy access of microbial pathogens and toxins into the system. In poultry production, the restrictions in the use of antibiotic growth promoters have increased the chances of birds being susceptible to different enteric diseases. Thus, understanding the mechanisms which compromise intestinal function is pertinent. Based on our previous observation which showed the primary chicken enterocytes in culture undergoing dystrophic changes on treatment with phorbol myristate acetate (PMA), we surmised that this model, which appeared to mimic increased intestinal permeability, may help to understand the mechanisms of this problem. As genomic and proteomic changes are associated with many physiological and pathological problems, we were interested to find whether certain proteomic changes underlie the morphological alterations in the enterocytes induced by PMA. We exposed primary enterocyte cultures to a sub-lethal concentration of PMA, extracted the proteins, and analyzed by mass spectrometry for differentially regulated proteins. Our results showed that PMA affected several biological processes which negatively affected their energy metabolism, nuclear activities, and differentially regulated the levels of several stress proteins, chaperon, cytoskeletal, and signal transduction proteins that appear to be relevant in the cause of enterocyte dystrophy. Phorbol myristate acetate-affected signal transduction activities also raise the possibilities of their increased susceptibility to pathogens. The changes in enterocyte integrity can make intestine vulnerable to invasion by microbial pathogens and disrupt gut homeostasis.</p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"10 ","pages":"1178641819840369"},"PeriodicalIF":0.0,"publicationDate":"2019-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178641819840369","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37183575","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":"Expression and Characterization of Human Fragile X Mental Retardation Protein Isoforms and Interacting Proteins in Human Cells.","authors":"Jiang Zhang,&nbsp;Guangli Wang,&nbsp;Wei-Wu He,&nbsp;Molly Losh,&nbsp;Elizabeth Berry-Kravis,&nbsp;William E Funk","doi":"10.1177/1178641818825268","DOIUrl":"https://doi.org/10.1177/1178641818825268","url":null,"abstract":"<p><p>Fragile X mental retardation protein is an mRNA-binding protein associated with phenotypic manifestations of fragile X syndrome, an X-linked disorder caused by mutation in the <i>FMR1</i> gene that is the most common inherited cause of intellectual disability. Despite the well-studied genetic mechanism of the disease, the proteoforms of fragile X mental retardation protein have not been thoroughly characterized. Here, we report the expression and mass spectrometric characterization of human fragile X mental retardation protein. <i>FMR1</i> cDNA clone was transfected into human HEK293 cells to express the full-length human fragile X mental retardation protein. Purified fragile X mental retardation protein was subjected to trypsin digestion and characterized by mass spectrometry. Results show 80.5% protein sequence coverage of fragile X mental retardation protein (Q06787, <i>FMR1</i>_HUMAN) including both the N- and C-terminal peptides, indicating successful expression of the full-length protein. Identified post-translational modifications include N-terminal acetylation, phosphorylation (Ser600), and methylation (Arg290, 471, and 474). In addition to the full-length fragile X mental retardation protein isoform (isoform 6), two endogenous fragile X mental retardation protein alternative splicing isoforms (isoforms 4 and 7), as well as fragile X mental retardation protein interacting proteins, were also identified in the co-purified samples, suggesting the interaction network of the human fragile X mental retardation protein. Quantification was performed at the peptide level, and this information provides important reference for the future development of a targeted assay for quantifying fragile X mental retardation protein in clinical samples. Collectively, this study provides the first comprehensive report of human fragile X mental retardation protein proteoforms and may help advance the mechanistic understanding of fragile X syndrome and related phenotypes associated with the <i>FMR1</i> mutation.</p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"10 ","pages":"1178641818825268"},"PeriodicalIF":0.0,"publicationDate":"2019-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178641818825268","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37041138","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":"An Improved 2-Dimensional Gel Electrophoresis Method for Resolving Human Erythrocyte Membrane Proteins.","authors":"Manoj Kumar,&nbsp;Rajendra Singh,&nbsp;Anil Meena,&nbsp;Bhagwan S Patidar,&nbsp;Rajendra Prasad,&nbsp;Sunil K Chhabra,&nbsp;Surendra K Bansal","doi":"10.1177/1178641817700880","DOIUrl":"https://doi.org/10.1177/1178641817700880","url":null,"abstract":"<p><p>The 2-dimensional gel electrophoresis (2-DE) technique is widely used for the analysis of complex protein mixtures extracted from biological samples. It is one of the most commonly used analytical techniques in proteomics to study qualitative and quantitative protein changes between different states of a cell or an organism (eg, healthy and diseased), conditionally expressed proteins, posttranslational modifications, and so on. The 2-DE technique is used for its unparalleled ability to separate thousands of proteins simultaneously. The resolution of the proteins by 2-DE largely depends on the quality of sample prepared during protein extraction which increases results in terms of reproducibility and minimizes protein modifications that may result in artifactual spots on 2-DE gels. The buffer used for the extraction and solubilization of proteins influences the quality and reproducibility of the resolution of proteins on 2-DE gel. The purification by cleanup kit is another powerful process to prevent horizontal streaking which occurs during isoelectric focusing due to the presence of contaminants such as salts, lipids, nucleic acids, and detergents. Erythrocyte membrane proteins serve as prototypes for multifunctional proteins in various erythroid and nonerythroid cells. In this study, we therefore optimized the selected major conditions of 2-DE for resolving various proteins of human erythrocyte membrane. The modification included the optimization of conditions for sample preparation, cleanup of protein sample, isoelectric focusing, equilibration, and storage of immobilized pH gradient strips, which were further carefully examined to achieve optimum conditions for improving the quality of protein spots on 2-DE gels. The present improved 2-DE analysis method enabled better detection of protein spots with higher quality and reproducibility. Therefore, the conditions established in this study may be used for the 2-DE analysis of erythrocyte membrane proteins for different diseases, which may help to identify the proteins that may serve as markers for diagnostics as well as targets for development of new therapeutic potential.</p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"8 ","pages":"1178641817700880"},"PeriodicalIF":0.0,"publicationDate":"2017-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178641817700880","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34966702","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":"Characterization of Vitreous and Aqueous Proteome in Humans With Proliferative Diabetic Retinopathy and Its Clinical Correlation.","authors":"Sankarathi Balaiya,&nbsp;Zimei Zhou,&nbsp;Kakarla V Chalam","doi":"10.1177/1178641816686078","DOIUrl":"https://doi.org/10.1177/1178641816686078","url":null,"abstract":"<p><strong>Aims: </strong>Proliferative diabetic retinopathy (PDR) is associated with microvascular complications that cause biochemical changes in the human retina and alter the proteome of vitreous humor and aqueous humor (AH).</p><p><strong>Methods: </strong>Human vitreous humor and AH of PDR subjects were collected. Subjects who had surgery for epiretinal membrane or macular hole served as controls. Protein profiles were obtained and analyzed after running the samples on a liquid chromatography-mass spectrometry/mass spectrometry.</p><p><strong>Results: </strong>In vitreous humor, 16 unique proteins were noted in PDR patients, but not in controls. Those were associated mainly with coagulation, complement, and kallikrein-kinin systems. Under coagulation, fibrinogen and prothrombin proteins were more evident and may emphasize the importance of angiogenesis in the development of PDR. Vitreous proteins showed replicative presence in AH too. As for AH samples, we detected 10 proteins found in PDR patients, which were related to transport, coagulation, and inflammatory responses.</p><p><strong>Conclusions: </strong>We found 57 proteins in human vitreous and 39 proteins in AH. Identification of these proteins that are involved in various pathways will be helpful to understand diabetic retinopathy pathogenesis and to develop proteome as a biomarker for PDR.</p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"8 ","pages":"1178641816686078"},"PeriodicalIF":0.0,"publicationDate":"2017-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1178641816686078","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34965280","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":"Proteomic Changes in Chicken Plasma Induced by Salmonella typhimurium Lipopolysaccharides","authors":"B. Packialakshmi, R. Liyanage, J. Lay, S. Makkar, N. Rath","doi":"10.4137/PRI.S31609","DOIUrl":"https://doi.org/10.4137/PRI.S31609","url":null,"abstract":"Lipopolysaccharides (LPS) are cell wall components of Gram-negative bacteria that produce inflammation and sickness in higher animals. The objective was to identify plasma proteomic changes in an avian model of inflammation. Chickens were treated with either saline or LPS, and blood was collected at 24 hours postinjection. The pooled plasma samples were depleted of high-abundant proteins and analyzed by matrix-assisted laser desorption ionization (MALDI)-time-of-flight mass spectrometry and liquid chromatography–tandem mass spectrometry (LC–MS/MS). MALDI analyses showed an increase in fibrinogen beta-derived peptide and a decrease in apolipoprotein-AII-derived peptide in LPS samples. Label-free quantitation of LC–MS/MS spectra revealed an increase in the levels of α1-acid glycoprotein, a chemokine CCLI10, and cathelicidin-2, but a decrease in an interferon-stimulated gene-12-2 protein in the LPS group. These differentially expressed proteins are associated with immunomodulation, cytokine changes, and defense mechanisms, which may be useful as candidate biomarkers of infection and inflammation.","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"7 1","pages":"1 - 9"},"PeriodicalIF":0.0,"publicationDate":"2016-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/PRI.S31609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70714029","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":"Proteomic Analysis of Soybean [Glycine max (L.) Merrill] Roots Inoculated with Bradyrhizobium japonicum Strain CPAC 15.","authors":"Adalgisa R Torres,&nbsp;Elisete P Rodrigues,&nbsp;Jesiane Ss Batista,&nbsp;Douglas F Gomes,&nbsp;Mariangela Hungria","doi":"10.4137/PRI.S13288","DOIUrl":"https://doi.org/10.4137/PRI.S13288","url":null,"abstract":"<p><p>This research intended to analyze the expression pattern of proteins in roots of the Brazilian soybean cultivar Conquista when inoculated with Bradyrhizobium japonicum CPAC 15, a strain broadly used in commercial inoculants in Brazil. At ten days after bacterial inoculation, whole-cell proteins were extracted from roots and separated by 2-D gel electrophoresis. Comparative analysis revealed significant changes in the intensity of 37 spots due to the inoculation (17 up-regulated and 20 down-regulated proteins), identified by MALDI-TOF/TOF-TOF. Identified proteins were associated with COG functional categories of information storage and processing, cellular processes and signaling, metabolism, and also in the \"poorly characterized\" and \"not in COG\" categories. Among the up-regulated proteins, we identified sucrose synthase (nodulin-100), β-tubulin, rubisco activase, glutathione-S-transferase, a putative heat-shock 70-kDa protein, pyridine nucleotide-disulphideoxidoreductase and a putative transposase. Proteomic analysis allowed for the identification of some putative symbiotic functions and confirmed the main biological processes triggered in the nitrogen-fixing symbiosis with soybean. </p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"6 ","pages":"7-11"},"PeriodicalIF":0.0,"publicationDate":"2013-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/PRI.S13288","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32724837","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":"Mutational effect of structural parameters on coiled-coil stability of proteins.","authors":"Amutha Selvaraj Maheshwari,&nbsp;Govindaraju Archunan","doi":"10.4137/PRI.S10988","DOIUrl":"https://doi.org/10.4137/PRI.S10988","url":null,"abstract":"<p><p>Understanding the parameters that influence the melting temperature of coiled-coils (CC) and their stability is very important. We have analyzed 45 CC mutants of DNA binding protein, electron transport protein, hydrolase, oxidoreductase, and transcription factors. Many mutants have been observed at Tm = 40 °C-60 °C with ΔS = 9-11 kcal/°C mol, ΔG = -400 to -450 kcal/mol, and Keq = 0.98-1.03. The multiple regression analysis of Tm reveals that influences of thermodynamic parameters are strong (R = 0.97); chemical parameters are moderate (R = 0.63); and the geometrical parameters are negligible (R = 0.19). The combination of all these three parameters exhibits a little higher influence on Tm (R = 0.98). From the analysis, it has been concluded that the thermodynamic parameters alone are very important in stability studies on protein coil mutants. Besides, the derived regression model would have been useful for the reliable prediction of the melting temperature of coil mutants. </p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"6 ","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2013-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/PRI.S10988","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32724836","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":"A survey of membrane proteins in human serum.","authors":"Nguyen Tien Dung,&nbsp;Phan Van Chi","doi":"10.4137/PRI.S9374","DOIUrl":"https://doi.org/10.4137/PRI.S9374","url":null,"abstract":"<p><p>Serum and membrane proteins are two of the most attractive targets for proteomic analysis. Previous membrane protein studies tend to focus on tissue sample, while membrane protein studies in serum are still limited. In this study, an analysis of membrane proteins in normal human serum was carried out. Nano-liquid chromatography-electrospray ionization mass spectrometry (NanoLC-ESI-MS/MS) and bioinformatics tools were used to identify membrane proteins. Two hundred and seventeen membrane proteins were detected in the human serum, of which 129 membrane proteins have at least one transmembrane domain (TMD). Further characterizations of identified membrane proteins including their subcellular distributions, molecular weights, post translational modifications, transmembrane domains and average of hydrophobicity, were also implemented. Our results showed the potential of membrane proteins in serum for diagnosis and treatment of diseases. </p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"5 ","pages":"1-19"},"PeriodicalIF":0.0,"publicationDate":"2012-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/PRI.S9374","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32724835","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":"How Many proteins are Missed in Quantitative proteomics Based on Ms/Ms sequencing Methods?","authors":"Claire Mulvey, Bettina Thur, Mark Crawford, Jasminka Godovac-Zimmermann","doi":"10.4137/PRI.S5882","DOIUrl":"10.4137/PRI.S5882","url":null,"abstract":"<p><p>Current bottom-up quantitative proteomics methods based on MS/MS sequencing of peptides are shown to be strongly dependent on sample preparation. Using cytosolic proteins from MCF-7 breast cancer cells, it is shown that protein pre-fractionation based on pI and MW is more effective than pre-fractionation using only MW in increasing the number of observed proteins (947 vs. 704 proteins) and the number of spectral counts per protein. Combination of MS data from the different pre-fractionation methods results in further improvements (1238 proteins). We discuss that at present the main limitation on quantitation by MS/MS sequencing is not MS sensitivity and protein abundance, but rather extensive peptide overlap and limited MS/MS sequencing throughput, and that this favors internally calibrated methods such as SILAC, ICAT or ITRAQ over spectral counting methods in attempts to drastically improve proteome coverage of biological samples.</p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"3 ","pages":"61-66"},"PeriodicalIF":0.0,"publicationDate":"2010-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33423461","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":"prospects for proteomics Directed Genomic and Genetic Analyses in Disease Discoveries.","authors":"Sanjoy K Bhattacharya","doi":"10.4137/pri.s3023","DOIUrl":"10.4137/pri.s3023","url":null,"abstract":"<p><p>Proteomic discoveries are usually made using database searches for identification of proteins in a given protein sample derived from cells or tissues. High throughput searches leave a number of peptides not analyzed for a variety of reasons, such as posttranslational modification or a mutation that results changes in the peptide that is not present in databases. Such mutations may be critically important in causing disease conditions. Accounts from ocular diseases are presented where the search provided results often from non-conventional databases (such as structural database instead of protein database) due to the presence of information about a mutant peptide. We contemplate that better algorithms and the ability to determine probabilities of different amino acids in the available sequence may permit combinatorial analysis with genomics which may help identify new disease associated mutations directly from the sequence of the captured peptides. In addition, the de novo analysis of spectra of the unidentified peptides may provide mutation or polymorphism information enabling additional insight about the disease association of a mutation or posttranslational modification.</p>","PeriodicalId":88975,"journal":{"name":"Proteomics insights","volume":"2 ","pages":"23-26"},"PeriodicalIF":0.0,"publicationDate":"2009-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2899679/pdf/nihms-148582.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29116343","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}