Current Proteomics最新文献

{"title":"Identification of Potential Immunogenic Epitopes against SARS-CoV-2 using In-Silico Method: An Immunoinformatics Study","authors":"Subikshaa. S, S. P., Chethan Jaya Sai Nandamuri, Shruti Ramanathan, Shobana Sugumar","doi":"10.2174/1570164619666220401115509","DOIUrl":"https://doi.org/10.2174/1570164619666220401115509","url":null,"abstract":"\u0000\u0000Severe Acute Respiratory Syndrome (SARS-CoV-2), a zoonotic virus, is the pathogenic causal agent for the ongoing pandemic. Despite the lethality of the disease, there are no therapeutic agents available to combat the disease outbreak; and the vaccines currently accessible are insufficient to control the widespread, fast-mutating virus infection.\u0000\u0000\u0000\u0000This research study focuses on determining potential epitopes by examining the entire proteome of the SARS-CoV-2 virus using an in-silico approach.\u0000\u0000\u0000\u0000To design a vaccine for the deadly virus, the entire proteome of the SARS-CoV-2 virus was screened for identification of potential epitopes in order to identify the potent peptide candidate which is both unique and simultaneously solves the purpose of the vaccine discovery. It is mandatory to identify the suitable B-cell and T-cell epitopes of the observed SARS-CoV-2 Surface Glycoprotein (QKN61229.1). These epitopes were subjected to various tests, including antigenicity, allergenicity, and other physicochemical properties. The T-cell epitopes that met all of the criteria were then subjected to Population Coverage Analysis. It helped better understand the response of epitopes to the target population, compute the conservancy of a peptide, and then cluster them based on their sequence match, MHC binding, and T-cell restriction sites. Lastly, the interactions between the T-Cell Receptor (TCR) and a peptide-MHC were studied to gain a thorough understanding of MHC-restriction to design a peptide-vaccine.\u0000\u0000\u0000\u0000The results showed that there were 4 B-Cell epitopes, 2 MHC-I epitopes, 4 MHC-II epitopes that qualified all the subjected tests and thus have an affinity to prominent antigens.\u0000\u0000\u0000\u0000ased on the results obtained from this study, the estimated peptides are a promising candidate for peptide-vaccine design and development.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"90 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83907966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A motif in metallopeptidase inhibitor decreases effectively the activity of macrophage metalloproteinases","authors":"G. Esfandiari, G. Ghasempour, Naser Kakavandi, A. Soleimani, Borhan Rahimi, Elham Bahraini, M. Najafi, M. Khosravi","doi":"10.2174/1570164619666220304162545","DOIUrl":"https://doi.org/10.2174/1570164619666220304162545","url":null,"abstract":"\u0000\u0000The tissue remodeling process and cellular migration relate to the activities of matrix metalloproteinases (MMPs). The aim of this study was to investigate the effects of a predicted motif from TIMPs on the MMP-2 and MMP-9 activities secreted from the differentiated macrophages.\u0000\u0000\u0000\u0000The monocytes were isolated from the healthy individuals by RosetteSep kit and were differentiated into macrophages using M-CSF. A 4-amino acid motif (TCAP) was predicted using bioinformatics tools. Zymography technique was applied for the measurement of MMP activities. The docking studies were also investigated between MMPs, tetrapeptide, and Batimastat.\u0000\u0000\u0000\u0000The TCAP inhibited significantly the differentiated macrophage MMP-2 and MMP-9 activities (p=0.0001and p=0.01, respectively). The docking results suggested the some MMP amino acids are involved with both tetrapeptide (TCAP), and Batimastat,\u0000\u0000\u0000\u0000The data showed that the small motif (TCAP) of TIMPs inhibits effectively the MMP-2 activity.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"91 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89965276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic profile analysis of pulmonary artery in a rat model under hypoxic pulmonary hypertensionc","authors":"Ma Shuang, L. Jie, Zhang Ruixia, Liu Chuanchuan, M. Yan","doi":"10.2174/1570164619666220204123709","DOIUrl":"https://doi.org/10.2174/1570164619666220204123709","url":null,"abstract":"\u0000\u0000Proteomic profile analysis of pulmonary artery in a rat model under hypoxic pulmonary hypertension\u0000\u0000\u0000\u0000Background: Hypoxic pulmonary hypertension (HPH) is a pathological condition exemplified by a constant rise in pulmonary artery pressure in high-altitudes.\u0000\u0000\u0000\u0000Objective: To investigated the proteome profile and response mechanisms of SD rats under hypoxia over a period of four-weeks.\u0000\u0000\u0000\u0000Method: Proteomic profile analysis of pulmonary artery in a rat model under hypoxic pulmonary hypertension.\u0000\u0000\u0000\u0000Results: With 3,204 proteins identified, 49 were up-regulated while 46 were down-regulated. Upregulated genes included Prolargin, Protein S100-A6 and Transgelin-2, whereas Nascent polypeptide-associated complex and Elongator complex protein 1 were down-regulated. KEGG enriched pathways had purine metabolism, cancer and lipolysis regulation as significantly enriched in hypoxic group.\u0000\u0000\u0000\u0000Conclusion: In conclusion, our findings submit basis for downstream studies on tissue hypoxia mechanisms alongside the associated physiological conditions.\u0000Hypoxic pulmonary hypertension (HPH) is a pathological condition exemplified by a constant rise in pulmonary artery pressure in high altitudes. Herein, we investigated the proteome profile and response mechanisms of Sprague-Dawley (SD) rats under hypoxia over a period of four weeks. Unbiased iTRAQ-based quantitative proteomics was utilized in proteome profile analysis of a rat model exposed to HPH. With 3,204 proteins identified, 49 were upregulated while 46 were downregulated. Upregulated genes included Prolargin, Protein, S100-A6 and Transgelin-2, whereas Nascent polypeptide-associated complex and Elongator complex protein 1 were downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched pathways had purine metabolism, cancer, and lipolysis regulation as significantly enriched in hypoxic group. In conclusion, the findings from this study submit a basis for downstream studies on tissue hypoxia mechanisms alongside the associated physiological conditions.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"21 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76647837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meet the Editorial Board Member","authors":"N. Taylor","doi":"10.2174/157016461901220119162454","DOIUrl":"https://doi.org/10.2174/157016461901220119162454","url":null,"abstract":"","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"3 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79843589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"iTRAQ-Based Quantitative Proteomics Analysis Reveals the Invasion Mechanism of Spiroplasma eriocheiris in 3T6 Cells","authors":"Peng Liu, Youyuan Ye, Shasha Xiang, Yuxin Li, Chengbin Zhu, Zixu Chen, Jie Hu, Ye Gen, Li Lou, Xuqi Duan, Juan Zhang, W. Gu","doi":"10.2174/1570164619666220113154423","DOIUrl":"https://doi.org/10.2174/1570164619666220113154423","url":null,"abstract":"\u0000\u0000Spiroplasma eriocheiris is a novel pathogen of freshwater crustaceans and\u0000is closely related to S. mirum. They have no cell wall and a helical morphology. They have the ability\u0000to infect mammals with an unclear mechanism.\u0000\u0000\u0000\u0000In this study, our aim was to investigate the profile of protein expression in 3T6 cells infected\u0000with S. eriocheiris.\u0000\u0000\u0000\u0000The proteome of 3T6 cells infected by S. eriocheiris was systematically investigated by\u0000iTRAQ.\u0000\u0000\u0000\u0000We identified and quantified 4915 proteins, 67 differentially proteins were found, including\u000030 up-regulated proteins and 37 down-regulated proteins. GO term analysis shows that dysregulation\u0000of adhesion protein , interferon and cytoskeletal regulation are associated with apoptosis. Adhesion\u0000protein Vcam1 and Interferon-induced protein GBP2, Ifit1, TAPBP, CD63 ,Arhgef2 were\u0000up-regulated. A key cytoskeletal regulatory protein, ARHGEF17 was down-regulated. KEGG pathway\u0000analysis showed the NF-kappa B signaling pathway, the MAPK signaling pathway , the Jak-STAT\u0000signaling pathway and NOD-like receptor signaling are closely related to apoptosis in vivo.\u0000\u0000\u0000\u0000Analysis of the signaling pathways involved in invasion may provide new insights for\u0000understanding the infection mechanisms of S. eriocheiris.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"78 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77294974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolomics of meat color: Practical implications","authors":"M. Denzer, F. Kiyimba, G. Mafi, R. Ramanathan","doi":"10.2174/1570164619666211230153145","DOIUrl":"https://doi.org/10.2174/1570164619666211230153145","url":null,"abstract":"\u0000\u0000Meat is biochemically active, and the various pre-and post-harvest processes\u0000can affect meat quality. Metabolomics is a valuable tool to elucidate metabolite changes in meat.\u0000The overall goal of this study was to provide an overview of various techniques, data analysis, and\u0000application of metabolomics in meat color research.\u0000\u0000\u0000\u0000Both targeted and non-targeted approaches have been used to determine metabolite profiles in meat. Researchers use gas-, liquid-chromatography, and nuclear magnetic resonance platforms to separate molecules. Metabolomics is used to characterize muscle-specific differences in\u0000color stability, meat tenderness, the impact of aging on meat color, and to determine metabolite profile differences between normal-pH and dark-cutting beef. Color stable muscles have more glycolytic metabolites than color labile muscles.\u0000\u0000\u0000\u0000The use of metabolomics has greatly enhanced our understanding of metabolites' role\u0000in meat quality. There are challenges in data analysis; thus, there is a need for multiple platforms in\u0000order to obtain comprehensive metabolite libraries specific to food. Metabolomics in combination\u0000with wet-laboratory techniques can provide novel insights on the relationship between postmortem\u0000metabolism and meat color.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"61 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84676639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subcellular Proteomic Analysis Reveals Dysregulation in Organization of Human A549 Cells Infected with Influenza Virus H7N9","authors":"L. Yin, Siyuan Liu, Huichun Shi, Yan-ling Feng, Yujiao Zhang, Dage Wu, Zhigang Song, Lijun Zhang","doi":"10.2174/1570164619666211222145450","DOIUrl":"https://doi.org/10.2174/1570164619666211222145450","url":null,"abstract":"\u0000\u0000H7N9 influenza virus poses a high risk to human beings and proteomic evaluations of these infections may help to better understand its pathogenic mechanisms in human systems. Objective: To find membrane proteins related to H7N9 infection. \u0000\u0000\u0000\u0000\u0000 Here, we infected primary human alveolar adenocarcinoma epithelial cells (A549) cells with H7N9 (including wild and mutant strains) and then produced enriched cellular membrane isolations which were evaluated by western blot. The proteins in these cell membrane fractions were analyzed using the isobaric Tags for Relative and Absolute Quantitation (iTRAQ) proteome technologies. \u0000\u0000\u0000\u0000\u0000 Differentially expressed proteins (n = 32) were identified following liquid chromatography-tandem mass spectrometry, including 20 down-regulated proteins such as CD44 antigen, and CD151 antigen, and 12 up-regulated proteins such as tight junction protein ZO-1, and prostaglandin reductase 1. Gene Ontology database searching revealed that 20 out of the 32 differentially expressed proteins were localized to the plasma membrane. These proteins were primarily associated with cellular component organization (n = 20), and enriched in the Reactome pathway of extracellular matrix organization (n = 4). \u0000\u0000\u0000\u0000\u0000These findings indicate that H7N9 may dysregulate cellular organization via specific alterations to the protein profile of the plasma membrane.\u0000\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"24 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86743952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic analysis of early phosphorylated proteins in acute pancreatitis model","authors":"Pengcheng Zhang, Yuan Zhou, Qiangqiang Fang, Houmin Lin, Juan Xiao","doi":"10.2174/1570164618666211130144858","DOIUrl":"https://doi.org/10.2174/1570164618666211130144858","url":null,"abstract":"\u0000\u0000 The exact mechanism of acute pancreatitis (AP), which is an inflammation of the pancreas, still remains unclear. In this study, we examined the protein phosphorylation changes during the early stage of AP in mice using proteomic analysis. \u0000\u0000\u0000\u0000\u0000AP model in mice was constructed using an intraperitoneal injection of cerulein. Blood samples and pancreas were collected at 1, 3, 6, 9h after the final injection (n=3 at each time point). Samples collected 3h after the final injection were separately mixed and named S (saline group) and C1 (cerulein group); samples collected 6h after the final injection from the cerulein group were mixed and named C2. Proteins from S, C1, and C2 were extracted, digested by trypsin, and subjected to LC-MS/MS analysis, bioinformatics analysis, and Western blotting.\u0000\u0000\u0000\u0000\u0000A total of 549 sites (426 proteins) were upregulated, and 501 sites (367 proteins) were downregulated in C1 compared to S; while 491 phosphorylation sites (377 proteins) were upregulated and 367 sites (274 proteins) were downregulated in C2 compared to S. Motif analysis showed that proline-directed kinase and basophilic kinase had a key role during early AP. During an early AP stage, the cellular distributions of proteins slightly changed. The types of domains changed with the development of AP. Phosphorylation proteins associated with calcium signaling, especially IP3R mediated calcium release, lysosome and autophagosome pathway, pancreatic digestive activation, and secretion, were found to be involved in the development of early AP independent of NF-kB activation. Moreover, the MAPK family was found to have a greater impact at the early stage of AP. We also found differentially expressed phosphorylations of amylase and trypsinogen and increased phosphorylation of MAPK6 S189 in early AP. \u0000\u0000\u0000\u0000\u0000IP3R mediated calcium release and activation of MAPK family are key events promoting the development of early AP. \u0000\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"6 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77825348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel Feature Representation and Machine Learning Methods in Computational Proteomics","authors":"Lei Chen","doi":"10.2174/157016461805210924161719","DOIUrl":"https://doi.org/10.2174/157016461805210924161719","url":null,"abstract":"In recent years, protein-related data have grown rapidly with the application of novel methods and techniques. Several online public databases have been set up, and investigators can easily retrieve various data reported in them. Traditional computational methods to deal with these data are becoming more and more inappropriate because they are in different forms. Thus, novel data-driven computational methods are increasingly needed. This thematic issue collects six excellent papers, out of which three papers reviewed newly proposed methods of essential problems in computational proteomics and three research articles proposed novel computational methods to deal with specific problems.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"29 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85288542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"M.P. Molloy","authors":"M. Molloy","doi":"10.2174/157016461805210924161310","DOIUrl":"https://doi.org/10.2174/157016461805210924161310","url":null,"abstract":"","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"61 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80286307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}