Current Proteomics最新文献

{"title":"ORF7a Palsies Macrophage to Worsen Diabetes by SMB/BPI/ABC Domains and PARP/Cap/Cyclin Enzyme System","authors":"Wenzhong Liu, Hualan Li","doi":"10.2174/1570164620666230314102530","DOIUrl":"https://doi.org/10.2174/1570164620666230314102530","url":null,"abstract":"\u0000\u0000Such factors as diabetes and obesity can dramatically worsen COVID-19 symptoms. In addition, macrophage accumulation in adipose tissue is related to obesity. Therefore, macrophages play a significant role in raising COVID-19 susceptibility and severity in diabetes and obese patients.\u0000\u0000\u0000\u0000Lipopolysaccharide activates the natural immune system response in obese and diabetic patients’ adipose tissue and increases the risk of susceptibility and severity of COVID-19.\u0000\u0000\u0000\u0000In this study, the functional impact of SARS-CoV-2 ORF7a on macrophages was analyzed using a domain-searching bioinformatics technique. Ca2+ binding domain, kinase and phosphatase, SMB/SRCR, LBP/BPI/CETP, ABC, TIR,PARP, Flavivirus Cap enzyme, Cyclin, and other domains have been identified in SARS-CoV-2 ORF7a. ORF7a binds to oxidized low-density lipoprotein cholesterol particles by the macrophage receptor-like domains such as SMB/SRCR and enters macrophages via macropinocytosis. Then, ORF7a prevents 18 S rRNA maturation and adds flavivirus cap 0/1/2 to mRNA to interfere with transcription and translation via PARP, Flavivirus Cap enzyme, and other associated domains.\u0000\u0000\u0000\u0000Meanwhile, ORF7a activates and promotes G2/M phase transition via cyclin-related enzymatic activity domains.\u0000\u0000\u0000\u0000The destructive activity of ORF7a hijacks the nitric oxide release pathway of macrophages and promotes macrophage death, enabling the virus to elude the innate immune system and aggravate diabetes-related problems in patients.\u0000\u0000\u0000\u0000We speculated that cells infected by the SARS-COV-2 virus often used its surface lipopolysaccharides to build expanded barriers to resist T cells, NK cells, and drugs.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"23 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2023-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91158532","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":"Pilot Study of the ex vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma","authors":"A. Nikolić, Kevin J. Mark, S. Dragicevic, T. Babic, K. Milosevic, B. Nestorović, V. Beškoski","doi":"10.2174/1570164620666230220112500","DOIUrl":"https://doi.org/10.2174/1570164620666230220112500","url":null,"abstract":"\u0000\u0000Leukocytes are key cellular effectors of inflammation in asthma and understanding their function in this disease is of crucial importance. Blood leukocytes reflect the actions of their counterparts in the lungs and they can be obtained through minimal invasive procedures as part of the peripheral blood.\u0000\u0000\u0000\u0000Leukocytes are key cellular effectors of inflammation in asthma and understanding their function in this disease is of crucial importance. Blood leukocytes reflect the actions of their counterparts in the lungs and they can be obtained through minimal invasive procedure as part of the peripheral blood.\u0000\u0000\u0000\u0000The aim of the study was to identify proteins in blood leukocyte proteomes that respond to ex vivo treatment by prednisone in order to pinpoint candidates for predictive biomarkers in corticosteroid-responsive asthma.\u0000\u0000\u0000\u0000The study included five children diagnosed with asthma and five healthy children. After the ex vivo treatment of blood samples with prednisone, lysis of erythrocytes was performed and proteins were extracted from the remaining leukocytes by ultrasonic disintegration. Protein extracts were analyzed by reversed phase nano-liquidchromatography–tandem mass spectrometry (LC–MS/MS).\u0000\u0000\u0000\u0000The stimulation of asthmatics' leukocytes with prednisone has led to an increase in the levels of FYB (fold change 3.4) and LYZ (fold change 2.2) with a statistical significance of p<0.005. The two proteins with expressions significantly altered upon the prednisone treatment should be further explored as tools to evaluate the patient's response before therapy administration, especially when lung function measurements are not possible, as is the case with young pediatric patients.\u0000\u0000\u0000\u0000The approach that entails ex vivo response of blood leukocytes to therapeutics can facilitate asthma management and help overcome the need for therapeutic adjustments in a clinical setting.\u0000\u0000\u0000\u0000/\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"270 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2023-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74731257","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":"Corrigendum to: Cancer Proteomics: New Horizons and Insights into Therapeutic Applications","authors":"Jaime Jacqueline Jayapalan, Perumal Subramanian, Puteri Shafinaz Abdul-Rahman","doi":"10.2174/157016462001230717161726","DOIUrl":"https://doi.org/10.2174/157016462001230717161726","url":null,"abstract":"Following the publication of the original article [1], the authors reported that the complete grant number of the funding was omitted. In this correction, the incorrect and correct grant numbers are mentioned. The original publication of this article has been corrected. <P> The funding acknowledgement published previously is as follows: <P> The study was funded by Fundamental Research Grant Scheme (FRGS) by the Ministry of Education, Malaysia, Grant number: FP067-2018A, Geran Penyelidikan Fakulti by the Faculty of Medicine, University of Malaya, Grant number: GPF001C- 2019, and UGC mid-career award, Grant number: F.19-221/2018 (BSR) dt. 28.03.2018. <P> We would like to request a revision to one of the funding numbers (in blue) in the funding acknowledgement below: The correct funding acknowledgement is: <P> The study was funded by Fundamental Research Grant Scheme (FRGS) by the Ministry of Education, Malaysia, Grant number: FRGS/1/2018/STG05/UM/02/5, Geran Penyelidikan Fakulti by the Faculty of Medicine, University of Malaya, Grant number: GPF001C-2019 and UGC mid-career award, Grant number: F.19-221/2018 (BSR) dt. 28.03.2018. <P> The original article can be found online at: https://www.eurekaselect.com/public/article/109117.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135147183","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":"Brian McDonagh","doi":"10.2174/157016462001230614161649","DOIUrl":"https://doi.org/10.2174/157016462001230614161649","url":null,"abstract":"","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"66 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135146256","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":"Proteomics of the skin secretion of Pulchrana glandulosa (Anura: Ranidae) (Boulenger, 1882), Langkawi Island, Kedah, Peninsular Malaysia","authors":"D. Ong, S. Shahrudin, M. Ismail","doi":"10.2174/1570164620666221209121936","DOIUrl":"https://doi.org/10.2174/1570164620666221209121936","url":null,"abstract":"\u0000\u0000The advancement of proteomics studies leads to various benefits in research. However, in Malaysia, proteomics studies are still in their early stage.\u0000\u0000\u0000\u0000Four adult Pulchrana glandulosa individuals were collected from the stream of Temurun Waterfall for their proteomics information.\u0000\u0000\u0000\u0000These frogs’ skin secretions were collected, extracted, and analysed for their protein antimicrobial peptide compounds and biomedical potentials using liquid chromatography-mass spectrometry.\u0000\u0000\u0000\u0000Forty-six proteins had been identified from the skin secretion of this species. They contained unreviewed proteins, enzymes, AMPs, receptors, regulatory, transport, hormone, and developmental proteins. In addition, 11 AMP had been identified, consisting of esculentin-2, brevinin 1, and other AMPs.\u0000\u0000\u0000\u0000These proteins and AMPs have a wide range of biomedical importance, such as antimicrobials, anti-tumour, anti-cancerous, anti-viral, wound healing, anti-inflammation, anti-ageing and maintaining homeostasis.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"75 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83786941","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":"Predicting the Secondary Structure of Proteins: A Deep Learning Approach","authors":"D. Mehrotra, Charu Kathuria, N. Misra","doi":"10.2174/1570164619666221010100406","DOIUrl":"https://doi.org/10.2174/1570164619666221010100406","url":null,"abstract":"\u0000\u0000The machine learning computation paradigm touched new horizons with the development of deep learning architectures. It is widely used in complex problems and achieved significant results in many traditional applications like protein structure prediction, speech recognition, traffic management, health diagnostic systems and many more. Especially, Convolution neural network (CNN) has revolutionized visual data processing tasks.\u0000\u0000\u0000\u0000Protein structure is an important research area in various domains extending from medical science, health sectors to drug designing. Fourier Transform Infrared Spectroscopy (FTIR) is the leading tool for protein structure determination. This review aims to study the existing deep learning approaches proposed in the literature to predict proteins' secondary structure and to develop a conceptual relation between FTIR spectra images and deep learning models to predict the structure of proteins.\u0000\u0000\u0000\u0000Various pre-trained CNN models are identified and interpreted to correlate the FTIR images of proteins containing Amide-I and Amide-II absorbance values and their secondary structure.\u0000\u0000\u0000\u0000The concept of transfer learning is efficiently incorporated using the models like Visual Geometry Group (VGG), Inception, Resnet, and Efficientnet. The dataset of protein spectra images is applied as input, and these models act significantly to predict the secondary structure of proteins.\u0000\u0000\u0000\u0000As deep learning is recently being explored in this field of research, it worked remarkably in this application and needs continuous improvement with the development of new models.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"235 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73641549","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":"S. Gonfloni","doi":"10.2174/157016461905221208115443","DOIUrl":"https://doi.org/10.2174/157016461905221208115443","url":null,"abstract":"<jats:sec>\u0000<jats:title />\u0000<jats:p />\u0000</jats:sec>","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"98 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89257059","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":"Unraveling major proteins of Mycobacterium tuberculosis envelope","authors":"D. Bisht, Rananjay Singh, D. Sharma, D. Sharma, S. Gautam, Mahendra K. Gupta","doi":"10.2174/1570164619666220908141130","DOIUrl":"https://doi.org/10.2174/1570164619666220908141130","url":null,"abstract":"\u0000\u0000Although treatable, resistant form of tuberculosis has posed a major impediment to the effective TB control programme. As the Mycobacterium tuberculosis cell envelope is closely associated with its virulence and resistance, it is very important to understand the cell envelope for better treatment of causative pathogens. Cell membrane plays a crucial role in imparting various cell functions. Proteins being the functional moiety, it is impossible to characterize the functional properties based on genetic analysis alone. Proteomic based research has indicated mycobacterial envelope as a good source of antigens/proteins. Envelope/membrane and associated proteins have an anticipated role in biological processes which could be of vital importance to the microbe and hence could qualify as drug targets. This review provides an overview of the prominent and biologically important cell envelope and highlights the different functions offered by the proteins associated with it. Selective targeting of the mycobacterial envelope offers an untapped opportunity to address the problems associated with the current drugs regimen and also will lead to the development of more potent and safer drugs against all forms of tuberculous infections.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"9 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72914178","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":"A. Bairoch","doi":"10.2174/157016461904220907111423","DOIUrl":"https://doi.org/10.2174/157016461904220907111423","url":null,"abstract":"<jats:sec>\u0000<jats:title />\u0000<jats:p />\u0000</jats:sec>","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"10 2 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90372564","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":"Heavy metal stress tolerance by Serratia nematodiphila sp. MB307: insights from mass spectrometry based proteomics","authors":"Z. Basharat, K. Moon, L. Foster, A. Yasmin","doi":"10.2174/1570164619666220617145437","DOIUrl":"https://doi.org/10.2174/1570164619666220617145437","url":null,"abstract":"\u0000\u0000Heavy metals impact living organism deleteriously when exceed the required limits. Their remediation by bacteria is a much pursued area of environmental research. In this study, we explored the quantitative changes for four heavy metals (Cadmium, Chromium, Zinc, Copper), on global and membrane proteome of gram negative S. nematodiphila MB307. This is a versatile bacterium, isolated from rhizosphere of heavy metal tolerating plant and equipped with characteristics ranging from useful biopeptide production to remediation of metals.\u0000\u0000\u0000\u0000We explored changes in its static end products of coding DNA sequences i.e. proteins after 24 incubation under metal stress, using LC-MS/MS. Data analysis was done using MaxQuant software coupled with Perseus package.\u0000\u0000\u0000\u0000Up and downregulated protein fractions consisted prominently of chaperones, membrane integrity proteins, mobility or transporter proteins. Comparative analysis with previously studied bacteria and functional contribution of these proteins in metal stress offers evidence for survival of S. nematodiphila under high concentrations of selected metals.\u0000\u0000\u0000\u0000The outcomes validate that this soil derived bacterium is well attuned to remove these metals from soil, water and may be additionally useful for boosting phytoremediation of metals. This study delivers interesting insights and overlays ground for further investigations into mechanistic activity of this bacterium under pollutant stress.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"396 5","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72448184","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}