Current Proteomics最新文献_第6页

Meet the Editorial Board Member 认识编辑委员会成员

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-06-01 DOI: 10.2174/157016461903220530111915

R. Abrol

引用次数: 0

Identification of human protein subcellular location with multiple networks 基于多网络的人蛋白亚细胞定位鉴定

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-05-31 DOI: 10.2174/1570164619666220531113704

Rui Wang, Lei Chen

{"title":"Identification of human protein subcellular location with multiple networks","authors":"Rui Wang, Lei Chen","doi":"10.2174/1570164619666220531113704","DOIUrl":"https://doi.org/10.2174/1570164619666220531113704","url":null,"abstract":"\u0000\u0000Protein function is closely related to its location within the cell. Determination of protein subcellular location is helpful to uncover its functions. However, traditional biological experiments to determine the subcellular location are of high cost and low efficiency, which cannot meet today’s needs. In recent years, lots of computational models have been set up to identify protein subcellular locations. Most models used features derived from protein sequences. Recently, features extracted from protein-protein interaction (PPI) network become popular to study various protein-related problems.\u0000\u0000\u0000\u0000A novel model with features derived from multiple PPI networks was proposed to predict protein subcellular location.\u0000\u0000\u0000\u0000Protein features were obtained by a new designed network embedding algorithm, Mnode2vec, which was a generalized version of the classic Node2vec algorithm. Two classic classification algorithms: support vector machine and random forest, were employed to build the model.\u0000\u0000\u0000\u0000Such model provided good performance and was superior to the model with features extracted by Node2vec. Also, this model outperformed some classic models. Furthermore, Mnode2vec can produce powerful features when the path length was small.\u0000\u0000\u0000\u0000The proposed model can be a powerful tool to determine protein subcellular location and Mnode2vec can efficiently extract informative features from multiple networks.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"38 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73668864","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}

引用次数: 10

Methanol and sorbitol affect the molecular dynamics of arginine deiminase: insights for improving its stability 甲醇和山梨醇影响精氨酸脱亚胺酶的分子动力学:提高其稳定性的见解

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-05-13 DOI: 10.2174/1570164619666220513123509

M. Zarei, S. Sabetian, M. Rahbar, M. Negahdaripour

{"title":"Methanol and sorbitol affect the molecular dynamics of arginine deiminase: insights for improving its stability","authors":"M. Zarei, S. Sabetian, M. Rahbar, M. Negahdaripour","doi":"10.2174/1570164619666220513123509","DOIUrl":"https://doi.org/10.2174/1570164619666220513123509","url":null,"abstract":"\u0000\u0000Arginine deiminase enzyme of Mycoplasma arginini (MaADI) is a potential anti-cancer agent for treating arginine-auxotrophic cancers. Investigating the protein stability in the presence of osmolytes can help to increase protein stability under various stressed conditions.\u0000\u0000\u0000\u0000In this study, the stability and dynamics of MaADI were investigated in pure water and solutions of 1 M sorbitol, 10% (v/v) methanol, and 50% (v/v) methanol using molecular dynamics simulation.\u0000\u0000\u0000\u0000Sorbitol was found to stabilize the protein, whereas high-concentrated methanol destabilized it. Sorbitol molecules interacted with the protein through hydrogen bonding and reduced the protein fluctuations as well. At 50% methanol, the flexibility of regions 4-8, 195-201, 314-324, and 332-337 in the MaADI was increased; whereas residues 195-201 showed the highest variations.\u0000\u0000\u0000\u0000Thus, these regions of MaADI, especially 195-201, are the most sensitive regions in the presence of denaturing agents and can be subjected to protein engineering toward improving the stability of MaADI.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"70 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86905155","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}

引用次数: 0

Proteomics, Peptidomics and Transcriptomic Analysis of the Venom from the Spider Macrothele yani (Mygalomorphae: Macrothelidae) 巨蛛毒液的蛋白质组学、肽组学和转录组学分析

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-04-30 DOI: 10.2174/1570164619666220430151150

X. Gu, Ying Wang, Chenggui Zhang, Xiu-Mei Wu, Huai Xiao, Yinnan Yang, Dasong Yang, Zhi-Bin Yang, Zijin Yang, Yu Zhao

{"title":"Proteomics, Peptidomics and Transcriptomic Analysis of the Venom from the Spider Macrothele yani (Mygalomorphae: Macrothelidae)","authors":"X. Gu, Ying Wang, Chenggui Zhang, Xiu-Mei Wu, Huai Xiao, Yinnan Yang, Dasong Yang, Zhi-Bin Yang, Zijin Yang, Yu Zhao","doi":"10.2174/1570164619666220430151150","DOIUrl":"https://doi.org/10.2174/1570164619666220430151150","url":null,"abstract":"\u0000\u0000Spider venom show abundant diversity in both peptides and proteins, which play essential roles in new drug development and agrochemistry. The venoms of Macrothele yani species have strong toxicity on the victims.\u0000Objective: The purpose of this study is to comprehensively characterize the profile of venom proteins and peptides of spider Macrothele yani mainly inhabiting in Yunnan province, China.\u0000\u0000\u0000\u0000Using a combination of RNA sequencing of the venom glands and venom proteomics based on Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry (LC-ESI-MS/MS), we provide the ﬁrst overview of the peptides and proteins produced by Macrothele yani.\u0000\u0000\u0000\u0000A total of 116 peptide sequences were analyzed, and 43 homologous proteins were matched, of which 38.10% were toxin proteins. High-throughput sequencing by the HiSeq-2000 (Illumina), followed by de novo assembly. As a result, 301,024 similar protein sequences were annotated in the available databases. A total of 68 toxins-related sequences were identiﬁed, comparative sequence analyses of these sequences indicated the presence of different types of enzymes and toxin-like genes, including Acetylcholinesterase, Hyaluronidase, cysteine-rich secretory proteins (CRISP), Astacin metalloprotease and other venom components.\u0000\u0000\u0000\u0000The venom of spider is a very abundant resources in nature. They were analyzed in order to determine their function in pathophysiology. Molecular templates with potential application value in medical and biological fields were obtained by classifying and characterizing the presumed components about spider venom of Macrothele yani, which laid a foundation for further study of the venom in the future.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"08 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89617330","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}

引用次数: 0

Proteomics and Computational Analysis of Cytosolic Proteome of a Thermoacidophilic Euryarchaeon Picrophilus torridus 嗜热嗜酸Euryarchaeon Picrophilus torridus的蛋白质组学和胞质蛋白质组学计算分析

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-04-29 DOI: 10.2174/1570164619666220429121247

N. Singhal, Anjali Garg, Nirpendra Singh, Manish Kumar, M. Goel

{"title":"Proteomics and Computational Analysis of Cytosolic Proteome of a Thermoacidophilic Euryarchaeon Picrophilus torridus","authors":"N. Singhal, Anjali Garg, Nirpendra Singh, Manish Kumar, M. Goel","doi":"10.2174/1570164619666220429121247","DOIUrl":"https://doi.org/10.2174/1570164619666220429121247","url":null,"abstract":"\u0000\u0000Picrophilus torridus is a thermoacidophilic archaeon which thrives in an extremely low pH (0-1) and high temperatures (50-60°C). Thus, it is a suitable organism to study microbial genetics and metabolic adaptations to extreme acidic and moderate thermal environment.\u0000\u0000\u0000\u0000In the present study we have conducted a global proteome analysis of P. torridus and discerned the cytosolic proteome of P. torridus using gel-free, liquid chromatography mass spectrometry (LC-MS/MS).\u0000\u0000\u0000\u0000The cytosolic proteins of P. torridus were extracted and identified using gel-free, LC-MS/MS. Gene Ontology based pathway analysis and protein-protein interaction studies were performed to understand the role of various cytosolic proteins in sustaining the thermoacidophilic environment. Also, domain analysis of hypothetical/uncharacterized proteins was performed.\u0000\u0000\u0000\u0000Using gel-free LC-MS/MS, 408 cytosolic proteins of P. torridus were identified, including 36 hypothetical/uncharacterized proteins. Thus, we could identify 26.58 % of the theoretical proteome of P. torridus. Majority of the cytosolic proteins were observed to be multi-functional and involved in activities related to microbial metabolism.\u0000\u0000\u0000\u0000Comparison with an earlier study which used gel-based LC-MS analysis to identify cytosolic proteins of P. torridus revealed that gel-free LC-MS was better in identifying more number of proteins and also, higher/lower molecular weight proteins. The information discerned in this study might add to the knowledge-base of P. torridus proteome and provide a useful basis for further proteomic studies on other thermoacidophilic archaea.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"95 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81245736","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}

引用次数: 0

Analysis of membrane proteins of streptomycin resistant Mycobacterium tuberculosis isolates 耐链霉素结核分枝杆菌分离株膜蛋白分析

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-04-28 DOI: 10.2174/1570164619666220428082752

Rananjay Singh, D. Sharma, D. Sharma, Mahendra K. Gupta, D. Bisht

{"title":"Analysis of membrane proteins of streptomycin resistant Mycobacterium tuberculosis isolates","authors":"Rananjay Singh, D. Sharma, D. Sharma, Mahendra K. Gupta, D. Bisht","doi":"10.2174/1570164619666220428082752","DOIUrl":"https://doi.org/10.2174/1570164619666220428082752","url":null,"abstract":"\u0000\u0000Drug resistant tuberculosis remains a health security threat and resistance to second-line drugs limits the options for treatment. Consequently, there is an utmost need for identifying and characterizing new biomarkers/drug targets of prime importance. Membrane proteins have an anticipated role in biological processes and could qualify as biomarkers/drug targets. Streptomycin (SM) is recommended as a second-line treatment regimen only when amikacin resistance has been confirmed. As extensively drug-resistant (XDR) isolates are frequently cross-resistant to second-line injectable drugs, an untapped potential for continued use of SM has been suggested.\u0000\u0000\u0000\u0000The study aimed to analyze the membrane proteins overexpressed in SM resistant isolates of Mycobacterium tuberculosis using proteomics approaches.\u0000\u0000\u0000\u0000Membrane proteins were extracted employing sonication and ultracentrifugation. Two-dimensional gel electrophoresis (2DGE) of membrane proteins was performed and identification of proteins was done by liquid chromatography-mass spectrometry (LCMS) and bioinformatics tools.\u0000\u0000\u0000\u0000On analyzing the two-dimensional (2D) gels, five protein spots were found overexpressed in the membrane of SM resistant isolates. Docking analysis revealed that SM might bind to the conserved domain of overexpressed proteins and Group-based prediction system-prokaryotic ubiquitin-like protein (GPS-PUP) predicted potential pupylation sites within them.\u0000\u0000\u0000\u0000These proteins might be of diagnostic importance for detecting the cases early and for exploring effective control strategies against drug-resistant tuberculosis, particularly SM.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"9 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85100742","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}

引用次数: 0

Proteomic Profiling of Maternal Serum for Early Risk Analysis of Preterm Birth 早产儿早期风险分析的母体血清蛋白质组学分析

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-04-12 DOI: 10.2174/1570164619666220412122959

Javeria Malik, Shaaf Ahmad, Humaira Aziz, N. Roohi, M. A. Iqbal

{"title":"Proteomic Profiling of Maternal Serum for Early Risk Analysis of Preterm Birth","authors":"Javeria Malik, Shaaf Ahmad, Humaira Aziz, N. Roohi, M. A. Iqbal","doi":"10.2174/1570164619666220412122959","DOIUrl":"https://doi.org/10.2174/1570164619666220412122959","url":null,"abstract":"\u0000\u0000The absence of absolute clinical indicators and suitable biomarkers hinders the timely diagnosis of women at risk of preterm birth. It influences roughly 12% of births. At\u0000delivery and clinical presentation, preterm births are generally inspected based on the gestational\u0000period. Different disturbed pathways are associated with the signs of at-risk pregnancies.\u0000\u0000\u0000\u0000The main purpose of this study is to analyze and explore the serum proteome of early deliveries and help health care professionals to improve the understanding of the progression of\u0000preterm birth.\u0000\u0000\u0000\u0000In the present study, 200 pregnant females of 20-30 years of age were selected. We collected samples of second and third-trimester pregnant females, out of which 40 females delivered\u0000preterm. We further divided them into three groups, i.e., extremely preterm group, very preterm,\u0000and controls. Overall comparison of serum profiles of all the three groups expressing fourteen proteins ranging between 200-10kDa was made. Serum proteins were isolated by one-dimensional\u0000sodium dodecyl sulfate-polyacrylamide gel electrophoresis and photographed by totalLab quant\u0000software. Groups were evaluated using the ANOVA Tukey’s Post Hoc analysis.\u0000\u0000\u0000\u0000Proteins of 69kDa and 15kDa expressed a significant decrease when compared with control subjects. In contrast, the proteins of 23kDa expressed a significant increase, while the proteins\u0000of 77kDa, 45kDa, and 25kDa demonstrated no considerable variation.\u0000\u0000\u0000\u0000The serum proteins showing significant difference as compared to the control group\u0000will serve as predictive biomarkers for at-risk pregnancies. The present study is expected to considerably improve the understanding of the disease pathogenesis along with improved diagnostic and\u0000therapeutic approaches leading to better management of pregnancy and reducing the risk of\u0000preterm birth.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"40 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85075925","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}

引用次数: 0

Proteome Profiling of Serum Exosomes from Newborns Delivered by Mothers with Preeclampsia 子痫前期母亲所生新生儿血清外泌体的蛋白质组分析

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-04-06 DOI: 10.2174/1570164619666220406121420

Haiying Li, Xiaoqun Zhang, Xianhui Hong, Shuxuan Zhang, Haijun Tang, Jinlong Shi, Hui Peng, Youjia Wu

{"title":"Proteome Profiling of Serum Exosomes from Newborns Delivered by Mothers with Preeclampsia","authors":"Haiying Li, Xiaoqun Zhang, Xianhui Hong, Shuxuan Zhang, Haijun Tang, Jinlong Shi, Hui Peng, Youjia Wu","doi":"10.2174/1570164619666220406121420","DOIUrl":"https://doi.org/10.2174/1570164619666220406121420","url":null,"abstract":"\u0000\u0000Preeclampsia (PE) is a common pregnancy-specific disease with potential adverse maternal and neonatal outcomes.\u0000\u0000\u0000\u0000We aimed to estimate proteomic profiles of serum-derived exosomes obtained from PE offspring with bioinformatics methods.\u0000\u0000\u0000\u0000Serum samples were collected from 12 h, 24 h, and 72 h newborns delivered by preeclamptic and normal pregnant women. Exosomes were extracted, and the concentration and size distribution were determined. The exosome surface markers CD9, CD63, CD81, and TSG101, were assayed by Western blot. The exosome proteins were screened by quantitative proteomics with tandem mass tag (TMT). All the identified proteins were subjected to the Weighted Gene Co-Expression Network Analysis (WGCNA), GO function, and KEGG pathway analysis. A protein-protein interaction network (PPI) was used to extract hub proteins through the Cytohubba plugin of Cytoscape\u0000\u0000\u0000\u0000The extracted exosomes were round or oval vesicular structures at a 100-200 nm concentration, and the size distribution was standard and uniform. Exosome surface markers CD9, CD63, and CD81 were detected, and TSG101 was not detected. A total of 450 expressed proteins were selected, and 444 proteins were mapped with gene names. A blue module with 66 proteins highly correlated with phenotype at 12 h. Functional analyses revealed that module proteins were mainly enriched in extracellular matrix. The top 10 selected hub proteins were identified as hub proteins, including COL6A2, HSPG2, COL4A1, COL3A1, etc.\u0000\u0000\u0000\u0000Our study provides important information for exploring molecular mechanisms of preeclampsia and potential biomarkers for future diagnosis and treatment in the clinic.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"59 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77553717","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}

引用次数: 0

Proteomic analysis of tumor-specific biomarkers in colon cancer 结肠癌肿瘤特异性生物标志物的蛋白质组学分析

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-04-06 DOI: 10.2174/1570164619666220406115339

Yu-An Chien, H. Chou, Chu-Chun Yang, Yi- Shiuan Wang, yu-shan Wei, H. Chan

{"title":"Proteomic analysis of tumor-specific biomarkers in colon cancer","authors":"Yu-An Chien, H. Chou, Chu-Chun Yang, Yi- Shiuan Wang, yu-shan Wei, H. Chan","doi":"10.2174/1570164619666220406115339","DOIUrl":"https://doi.org/10.2174/1570164619666220406115339","url":null,"abstract":"\u0000\u0000With the development of medicine and technological advancement, the concept of precision medicine is rising, and the traditional principle of all-in-one therapy is gradually broken. Utilizing the detection of genome, transcriptome, proteome, and metabolome, combined with big data analysis to discover new pathogenic mechanisms, provide more effective prescriptions with fewer side effects, and even shift the emphasis of medicine from disease treatment to disease prevention.\u0000\u0000\u0000\u0000Proteomics is one of the potential tools for monitoring the alternations of protein expression. This study analyzed the proteomic alternations between normal colon tissue and cancerous colon tissue via two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to select the potential target proteins.\u0000\u0000\u0000\u0000The experimental results demonstrated that a total of 90 proteins were identified with significantly expressed. These proteins were classified according to their functions. These proteins are mainly associated with cytoskeleton regulation, glycolysis, and protein folding. Furthermore, immunoblotting was used to verify the differentially expressed proteins, and the results showed positive agreement with the trends in the proteomic analysis.\u0000\u0000\u0000\u0000To sum up, these differentially expressed proteins could be used as potential and precise biomarkers in the diagnosis or treatment of colorectal cancer.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"32 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2022-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75236936","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}

引用次数: 0

Meet the Editorial Board Member 与编辑委员会成员见面

IF 0.8 4区生物学

Current Proteomics Pub Date : 2022-04-01 DOI: 10.2174/157016461902220221140544

N. B. Maheswarappa

引用次数: 0