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Gly-LysPred: Identification of Lysine Glycation Sites in Protein Using Position Relative Features and Statistical Moments via Chou’s 5 Step Rule

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Computers, Materials & Continua 2021年第2期66卷 2165-2181页

作者： Shaheena Khanum Muhammad Adeel Ashraf Asim Karim Bilal Shoaib Muhammad Adnan Khan Rizwan Ali Naqvi Kamran Siddique Mohammed Alswaitti Department of Computer Science Lahore University of Management SciencesLahore54792Pakistan Department of Computer Science University of Management and TechnologyLahore54770Pakistan School of Computer Science Minhaj University LahoreLahore54770Pakistan Department of Computer Science Lahore Garrison UniversityLahore54000Pakistan Department of Unmanned Vehicle Engineering Sejong UniversitySeoulKorea Department of Information and Communication Technology School of Electrical and Computer EngineeringXiamen University MalaysiaSepang43900Malaysia

Glycation is a non-enzymatic post-translational modification which assigns sugar molecule and residues to a *** is a clinically important attribute to numerous age-related,metabolic,and chronic diseases such as diabetes,Alzheimer’s,renal failure,*** of a non-enzymatic reaction are quite challenging in *** identification in labs is a very costly and timeconsuming *** this research,we developed an accurate,valid,and a robust model named as Gly-LysPred to differentiate the glycated sites from non-glycated *** techniques using position relative features are used for feature *** algorithm named as a random forest with some preprocessing techniques and feature engineering techniques was developed to train a computational *** types of testing techniques such as self-consistency testing,jackknife testing,and cross-validation testing are used to evaluate the *** overall model’s accuracy was accomplished through self-consistency,jackknife,and cross-validation testing 100%,99.92%,and 99.88%with MCC 1.00,0.99,and 0.997 *** this regard,a user-friendly webserver is also urbanized to accumulate the whole *** features vectorization methods suggest that they can play a critical role in other web servers which are developed to classify lysine glycation.

关键词： Gly-LysPred PseAAC post-translational modification lysine glycation Chou’s 5 step rule position relative features

Comprehensive profiling of lysine acetylome in Staphylococcus aureus

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Science China Chemistry 2014年第5期57卷 732-738页

作者： ZHANG Yi WU ZhiXiang WAN XueLian LIU Ping ZHANG JiBao YE Yang ZHAO YingMing TAN MinJia Chemical Proteomics Center & State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of Sciences Natural Products Chemistry Department & State Key Laboratory of Drug Research Shanghai Instituteof Materia Medica Chinese Academy of Sciences Ben May Department for Cancer Research University of Chicago

The Gram-positive bacterium Staphylococcus aureus(***)is a wide spread common opportunistic pathogen that causes a wide variety of infectious diseases,from benign skin infections to life-threatening diseases such as the methicillin-resistant Staphylococcus aureus(MRSA)*** emerging evidence suggests that lysine acetylation may play critical roles in bacterial physiology,the atlas of acetylome in *** has not been *** comprehensively profile protein lysine acetylation in ***,we used an integrated approach that combined immune affinity peptide enrichment using anti-lysine acetylation antibody,high-pH HPLC fractionation,and HPLC/mass spectrometry *** study led to the identification of 1361 non-redundant acetylation sites on 412 proteins found in a search of *** protein database extracted from the Swiss-Prot *** further performed bioinformatic analysis to characterize this modification,including gene ontology annotation,protein-protein interaction,and domain analysis of the acetylation *** found that the acetylated proteins were enriched in multiple biological pathways,such as ribosomal function and energy *** data provides a rich source for functional studies of lysine acetylation in ***.

关键词： proteomics post-translational modification acetylation Staphylococcus aureus

Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis *** 6803

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Genomics, Proteomics & Bioinformatics 2020年第3期18卷 289-304页

作者： Xiaohuang Lin Mingkun Yang Xin Liu Zhongyi Cheng Feng Ge State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China Key Laboratory of Algal Biology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China University of Chinese Academy of Sciences Beijing 100039China Jingjie PTM BioLab(Hangzhou)Co.Ltd Hangzhou 310018China

Protein lysine methylation is a prevalent post-translational modification(PTM)and plays critical roles in all domains of ***,its extent and function in photosynthetic organisms are still largely *** are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental *** we integrated propionylation of monomethylated proteins,enrichment of the modified peptides,and mass spectrometry(MS)analysis to identify monomethylated proteins in Synechocystis *** 6803(Synechocystis).Overall,we identified 376 monomethylation sites in270 proteins,with numerous monomethylated proteins participating in photosynthesis and carbon *** subsequently demonstrated that Cpc M,a previously identified asparagine methyltransferase in Synechocystis,could catalyze lysine monomethylation of the potential aspartate aminotransferase Sll0480 both in vivo and in vitro and regulate the enzyme activity of *** loss of Cpc M led to decreases in the maximum quantum yield in primary photosystemⅡ(PSⅡ)and the efficiency of energy transfer during the photosynthetic reaction in *** report the first lysine monomethylome in a photosynthetic organism and present a critical database for functional analyses of monomethylation in *** large number of monomethylated proteins and the identification of Cpc M as the lysine methyltransferase in cyanobacteria suggest that reversible methylation may influence the metabolic process and photosynthesis in both cyanobacteria and plants.

关键词： Cyanobacteria Lysine monomethylation Lysine methyltransferase post-translational modification Aspartate aminotransferase

Structure and function of WD40 domain proteins

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Protein & Cell 2011年第3期2卷 202-214页

作者： Chao Xu Jinrong Min Structural Genomics Consortium University of Toronto101 College St.TorontoOntarioM5G 1L7Canada Department of Physiology University of TorontoTorontoOntario M5S 1A8Canada

The WD40 domain exhibits aβ-propeller architecture,often comprising seven *** WD40 domain is one of the most abundant domains and also among the top interacting domains in eukaryotic *** this review,we will discuss the identification,definition and architecture of the WD40 ***40 domain proteins are involved in a large variety of cellular processes,in which WD40 domains function as a protein-protein or protein-DNA interaction ***40 domain mediates molecular recognition events mainly through the smaller top surface,but also through the bottom surface and *** far,no WD40 domain has been found to display enzymatic *** will also discuss the different binding modes exhibited by the large versatile family of WD40 domain *** the last part of this review,we will discuss how post-translational modifications are recognized by WD40 domain proteins.

关键词： WD40 beta-propeller protein-protein interaction scaffold post-translational modification

PRMT6 promotes tumorigenicity and cisplatin response of lung cancer through triggering 6PGD/ENO1 mediated cell metabolism

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Acta Pharmaceutica Sinica B 2023年第1期13卷 157-173页

作者： Mingming Sun Leilei Li Yujia Niu Yingzhi Wang Qi Yan Fei Xie Yaya Qiao Jiaqi Song Huanran Sun Zhen Li Sizhen Lai Hongkai Chang Han Zhang Jiyan Wang Chenxin Yang Huifang Zhao Junzhen Tan Yanping Li Shuangping Liu Bin Lu Min Liu Guangyao Kong Yujun Zhao Chunze Zhang Shu-Hai Lin Cheng Luo Shuai Zhang Changliang Shan State Key Laboratory of Medicinal Chemical Biology College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjin 300350China Biomedical translational Research Institute Jinan UniversityGuangzhou 510632China State Key Laboratory of Cellular Stress Biology Innovation Center for Cell Signaling NetworkSchool of Life SciencesXiamen UniversityXiamen 361102China School of Integrative Medicine Tianjin University of Traditional Chinese MedicineTianjin 301617China Department of Pathology and Institute of Precision Medicine Jining Medical UniversityJining 272067China Department of Pathology Medical SchoolDalian UniversityDalian 116622China Department of Biochemistry and Molecular Biology School of Basic Medical SciencesHengyang Medical SchoolUniversity of South ChinaHengyang 421001China School of Laboratory Medicine and Life Sciences Wenzhou Medical UniversityWenzhou 325035China Institute of Biomedical Sciences Shandong Provincial Key Laboratory of Animal Resistance BiologyCollaborative Innovation Center of Cell Biology in Universities of ShandongCollege of Life SciencesShandong Normal UniversityJinan 250014China National Local Joint Engineering Research Center of Biodiagnostics and Biotherapy the Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'an 710004China State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China Department of Colorectal Surgery Tianjin Union Medical Center Nankai UniversityTianjin 300121China

Metabolic reprogramming is a hallmark of cancer,including lung ***,the exact underlying mechanism and therapeutic potential are largely *** we report that protein arginine methyltransferase 6(PRMT6)is highly expressed in lung cancer and is required for cell metabolism,tumorigenicity,and cisplatin response of lung ***6 regulated the oxidative pentose phosphate pathway(PPP)flux and glycolysis pathway in human lung cancer by increasing the activity of 6-phosphogluconate dehydrogenase(6PGD)and a-enolase(ENO1).Furthermore,PRMT6 methylated R324 of 6PGD to enhancing its activity;while methylation at R9 and R372 of ENO1 promotes formation of active ENO1 dimers and 2-phosphoglycerate(2-PG)binding to ENO1,***,targeting PRMT6 blocked the oxidative PPP flux,glycolysis pathway,and tumor growth,as well as enhanced the antitumor effects of cisplatin in lung ***,this study demonstrates that PRMT6 acts as a posttranslational modification(PTM)regulator of glucose metabolism,which leads to the pathogenesis of lung *** was proven that the PRMT6-6PGD/ENO1 regulatory axis is an important determinant of carcinogenesis and may become a promising cancer therapeutic strategy.

关键词： Lung cancer Metabolic reprogramming post-translational modification PRMT6 Pentose phosphate pathway flux Glycolysis 6-Phospho-gluconate dehydrogenase a-enolase ENO1

The pathogenic mechanism of TAR DNA-binding protein 43(TDP-43)in amyotrophic lateral sclerosis

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Neural Regeneration Research 2024年第4期19卷 800-806页

作者： Xinxin Wang Yushu Hu Renshi Xu Medical College of Nanchang University Department of Neurology Jiangxi Provincial People's HospitalThe First Affiliated Hospital of Nanchang Medical CollegeThe Clinical College of Nanchang Medical College

The onset of amyotrophic lateral sclerosis is usually characterized by focal death of both upper and/or lower motor neurons occurring in the motor cortex,basal ganglia,brainstem,and spinal cord,and commonly involves the muscles of the upper and/or lower extremities,and the muscles of the bulbar and/or respiratory ***,as the disease progresses,it affects the adjacent body regions,leading to generalized muscle weakness,occasionally along with memory,cognitive,behavioral,and language impairments;respiratory dysfunction occurs at the final stage of the *** disease has a complicated pathophysiology and currently,only riluzole,edaravone,and phenylbutyrate/taurursodiol are licensed to treat amyotrophic lateral sclerosis in many industrialized *** TAR DNA-binding protein 43 inclusions are observed in 97%of those diagnosed with amyotrophic lateral *** review provides a preliminary overview of the potential effects of TAR DNAbinding protein 43 in the pathogenesis of amyotrophic lateral sclerosis,including the abnormalities in nucleoplasmic transport,RNA function,post-translational modification,liquid-liquid phase separation,stress granules,mitochondrial dysfunction,oxidative stress,axonal transport,protein quality control system,and non-cellular autonomous functions(e.g.,glial cell functions and prion-like propagation).

关键词： amyotrophic lateral sclerosis axonal transport liquid-liquid phase separation noncellular autonomous functions oxidative stress pathogenesis post-translational modification protein quality control system stress granules TAR DNA-binding protein 43(TDP-43)

Nphos:Database and Predictor of Protein N-phosphorylation

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Genomics, Proteomics & Bioinformatics 2024年第3期22卷 139-151页

作者： Ming-Xiao Zhao Ruo-Fan Ding Qiang Chen Junhua Meng Fulai Li Songsen Fu Biling Huang Yan Liu Zhi-Liang Ji Yufen Zhao Institute of Drug Discovery Technology Ningbo UniversityNingbo 315211China Department of Chemical Biology Key Laboratory for Chemical Biology of Fujian ProvinceCollege of Chemistry and Chemical EngineeringXiamen UniversityXiamen 361005China State Key Laboratory of Cellular Stress Biology School of Life SciencesFaculty of Medicine and Life SciencesXiamen UniversityXiamen 361102China Zhejiang Key Laboratory of Pathophysiology Department of Biochemistry and Molecular BiologyHealth Science CenterNingbo UniversityNingbo 315211China BGI Genomics BGI-ShenzhenShenzhen 518083China Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical Biology Department of ChemistryTsinghua UniversityBeijing 100084China

Protein N-phosphorylation is widely present in nature and participates in various biological ***,current knowledge on N-phosphorylation is extremely limited compared to that on *** this study,we collected 11,710 experimentally verified N-phosphosites of 7344 proteins from 39 species and subsequently constructed the database Nphos to share up-to-date information on protein *** these substantial data,we characterized the sequential and structural features of protein ***,after comparing hundreds of learning models,we chose and optimized gradient boosting decision tree(GBDT)models to predict three types of human N-phosphorylation,achieving mean area under the receiver operating characteristic curve(AUC)values of 90.56%,91.24%,and 92.01%for pHis,pLys,and pArg,***,we discovered 488,825 distinct N-phosphosites in the human *** models were also deployed in Nphos for interactive N-phosphosite *** summary,this work provides new insights and points for both flexible and focused investigations of *** will also facilitate a deeper and more systematic understanding of protein N-phosphorylation modification by providing a data and technical *** is freely available at http://***/Nphos/and http://***/Nphos/.

关键词： N-phosphorylation post-translational modification Machine learning Database Benchmark dataset

Novel post-translational modifications and Host Subversion by Bacterial Pathogens

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Novel Post-translational Modifications and Host Subversion b...

Evidence for a mouse brain-specific variant of α-tubulin

中国生物化学与分子生物学会第十二届全国会员代表大会暨2018年全国学术会议

作者： Yongqun Zhu Life Sciences Institute Zhejiang University

Gram-negative bacterial pathogens deliver virulent effector proteins into host cells through specialized protein secretion systems,such as type III and IV secretion *** injected effectors often harbor novel enzymatic activities and catalyze unique post-translational modifications on host key signaling molecules to activate or inactivate the host signaling pathways for bacterial infection and *** subversion of the host cellular processes by bacterial effector proteins plays the central role in bacterial ***,we utilized multiple-disciplinary approaches of microbiology,biochemistry and cell biology,and identified the biochemical activities and host targets of several important effector *** effectors employed novel mechanisms to modulate the host *** this talk,we will present the novel post-translational modifications and mechanisms by two of these effectors.

关键词： Bacterial effector Host target post-translational modification

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Cell Research 1999年第4期9卷 315-325页

作者： KONG LING WEI XIAO YAN DING HIROSHIKITANI ROBERT SHIURBA NAI HE JING( Shanghai Institute of Biochemistry, Chinese Academyof Sciences, 320 Yue Yang Road, Shanghai 200031,China)( Shanghai Institute of Cell Biology, Chinese Academyof Sciences, 320 Yue Ya Misato Plaheat Mfg. Ltd. 521-18 Kamiuwada Satte-shi Saitama 340-0124 Japan

INTRODUCTIONTOinvestigatenestinintermediatefilamentproteinll]expressionduringmousebraindevelopment,weraisedanantibodytoasynthetic20-*******:86-21-... 详细信息

INTRODUCTIONTOinvestigatenestinintermediatefilamentproteinll]expressionduringmousebraindevelopment,weraisedanantibodytoasynthetic20-*******:86-21-...

关键词： Brain-specific a-tubulin post-translational modification Nestin.