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PLMD：An updated data resource of protein lysine modifications

Journal of Genetics and Genomics 2017年第5期44卷 243-250页

作者： Haodong Xu Jiaqi Zhou Shaofeng Lin wankun deng Ying Zhang Yu Xue Key Laboratory of Molecular Biophysics of Ministry of Education College of Life Science and Technology and the Collaborative Innovation Center for Brain ScienceHuazhong University of Science and Technology Wuhan 430074 China

Post-translational modifications（PTMs） occurring at protein lysine residues,or protein lysine modifications（PLMs）,play critical roles in regulating biological *** to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types,here we greatly updated our previous studies,and presented a much more integrative resource of protein lysine modification database（PLMD）.In PLMD,we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs,including ubiquitination, acetylation, sumoylation, methylation ,succinylation,malonylation,glutarylation,giycation,formylation,hydroxylation,butyrylation,propionylation,crotonylation,pupylation,neddylation,2-hydroxyisobutyrylation,phosphoglycerylation,carboxylation,lipoylation and *** the data set,a motif-based analysis was performed for each PLM type,and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the ***,various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other,and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine ***,various options were provided for accessing the data,while original references and other annotations were also present for each PLM *** together,we anticipated the PLMD database can serve as a useful resource for further researches of *** 3.0 was implemented in PHP ＋ MySQL and freely available at http：//***.

关键词： Post-translational modification(PTM) Protein lysine modification(PLM) Ubiquitination Acetylation PTM crosstalk

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PTMD: A Database of Human Disease-associated Post-translational Modifications

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 244-251页

作者： Haodong Xu Yongbo Wang Shaofeng Lin wankun deng Di Peng Qinghua Cui Yu Xue Department of Bioinformatics & Systems Biology MOE Key Laboratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering Huazhong University of Science and Technology Department of Biomedical Informatics School of Basic Medical Sciences MOE Key Laboratory of Molecular Cardiovascular Sciences Center for Non-coding RNA Medicine Peking University

Various posttranslational modifications （PTMs） participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM–disease associations （PDAs）would be a great help for both academic research and clinical use. In this work, we reported PTMD,a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of diseaseassociated PTM events. By reconstructing a disease–gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http：//***.

关键词： Posttranslational modification Phosphorylation PTM-disease association Disease-gene network AKT1

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WocEA:The visualization of functional enrichment results in word clouds

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Journal of Genetics and Genomics 2018年第7期45卷 415-417页

作者： Wanshan Ning Shaofeng Lin Jiaqi Zhou Yaping Guo Ying Zhang Di Peng wankun deng Yu Xue Key Laboratory of Molecular Biophysics of Ministry of Education College of Life Science and Technology and the Collaborative Innovation Center for Biomedical EngineeringHuazhong University of Science and Technology

The integration, analysis and visualization of the big omics data are critical for addressing a broad spectrum of biological questions. One of the most frequently conducted procedures is enrichment analysis, which statistically tests whether individual functional an- notations of Gent Ontology （GO） or Kyoto Encyclopedia of Genes and Genomes （KEGG） are significantly over-or under-represented in an ＂interesting＂ gene or protein list against the reference set （Tavazoie et al., 1999）.

关键词： WocEA he visualization of functional enrichment results word clouds

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A Decade Effort of PTM Bioinformatics for Epigenetic Modifications

A Decade Effort of PTM Bioinformatics for Epigenetic Modific...

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中国生物工程学会第二届青年科技论坛暨首届青年工作委员会...

作者：薛宇 Shuang Zhang wankun deng Yu Xue 华中科技大学生命科学与技术学院 Department of Bioinformatics & Systems Biology College of Life Science and Technology Huazhong University of Science and Technology

As an important epigenetic mechanism,post-translational modifications(PTMs)of histones or histone modifications combinatorially and dynamically constitute?histone code‘,which accurately regulates a variety of DNA-templated *** as gene transcription,chromosome segregation and *** and methylation are two predominant types of histone *** acetylation neutralizes the positive charges of lysine residues,

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A decade effort of PTM Bioinformatics for epigenetic modifications

A decade effort of PTM Bioinformatics for epigenetic modific...

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中国生物工程学会第二届青年科技论坛暨首届青年工作委员会...

作者： Yang Xu Shuang Zhang wankun deng Yu Xue Department of Bioinformatics & Systems Biology College of Life Science and Technology Huazhong University of Science and Technology

As an important epigenetic mechanism, post-translational modifications(PTMs) of histones or histone modifications combinatorially and dynamically constitute ‘histone code’, which accurately regulates a variety of DNA-templated processes. such as gene transcription, chromosome segregation and DNArepair. Acetylation and methylation are two predominant types of histone modifications. Histone acetylation neutralizes the positive charges of lysine residues, disrupts the association between histones and DNA, and is a hallmark of open chromatin that can be more accessible to DNA and RNA polymerases as well as transcription factors, resulting in the activation of gene transcription. Histone methylation mainly occurs on arginine and lysine residues, enhances the basicity and hydrophobicity of histone tails, influences the interaction affinity between DNA and transcription factors, and can either activate or repress gene expression. Besides histones, acetylation and methylation also widely occur in non-histone proteins, and play central roles in the regulation of biological processes. In 2006, we developed two tools, Me Mo and PAIL, for the prediction of methylation and acetylation sites from protein sequences. Later, we developed an integrative database of CPLA for lysine acetylated substrates with their sites, containing 7151 experimentally identified acetylation sites in 3311 targets manually collected the literature. CPLM was then updated into CPLM, which contained 203,972 modification events of 12 types of protein lysine modifications including lysine acetylation and methylation, on 189,919 modified lysines in 45,748 proteins for 122 species. Using this data set, we improved our tools, and developed GPS-MSP and GPS-PAIL for a better prediction of methylation and acetylation sites in proteins. More recently, we developed a database WERAM for histone acetyltransferases, histone deacetylases, histone methyltransferases, histone demethylases and acetyl-or methyl-binding prot

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Systematic analysis of plant phosphoproteomes reveals that site-specific kinase-substrate networks are highly involved in stress response and disease resistance

Systematic analysis of plant phosphoproteomes reveals that s...

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中国生物工程学会2014年学术年会暨全国生物技术大会

作者：程涵 wankun deng Yongbo Wang Zexian Liu Zhicheng Pan Yu Xue 华中科技大学 College of Life Science and Technology Huazhong University of Science and Technology

Protein phosphorylation is one of the most important and essential post-translational modifications(PTMs). It plays a crucial role in regulating the decision processes and dynamic behaviors in cells such as metabolism and signal transduction. Although nearly 6 phosphorylation prediction programs for plants were developed, they all lack the exact kinase information for the given phosphorylation sites(p-sites). So currently, our understanding of site-specific kinase-substrate networks(ssKSNs) remains still very limited. In this work, first, 1,052 Arabidopsis thaliana and 1,511 Oryza sativa protein kinases(PKs) which have been classified into three levels in hierarchy containing group, family and single PK based on previously established theories were downloaded from our newly developed database of EKPD. Then the GPS 2.1 algorithm coupled with the GPS predictors for these two plants PKs if available in GPS 2.1 were employed to predict the potential PKs for experimentally identified p-sites, while the corresponding ssKSRs were determined. Further, the prediction results were filtered with the public available protein-protein interaction(PPI) data to reduce the false-positive hits. Also, the prediction performance of this methodology was examined through the testing dataset of 76 experimentally kinase-specific p-sites in Arabidopsis thaliana by literature reading. The Sn and Sp were 39.47% and 97.99% which demonstrated that the methodology of iGPS algorithm(GPS algorithm with the interaction filter, or in vivo GPS) is feasible and reliable to predict the ssKSRs in vivo for plants. With this strategy, we predicted 13,452 ssKSRs among 583 PKs and 1,047 substrates for 2,606 p-sites with an average of 5.2 upstream PKs per p-site in Arabidopsis thaliana and 4,582 ssKSRs between 548 PKs and 638 substrates for 1,174 p-sites with an average of 3.9 upstream PKs per p-site in Oryza sativa. Furthermore, the ssKSNs of these two plants were constructed and visualized based on the pre

关键词： Phosphorylation Kinase site-specific kinase-substrate networks Stress response Disease resistance

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两种实习教学方式对医学生临床能力提升的对比分析

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中国高等医学教育 2019年第4期 84-85页

作者：蔡东峰邓婉坤洪嵩熊伟刘毅彭笳宸遵义医科大学附属医院

目的:比较全程参与式与传统教学方式的优劣。方法:招募2017年1月至10月在我院骨科实习的医生。随机分为全程参与式教学组与传统教学组,比较两组实习医生各项考核指标。结果:全程参与式教学组与传统教学组比较,出科考核成绩、沟通能力、... 详细信息

目的:比较全程参与式与传统教学方式的优劣。方法:招募2017年1月至10月在我院骨科实习的医生。随机分为全程参与式教学组与传统教学组,比较两组实习医生各项考核指标。结果:全程参与式教学组与传统教学组比较,出科考核成绩、沟通能力、成绩提升、沟通能力提升差异具有统计学意义(P<0.05)。结论:全程参与式教学组在基本理论知识掌握、沟通能力及纪律性等方面优于对照组。

关键词：临床实习全程参与式教学传统教学

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杜仲橡胶-丁苯橡胶复合体系的共硫化及其动静态力学性能

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复合材料学报 2022年第12期39卷 5892-5900页

作者：邓琳僡殷德贤向万坤孙泉丁晓冬赵秀英北京化工大学北京市新型高分子材料制备与加工重点实验室北京100029 中国船舶工业系统工程研究院北京100094

将杜仲橡胶(EUG)与丁苯橡胶(SBR)共混,制备了EUG-SBR橡胶复合材料。通过剥离实验和拉伸实验表征其共硫化的情况;通过拉伸实验,SEM、DMA和XRD研究了EUG含量对复合材料动静态性能的影响。结果表明,硫化体系:促进剂N,N-二环己基-2-苯并噻... 详细信息

将杜仲橡胶(EUG)与丁苯橡胶(SBR)共混,制备了EUG-SBR橡胶复合材料。通过剥离实验和拉伸实验表征其共硫化的情况;通过拉伸实验,SEM、DMA和XRD研究了EUG含量对复合材料动静态性能的影响。结果表明,硫化体系:促进剂N,N-二环己基-2-苯并噻唑磺酰胺(DZ)的质量比为1.0%(以EUG-SBR的质量为基准,下同)、促进剂二硫化四甲基秋兰姆(TMTD)0.1%、硫磺1.5%可以使两种橡胶达到更好的共硫化,剥离强度达到4.2 kN/m,EUG-SBR(EUG∶SBR质量比为70∶30)复合材料的拉伸强度达到6.3 MPa。复合材料中的EUG晶区主要以β晶型存在,随着EUG含量增多,复合材料的结晶度和熔融温度明显提高。EUG相的引入会使复合材料的损耗因子峰值tanδ_(max)下降,同时大幅提高复合材料的储能模量,在10℃时EUG-SBR复合材料的储能模量会从质量比5%EUG时的3.0×10^(6) Pa提高到35%EUG时的1.7×10^(7) Pa。同时晶区的存在起到物理交联点的作用,提升复合材料的拉伸强度和定伸应力。

关键词：杜仲橡胶丁苯橡胶共硫化阻尼模量晶体渝渗

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天然杜仲胶乳的制备及表征

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北京化工大学学报（自然科学版） 2022年第4期49卷 56-64页

作者：孙泉苏琳刘桂杰邓琳僡向万坤赵秀英北京化工大学北京市新型高分子材料制备与加工重点实验室北京100029 中国船舶工业系统工程研究院北京100094

采用溶液乳化法制备了杜仲胶乳,考察了乳化配方及乳化工艺对乳化效果的影响,确定了如下制备条件:以杜仲胶的环己烷溶液(杜仲胶的质量分数为6%)为油相胶液,采用1%Brij-52、0.5%Tween-20、0.5%十二烷基苯磺酸钠的三相复配乳化剂体系,油水... 详细信息

采用溶液乳化法制备了杜仲胶乳,考察了乳化配方及乳化工艺对乳化效果的影响,确定了如下制备条件:以杜仲胶的环己烷溶液(杜仲胶的质量分数为6%)为油相胶液,采用1%Brij-52、0.5%Tween-20、0.5%十二烷基苯磺酸钠的三相复配乳化剂体系,油水体积比为1∶1.5,乳化方式为高速搅拌(8000 r/min,10 min),除溶剂方式为旋转蒸发(-0.09 MPa,40℃),浓缩方式为离心浓缩(10000 r/min,10 min)。在优化条件下制备的杜仲胶乳的固含量可达54%,粒径约为330 nm,Zeta电位的绝对值可达57 mV。采用X射线衍射法(XRD)、差示扫描量热法(DSC)、傅里叶变换红外光谱法(FT-IR)、扫描电子显微镜(SEM)和偏光显微镜(POM)对制备的杜仲胶乳进行了表征,结果表明:乳化没有破坏杜仲胶的结晶性能,杜仲胶乳中仍存在大量的微结晶,杜仲胶乳的晶型中以β晶型为主。

关键词：杜仲胶溶液乳化法乳化剂乳化工艺结晶

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天然橡胶/杜仲胶并用胶的性能研究

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橡胶工业 2022年第12期69卷 899-909页

作者：向万坤孙崇志孙泉邓琳僡陈智刘力赵秀英北京化工大学北京市新型高分子材料制备与加工重点实验室北京100029

将天然橡胶(NR)与杜仲胶(EUG)并用,研究NR/EUG并用比对NR/EUG并用胶(未加补强剂)和白炭黑补强NR/EUG并用胶性能的影响。结果表明:随着EUG用量的增大,NR/EUG并用胶的EUG岛相结构的占比和尺寸增大,表面的“山脊状”纹路越明显;NR/EUG并用... 详细信息

将天然橡胶(NR)与杜仲胶(EUG)并用,研究NR/EUG并用比对NR/EUG并用胶(未加补强剂)和白炭黑补强NR/EUG并用胶性能的影响。结果表明:随着EUG用量的增大,NR/EUG并用胶的EUG岛相结构的占比和尺寸增大,表面的“山脊状”纹路越明显;NR/EUG并用比为80/20的NR/EUG并用胶的拉伸强度最大,为28.8 MPa,裂纹扩展速率最小,为23.5 nm·c^(-1);NR/EUG并用比为70/30的NR/EUG并用胶的拉伸疲劳次数最大,为200万。随着EUG用量的增大,白炭黑补强NR/EUG并用胶的邵尔A型硬度、撕裂强度和储能模量增大,拉断永久变形减小;NR/EUG并用比为85/15的白炭黑补强NR/EUG并用胶的切割量较小,压缩温升最低,阿克隆磨耗量最小。

关键词：天然橡胶杜仲胶并用胶白炭黑补强拉伸性能裂纹扩展速率抗切割性能压缩生热

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