翻译后修饰是蛋白质组学研究的前沿和重点,它不仅调节着蛋白质的折叠、状态、活性、定位以及蛋白质间的相互作用,也能帮助科学家更全面地了解生物体的生命过程,为疾病的预测、诊断和治疗提供更加强大的支撑和依据。翻译后修饰产物(例如...翻译后修饰是蛋白质组学研究的前沿和重点,它不仅调节着蛋白质的折叠、状态、活性、定位以及蛋白质间的相互作用,也能帮助科学家更全面地了解生物体的生命过程,为疾病的预测、诊断和治疗提供更加强大的支撑和依据。翻译后修饰产物(例如磷酸化肽和糖肽)丰度很低,且存在着强烈的背景干扰,很难直接用质谱进行分析,因此迫切需要开发高效的富集材料和技术来选择性富集翻译后修饰产物。近年来,智能聚合物基材料通过外部物理、化学或生物刺激可逆地改变其结构和功能,实现对磷酸化肽和糖肽高度可控的吸附和脱附,进而衍生开发出一系列新颖的富集方法,极大地吸引研究者们的兴趣。一方面,智能聚合物基材料的响应变化包括材料疏水性的增加或减少、形状和形貌的改变、表面电荷的重新分布以及亲和配体的暴露或隐藏等特性。这些特性使得目标物和智能聚合物基材料之间的亲和力可以通过简单改变外部条件(如温度、pH值、溶剂极性和生物分子等)实现更可控和更智能的精细调节。另一方面,智能聚合物基材料为集成功能模块提供了便捷的可扩展平台,例如特定的识别组件,显著提高了目标物质的分离选择性。智能聚合物基材料在分离方面展现出巨大的潜力,这为蛋白质翻译后修饰产物的分析和研究带来了希望。围绕上述主题,该文依据Web of Science近20年来近50篇代表性文献,概述了智能聚合物基材料在磷酸化肽和糖肽分离及富集中的发展方向。展开更多
Post-translational modifications（PTMs） occurring at protein lysine residues,or protein lysine modifications（PLMs）,play critical roles in regulating biological processes.Due to the explosive expansion of the amount...Post-translational modifications（PTMs） occurring at protein lysine residues,or protein lysine modifications（PLMs）,play critical roles in regulating biological processes.Due 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 biotinylation.Using 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 modifications.Moreover,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 residues.Finally,various options were provided for accessing the data,while original references and other annotations were also present for each PLM substrate.Taken together,we anticipated the PLMD database can serve as a useful resource for further researches of PLMs.PLMD 3.0 was implemented in PHP ＋ MySQL and freely available at http：//plmd.biocuckoo.org.展开更多
文摘翻译后修饰是蛋白质组学研究的前沿和重点,它不仅调节着蛋白质的折叠、状态、活性、定位以及蛋白质间的相互作用,也能帮助科学家更全面地了解生物体的生命过程,为疾病的预测、诊断和治疗提供更加强大的支撑和依据。翻译后修饰产物(例如磷酸化肽和糖肽)丰度很低,且存在着强烈的背景干扰,很难直接用质谱进行分析,因此迫切需要开发高效的富集材料和技术来选择性富集翻译后修饰产物。近年来,智能聚合物基材料通过外部物理、化学或生物刺激可逆地改变其结构和功能,实现对磷酸化肽和糖肽高度可控的吸附和脱附,进而衍生开发出一系列新颖的富集方法,极大地吸引研究者们的兴趣。一方面,智能聚合物基材料的响应变化包括材料疏水性的增加或减少、形状和形貌的改变、表面电荷的重新分布以及亲和配体的暴露或隐藏等特性。这些特性使得目标物和智能聚合物基材料之间的亲和力可以通过简单改变外部条件(如温度、pH值、溶剂极性和生物分子等)实现更可控和更智能的精细调节。另一方面,智能聚合物基材料为集成功能模块提供了便捷的可扩展平台,例如特定的识别组件,显著提高了目标物质的分离选择性。智能聚合物基材料在分离方面展现出巨大的潜力,这为蛋白质翻译后修饰产物的分析和研究带来了希望。围绕上述主题,该文依据Web of Science近20年来近50篇代表性文献,概述了智能聚合物基材料在磷酸化肽和糖肽分离及富集中的发展方向。
基金supported by grants from the National Basic Research Program(973 projectNo.2013CB933900)+1 种基金the Natural Science Foundation of China(Nos.31671360 andJ1103514)the International Science & Technology Cooperation Program of China (No.2014DFB30020)
文摘Post-translational modifications（PTMs） occurring at protein lysine residues,or protein lysine modifications（PLMs）,play critical roles in regulating biological processes.Due 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 biotinylation.Using 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 modifications.Moreover,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 residues.Finally,various options were provided for accessing the data,while original references and other annotations were also present for each PLM substrate.Taken together,we anticipated the PLMD database can serve as a useful resource for further researches of PLMs.PLMD 3.0 was implemented in PHP ＋ MySQL and freely available at http：//plmd.biocuckoo.org.
