文献类型：期刊文献

中文题名：基于三元残基组合对的蛋白质相互作用研究

英文题名：Study of protein interaction based on the triplets combination pairs of the residue groups

作者：肖薇[1,2];何增辉[2];李诗良[2];李洪林[1,2]

机构：[1]华东理工大学信息科学与工程学院,上海200237;[2]华东理工大学药学院,上海市新药设计重点实验室,上海200237

年份：2017

卷号：52

期号：10

起止页码：1578

中文期刊名：药学学报

外文期刊名：Acta Pharmaceutica Sinica

收录：CSTPCD;;Scopus;北大核心:【北大核心2014】；CSCD:【CSCD2017_2018】；PubMed;

基金：国家重点研发计划资助课题(2016YFA0502304);中央高校基本科研业务费(222201717024)

语种：中文

中文关键词：蛋白质-蛋白质相互作用;“三棱柱”模型;三元残基组合对

外文关键词：protein-protein interaction; ＇tri-prism＇ model; the triplets combination pairs of the residue group

摘要：蛋白质-蛋白质相互作用的作用机制对生命科学研究有着重要意义。目前已有的方法多偏向于氨基酸残基的偏好性研究,并没有给出对应的残基组合的空间信息,而这些空间信息对设计蛋白质-蛋白质相互作用至关重要。通过深入挖掘已有的蛋白质相互作用模式,并提炼残基相互作用对的偏好和相对位置信息,本文提出了一种全新的既能表征三元残基组合的偏好,又能给出三元残基组合对的空间信息的"三棱柱"模型。该模型主要从偏好因子、氨基酸组成和蛋白质二级结构分布等多个方面对三元残基组合对进行分析。此外,还将该模型应用于PD-1/PD-L2蛋白质的界面研究。通过分析PD-1/PD-L2蛋白质的界面残基组合对与预测残基组合对在组成和空间信息上的差异,给出了具体的残基突变建议,从而为蛋白质-蛋白质相互作用的设计提供了一种新的方法。
The protein-protein interactions play an important role in life science. At present, many methods are developed with preferences of the amino acid residues, which do not offer the relative spatial information for the residue groups. However, the spatial information for the residue groups is important in the design of the protein-protein interactions. We proposed a new model, which is named ‘tri-prism＇ model, by deep mining the existing protein-protein interaction patterns and refining the preference and the relative spatial information for the combination pairs of the residue groups. The model not only provided the preferences, but also offered the relative spatial information for the triplets combination pairs of the residue groups. The model was able to analyze the triplets combination pairs of the residue groups based on the preference factor, amino acid composition, and protein secondary structure. The model was applied to the interface of the PD-1/PD-L2 protein. According to the diversity characters of the composition and the spatial information between the combination pairs of the residue groups at the interface of the PD-1/PD-L2 protein and the predicted ones, we put forward the suggestions for the mutations of the residues, which offered a new view in the study of protein-protein interactions.