蛋白质-DNA复合物中残基界面偏好性分析及在识别界面中的应用  

Analysis of Residue Interface Preference in Protein-DNA Complexes and Its Application in Recognition of Binding Interface

作　　者：杨爽 李春华[1] 

机构地区：[1]北京工业大学环境与生命学部,北京

出　　处：《生物物理学》2022年第4期47-54,共8页Biophysics

摘　　要：蛋白质-DNA识别在生物过程中起着重要作用,其结合是由序列特异性识别和结构特征共同影响的。为了研究残基类型和蛋白质二级结构对结合的贡献,本文构建了一个新的非冗余蛋白质-DNA复合物数据库,其中包含1545个结构。经过统计分析发现,残基和二级结构类型对蛋白质与DNA结合有很大贡献,二级结构中π-helix和β-ladder是最偏好界面的类型。对蛋白质二级结构按界面偏好进行分类,构建了60 ×4氨基酸–核苷酸成对界面偏好性。从该偏好性中获得氨基酸界面偏好性,并探讨了将该信息用于预测蛋白质-DNA结合界面的可能性,研究对象为对接基准数据集中的47个复合物体系。结果发现成对界面偏好性信息可以将87.23%的体系的真实界面打分排在所有表面区域的前10%。这说明本文构建的60 ×4氨基酸–核苷酸成对界面偏好性很好地反映了蛋白质-DNA的界面识别,对界面和复合物结构预测具有重要意义。Protein-DNA recognition plays an important role in biological processes, and its binding is influ-enced by sequence specific recognition and structural characteristics. To investigate the contribu-tion of residue types and protein secondary structure elements to binding, a new non-redundant protein-DNA database with 1545 complex structures was constructed. Statistical analysis reveals that protein residue and secondary structure types have significant contributions to its binding with DNA. Among the secondary structures, π-helix and β-ladder have the highest preferences. We classified the protein secondary structures according to their interface preferences, and construct-ed the 60 ×4 amino acid-nucleotide pairwise interface preferences. The amino acid interface pref-erences obtained from the pairwise ones were used to explore the possibility of predicting pro-tein-DNA binding interfaces for 47 complex systems from the docking benchmark dataset. The re-sult shows that the pairwise interface preferences can rank the real interfaces in the top 10% of all surface patches for 87.23% of all cases. These results indicate that the 60 ×4 amino acid-nucleotide pairwise interface preferences constructed by us can well reflect protein-DNA recognition, which is of great significance for interface and complex structure predictions.

关 键 词：DNA识别 蛋白质二级结构 数据库 偏好性 统计分析 序列特异性 界面识别 

分 类 号：TP3[自动化与计算机技术—计算机科学与技术]