南方医科大学学报

南方医科大学学报 ›› 2024, Vol. 44 ›› Issue (1): 179-186.doi: 10.12122/j.issn.1673-4254.2024.01.21

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早幼粒细胞白血病蛋白与TAK1结合蛋白相互作用的生物信息学分析与验证

成佳聪，李智慧，刘 鳐，李 成，黄 鑫，田颖鑫，沈富兵   

  1. 成都医学院检验医学院，药学院，四川 成都 610500
  • 发布日期:2024-01-19

Bioinformatics analysis and validation of the interaction between PML protein and TAB1 protein

CHENG Jiacong, LI Zhihui, LIU Yao, LI Cheng, HUANG Xin, TIAN Yinxin, SHEN Fubing   

  1. School of Laboratory Medicine, School of Pharmacy, Chengdu Medical College, Chengdu 610500, China
  • Published:2024-01-19

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摘要： 目的 通过生物信息学方法预测早幼粒细胞白血病蛋白与TAK1结合蛋白的相互作用，并通过免疫共沉淀方法进行实验验证。方法 使用Rosetta软件，采用比较建模的方法，构建TAB1蛋白的三维模型；在PDB数据库中检索PML蛋白二级结构，并解析其晶体结构和三维结构。Zdock3.0.2软件进行PML与TAB1的蛋白-蛋白对接，并提取最佳构象进行对接模型的分子结构分析。α-MMC处理的M1炎性巨噬细胞，利用免疫共沉淀技术检测两种蛋白的相互作用。结果 以PML的6IMQ为对接部位时，PML蛋白与TAB1蛋白能形成3个盐桥、6个氢键和6个疏水作用；以PML的5YUF为对接部位时，PML蛋白与TAB1蛋白能形成1个氢键、3个静电相互作用和9个疏水作用，两种对接模式皆能形成良好的分子对接和相互作用；在α-MMC处理4 h后，其PML-IP组的细胞裂解沉淀液中分别能检测到显著的PML和TAB1阳性蛋白条带。结论 PML蛋白与TAB1蛋白能发生较强的相互作用。

关键词: TAB1蛋白；PML蛋白；生物信息学；蛋白-蛋白对接；免疫共沉淀

Abstract: Objective To analyze the interaction between PML protein and TAB1 protein using bioinformatic approaches and experimentally verify the results. Methods Using Rosetta software, a 3D model of TAB1 protein was constructed through a comparative modeling approach; the secondary structure of PML protein was retrieved in the PDB database and its crystal structure and 3D structure were resolved. Zdock 3.0.2 software was used to perform protein-protein docking of PML and TAB1, and the best conformation was extracted for molecular structure analysis of the docking model. The interaction between the two proteins was detected using immunoprecipitation in α-MMC- treated M1 inflammatory macrophages. Results When 6IMQ of PML was used as the docking site, PML protein formed 3 salt bridges, 6 hydrogen bonds and 6 hydrophobic interactions with TAB1 proteins; when 5YUF of PML was used as the docking site, PML protein formed 1 hydrogen bond, 3 electrostatic interactions and 9 hydrophobic interactions with TAB1 proteins, and both of the docking modes formed good molecular docking and interactions. In the M1 inflammatory macrophages treated with α-MMC for 4 h, positive protein bands of PML and TAB1 were detected in the cell lysates in PML-IP group. Conclusion PML protein can interact strongly with TAB1 protein.

Key words: TAB1 protein; PML protein; bioinformatics; protein-protein docking; co-immunoprecipitation