IL-18与IL-18R分子对接计算发展模拟蛋白质互作研究方法

研究蛋白质互作的化学生物学方法主要有荧光共振能量转移(Fluorescence resonance energy transfer, FRET)、酵母双杂交(Yeast two-hybrid technology, YTH)、免疫共沉淀(Co-immunoprecipitation, Co-IP)等。在此基础上，为了发展一种新的研究生物大分子互作，特别是膜蛋白相互作用的定量计算方法，依据前期研究发现，应用ELISA方法与QAH-NEU-1定量芯片技术检测NLRP2:ShRNAs慢病毒(Lentivirus)感染人脑微血管内皮细胞(Human brain microvascular endothelial cells, HBMEC), 敲除(Knocking down)NLRP2基因后的IL-18的分泌量与对照组比较, 显著提高(IL-18: 998 pg/mL)，表明它在炎症免疫中起关键调控作用。本文采用高性能的Discovery Studio 2021(DS2018R2)大分子计算模拟软件，在RCSB PDB数据库中调用蛋白质文件建立其立体结构，应用ZDOCK程序算法探究IL-18亚基(AB亚基或B亚基)与IL-18R互作的空间结构与构象变化，计算找到了相互作用界面的氨基酸的一级序列与二级结构，以及它们之间的相互作用力，并用拉氏图评估对接构象，研究发现B亚基在IL-18与IL-18R的结合中起主要作用。该计算方法与实验方法比较，可快速找到蛋白-蛋白相互作用的构象空间，优化膜蛋白互作的精度；能从原子与量子水平探究细胞因子与膜蛋白受体的互作；更深入解析分子机理，数据精确定量。研究结果表明本文应用ZDOCK算法建立了通过计算模拟膜蛋白生物大分子互作的新领域，为细胞因子与化学因子的多肽类药物开发提供新的思路; 为细菌病毒感染/肿瘤疾病的防治提供科学理论依据; 在分子识别，神经元网络深度学习，生物信息处理领域具有广泛的应用。

IL-18 and IL-18R Docking Calculation to Develop the Research Approach of the Simulation of Protein Interaction

Recently, the main biological technologies to study the functional activity of proteins are fluorescence resonance energy transfer (FRET), yeast two-hybrid technology (YTH), and co-immunoprecipitation(Co-IP), etc. On this basis, in order to develop a new quantitative calculative approach for studying biological macromolecular interaction, especially membrane protein interactions, NLRP2:ShRNAs lentivirus were constructed to knock down NLRP2 gene in the human brain microvascular endothelial cells (HBMEC). Both ELISA and QAH-NEU-1 quantitative chip assay detected results showed that the secretion of IL-18 inflammatory factor (IL-18: 998pg/mL) was significantly increased compared with the control group, which indicated that IL-18 plays a key regulatory role in inflammation and immunity. In this paper, the high-performance Discovery Studio 2021 (DS2018R2) macromolecular simulation software is applied to call the protein three-dimensional structure file in the RCSB PDB protein structure database to establish the three-dimensional (3D) structure of the protein, and the ZDOCK program algorithm to study the spatial structure and conformation variation of the interaction between IL-18 subunit (B subunit or AB subunit) and IL-18R. The primary sequence and secondary structure of amino acids at the interaction interface, and the interaction forces between them were found by the calculation. Furthermore, the docking conformation was evaluated by Laplace diagram. It was revealed that B subunit played a major role in the binding of IL-18 and IL-18R. Compared with the experimental method, the computational approach can quickly find the conformational space of protein-protein interaction, optimize the accuracy of the membrane protein interaction process, and explore the interaction between cytokines and membrane protein receptors at the atomic and quantum levels, which can analyze the molecular mechanism more deeply for the data which can be accurately quantified. The research results demonstrated that the application of ZDOCK algorithm established a new field of simulation of the biological macromolecular interaction of membrane proteins by calculation, which provided a new reference for the development of polypeptide drugs of cytokines and chemokines, and a scientific theoretical basis for the prevention and treatment of bacteria/virus infection/tumor diseases. It has a wide range of applications in the fields of molecular recognition, neural network deep learning and biological information processing.