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过程工程学报 ›› 2021, Vol. 21 ›› Issue (2): 219-229.DOI: 10.12034/j.issn.1009-606X.220085

• 生化工程 • 上一篇    下一篇

HBc-VLP的分子动力学模拟和结合自由能计算

马艳艳1,2, 李正军3, 张松平3, 陈 卫1,4*, 任 瑛1,5*   

  1. 1. 中国科学院过程工程研究所多相复杂系统国家重点实验室,北京 100190 2. 中国科学院大学化学工程学院,北京 100049 3. 中国科学院过程工程研究所生化工程国家重点实验室,北京 100190 4. 中国科学院洁净能源创新研究院,辽宁 大连 116023 5. 中国科学院绿色过程制造创新研究院,北京 100190
  • 收稿日期:2020-03-14 修回日期:2020-04-24 出版日期:2021-02-22 发布日期:2021-03-01
  • 通讯作者: 任瑛
  • 基金资助:
    MgCl26H2O-Mg(OH)2-MgO技术路线制备高纯镁砂过程基础研究;MgCl26H2O-Mg(OH)2-MgO技术路线制备高纯镁砂过程基础研究;MgCl26H2O-Mg(OH)2-MgO技术路线制备高纯镁砂过程基础研究;中国科学院绿色制造创新研究院自署布置课题

Molecular dynamics simulation and calculation of binding free energy of a HBc-VLP

Yanyan MA1,2, Zhengjun LI3, Songping ZHANG3, Wei CHEN1,4*, Ying REN1,5*   

  1. 1. State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China 2. School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China 3. State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China 4. Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, Liaoning 116023, China 5. Innovation Academy of Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
  • Received:2020-03-14 Revised:2020-04-24 Online:2021-02-22 Published:2021-03-01

摘要: 乙型肝炎核心病毒样颗粒HBc-VLPs (Hepatitis B Core Antigen Virus-like Particles)因稳定性好且易于改造,被作为疫苗载体广泛使用,但影响VLPs稳定性的控制机制尚不清楚。采用分子动力学模拟研究了HBc-VLP中蛋白亚基二聚体、五聚体及六聚体复合物的稳定性,计算了体系中蛋白亚基的介电常数,避免了以往研究中直接使用经验参数的做法;通过分子力学-泊松玻尔兹曼溶剂可及表面积(MM-PBSA)方法计算亚基分子间的结合自由能,表明范德华作用能和非极性溶剂化作用能有利于促进相邻蛋白亚基间的亲和作用;根据计算结果可推测HBc-VLPs中六聚体比五聚体的稳定性更强,而两个六聚体之间或五聚体同六聚体之间形成的二聚体有助于进一步形成结构更加稳定的HBc-VLPs。该结论有助于生物工程中对HBc-VLPs的蛋白质改造,从而提高HBc-VLPs为载体的候选疫苗的稳定性。

关键词: HBc-VLPs, 分子动力学模拟, 介电常数, MM-PBSA, 结合自由能, 稳定性

Abstract: Hepatitis B core antigen virus-like particles (HBc-VLPs) are widely used as vaccine vectors due to their good stability and easy modification, and the investigations of VLPs is one of the hot spots in the field of bio-pharmaceutical engineering. However, VLPs may disassemble or aggregate due to their sensitivity to temperature, pH and other factors, which becomes the bottleneck hindering the widely application, and the underlying mechanisms which governs the structure and thus stability of VLPs is still ambiguous. In this work, molecular dynamics simulation was utilized to investigate the stability of the dimer, pentamer and hexamer formed by protein subunits in HBc-VLP. Instead of using empirical values in previous studies, the parameters of protein dielectric constant in aqueous solution were obtained by molecular dynamics simulations, and the results suggested that both the aqueous solvent and the arrangement of protein subunits in the complex could significantly change the dielectric constant, which further affected the binding free energy. Furthermore, with the dielectric constant of protein subunits, the binding free energy between protein subunits were calculated by the molecular mechanics-Poisson Boltzmann solvent accessible surface area (MM-PBSA) method. Finally, according to the calculation results, it was speculated that the stability of the hexamer was better than the pentamer, and the dimers formed between two adjacent hexamers or between a pentamer and a hexamer can further lead to a more stable structure. These understandings could provide theoretical guidance for the modification of candidate vaccine with HBc-VLPs as the carrier.

Key words: HBc-VLPs, molecular dynamics simulations, dielectric constant, MM-PBSA, binding free energy, stability