Knowledge Management System Of Institute of process engineering,CAS
|Thesis Advisor||任瑛, 陈卫, 李粮生|
病毒样颗粒VLPs (virus-like particles)是生物制药工程领域的研究热点之一，但因其在生产及储运过程中易受温度、pH值等因素的影响而发生裂解、聚集或沉淀，严重限制了VLPs疫苗的工业转化和普遍应用。分子模拟通过分子力学-泊松玻尔兹曼溶剂可及表面积(MM-PBSA)法可计算VLPs中蛋白亚基之间的结合自由能，从而为VLPs稳定性调控奠定理论基础；但该方法中的蛋白质介电常数多采用经验值，未考虑蛋白质分子结构及溶剂环境影响，从而影响结合自由能计算结果的准确性。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。本工作以乙型肝炎核心病毒样颗粒HBc-VLP为研究对象，采用分子动力学模拟研究HBc-VLP中不同结构的亚基复合物的稳定性。论文提出根据蛋白亚基所处的大分子拥挤环境及溶剂环境对其介电常数进行统计计算，进而计算亚基分子间的结合自由能，获得该复合物结构的稳定性强弱。本文的主要研究内容如下：(1) 分别以HBc-VLP中的二聚体、五聚体、六聚体及一个五聚体同两个六聚体形成的大复合物为研究对象，摒弃传统自由能计算方法中采用的蛋白亚基介电常数的经验性数值，提出通过研究蛋白亚基分子的偶极矩计算其介电常数。结果表明，蛋白亚基的介电常数受溶剂环境及不同复合物结构中蛋白亚基间的自组装结构的影响，进而影响溶剂化静电能。(2) 采用上述计算所得不同体系中蛋白亚基的介电常数，通过MM-PBSA法计算HBc-VLP的不同复合物结构中蛋白亚基间的结合自由能。游离态多聚体中，蛋白亚基间的亲和作用强弱：二聚体>五聚体>六聚体。大复合物中，蛋白亚基间的亲和作用强弱：二聚体>六聚体>五聚体。对于所有模拟体系，范德华能和非极性溶剂化能均有利于维持各个复合物的稳定，静电能和极性溶剂化能则会减弱蛋白亚基间的亲和作用。如采用蛋白介电常数的经验值计算亚基间结合自由能，因未考虑蛋白分子在局部环境中呈现的电荷分布及静电作用，所得结果准确度不高。(3) 高浓度离子产生的电偶极矩会改变溶剂的介电性质，进而改变蛋白亚基的介电常数及结合自由能。在大复合物体系中添加1.5 mol/L的NaCl，模拟结果表明，五聚体内亚基间亲和作用增强，其它复合物中亚基间亲和作用减弱。因此，研究盐离子对VLPs体系亚基间结合能的影响需要根据离子浓度及蛋白亚基的自组装形式进行具体分析。;VLPs (virus-like particles) is one of the research hotspots in the field of biological pharmaceutical engineering. However, VLPs may undergo cracking, aggregation or precipitation as the change of temperature, pH value and other factors during production, storage and transportation, which severely limits the industrialization of VLPs vaccine. The binding affinity between protein subunits in VLPs can be simulated by molecular simulations and the binding free energies can be calculated by Molecular Mechanism-Poisson Boltzmann Solvent Accessible surface area (MM-PBSA) method, thus laying a theoretical foundation for the investigation of the stability of VLPs. However, currently, the empirical values of dielectric constants are usually used in the method, resulting in underestimation of the effects of protein molecular structures and the solvent environment. Hepatitis B core virus-like particles HBc-VLPs (hepatitis B core antigen virus-like particles) are widely used as vaccine vectors due to their good stability and easy modification, but the dominant mechanisms affecting the stability of VLPs is still unclear.In this work, the stability of protein complexes with different structures in HBc-VLP was studied by molecular dynamics simulation. The dielectric properties of the protein subunits were calculated statistically according to the macromolecular crowding environment and solvent properties, and then the binding free energies were calculated to obtain the stability of the protein complex structure. The main research contents of this work are as follows:(1) The protein complex of dimer, pentamer, hexamer and a large complex formed by one pentamer and two hexamers were studied by molecular dynamics with emphasis on the investigation of dielectric properties. Instead of the popular practice of using the empirical values of the dielectric constant, this work proposes to study the dynamics of the molecular dipole moments of the protein subunits and further obtain the dielectric constants based on Fröhlich-Kirkwood model. The results suggest that the dielectric constant of the protein subunit is affected by the solvent properties and the self-assembly structure of the protein subunit in different complex structures, which would further affect the solvation electrostatic energy.(2) With the dielectric constants of protein subunits calculated, the binding free energy between protein subunits in the corresponding complex structures of HBc-VLP was calculated by MM-PBSA method, and the order of affinity between protein subunits is dimer > pentamer > hexamer. However, the hexamer in the large complex is more stable than the pentameter, and the dimer formed at the interface between the pentameter and the hexamer is the most stable. For all the simulated systems, the van der Waals energy and the non-polar solvation energy promote the stability of each complex, while the electrostatic energy and polar solvation energy will weaken the affinity between the protein subunits. The free energy of binding between subunits obtained by using the empirical value of protein dielectric constant does not consider the charge distribution and electrostatic effect of protein molecules in the local environment, so the accuracy of the obtained free energy of binding is not high.(3) The electric dipole moment generated by the high concentration of ions will change the dielectric properties of the solvent, which in turn will change the dielectric constant of the protein and the calculated value of the binding free energy. The addition of 1.5 mol/L NaCl to the large complex system would enhance the affinity between protein subunits in the pentameter, while the stability of other complexes is slightly weakened. Therefore, the influence of salt ions on the affinity between subunits of the VLPs system needs to be specifically analyzed according to the ion concentration and the aggregation form of protein subunits.
|马艳艳. 乙肝核心病毒样颗粒稳定性的分子动力学模拟研究[D]. 中国科学院大学,2020.|
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