Abstract：
Self-assembling protein nanoparticles showed promise for vaccine design due to efficient antigen presentations and safety. However, the unpredictable formations of epitopes-fused protein assemblies remain challenging in the upstream design. This study suggests employing molecular dynamic (MD) simulations to investigate the assembly properties of Hepatitis B core protein (HBc) from thermodynamic perspectives. Eight HBc derivatives were expressed in E. coli, with their self-assembly properties characterised by high-performance liquid chromatography and transmission electron microscopy. MD simulations on the dimers, based on AlphaFold-predicted 3D structures, analysed the derivative at the atomic level. Results revealed that HBc derivatives can form dissociative polymers or large multi-subunit structures due to assembly failures. The instability of the dimer in aqueous solvents or inappropriate intradimer distances could cause major assembly failures. Polar solvation energies played a vital role too in forming assemble-incompetent dimers. Importantly, our study demonstrated that MD simulations on dimers can provide preliminary predictions on the assembly properties of HBc derivatives, thus aiding vaccine design by lowering the risk of self-assembling failures in engineered proteins.Communicated by Ramaswamy H. Sarma.
摘要：
由于有效的抗原呈递和安全性，自组装蛋白质纳米颗粒显示出疫苗设计的希望。然而,在上游设计中，表位融合蛋白组装体的不可预测的形成仍然具有挑战性。本研究建议采用分子动力学（MD）模拟从热力学角度研究乙型肝炎核心蛋白（HBc）的组装特性。八种HBc衍生物在大肠杆菌中表达,具有高效液相色谱和透射电子显微镜表征的自组装特性。对二聚体的MD模拟，基于AlphaFold预测的3D结构，在原子水平上分析了导数。结果表明，由于组装失败，HBc衍生物可以形成解离聚合物或大的多亚基结构。二聚体在水性溶剂中的不稳定性或不适当的内部距离可能导致主要的组装失败。极性溶剂化能量在形成无组装能力的二聚体中也起着至关重要的作用。重要的是,我们的研究表明，对二聚体的MD模拟可以提供对HBc衍生物的组装性质的初步预测，从而通过降低工程蛋白质自组装失败的风险来帮助疫苗设计。由RamaswamyH.Sarma沟通。
