Impact and Crashworthiness Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts.
Department of Mechanical and Aerospace of Engineering, University of Central Florida, Orlando, Florida.
Biophys J. 2022 Jun 21;121(12):2353-2370. doi: 10.1016/j.bpj.2022.05.021. Epub 2022 May 20.
The newly developed finite element (FE) modeling at the atomic scale was used to predict the static and dynamic response of the α-helix (AH) and tropocollagen (TC) protein fragments, the main building blocks of the spike of the SARS-CoV-2. The geometry and morphology of the spike's stalk and its connection to the viral envelope were determined from the combination of most recent molecular dynamics (MD) simulation and images of cryoelectron microscopy. The stiffness parameters of the covalent bonds in the main chain of the helix were taken from the literature. The AH and TC were modeled using both beam elements (wire model) and shell elements (ribbon model) in FE analysis to predict their mechanical properties under tension. The asymptotic stiffening features of AH and TC under tensile loading were revealed and compared with a new analytical solution. The mechanical stiffnesses under other loading conditions, including compression, torsion, and bending, were also predicted numerically and correlated with the results of the existing MD simulations and tests. The mode shapes and natural frequencies of the spike were predicted using the built FE model. The frequencies were shown to be within the safe range of 1-20 MHz routinely used for medical imaging and diagnosis by means of ultrasound. These results provide a solid theoretical basis for using ultrasound to study damaging coronavirus through transient and resonant vibration at large deformations.
新开发的原子尺度有限元（FE）建模用于预测 SARS-CoV-2 刺突的主要构建块α-螺旋（AH）和原胶原（TC）蛋白片段的静态和动态响应。刺突柄的几何形状和形态及其与病毒包膜的连接，是从最新的分子动力学（MD）模拟和冷冻电子显微镜图像的组合中确定的。螺旋主链中共价键的刚度参数取自文献。在 FE 分析中，使用梁元素（线模型）和壳元素（带状模型）对 AH 和 TC 进行建模，以预测它们在拉伸下的机械性能。揭示了 AH 和 TC 在拉伸载荷下的渐近硬化特征，并与新的解析解进行了比较。还通过数值预测了其他加载条件下的机械刚度，包括压缩、扭转和弯曲，并与现有 MD 模拟和测试的结果相关联。使用构建的 FE 模型预测了刺突的振型和固有频率。结果表明，这些频率处于安全范围内，即 1-20MHz，这是医学成像和诊断中常用的超声范围。这些结果为使用超声通过大变形时的瞬态和共振振动来研究破坏性冠状病毒提供了坚实的理论基础。
