This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently-determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully-glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19), so researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.

中文翻译：

---

病毒膜中全糖基化全长 SARS-CoV-2 刺突蛋白的建模和模拟。

这项技术研究描述了病毒膜中完全糖基化的全长 SARS-CoV-2 刺突 (S) 蛋白的全原子建模和模拟。首先，从 PDB:6VSB 和 6VXX 开始，使用 GALAXY 建模套件中的基于模板的建模、从头蛋白质结构预测和循环建模技术对全长 S 蛋白结构进行建模。然后，使用最近确定的占据最多的糖型，使用 CHARMM-GUI 中的 Glycan Reader & Modeler 对每个单体的 22 个 N-聚糖和 1 个 O-聚糖进行建模。使用 ISOLDE 对这些完全糖基化的全长 S 蛋白模型结构进行了评估，并针对其各自实验图中的低分辨率数据进一步细化。然后，我们使用 CHARMM-GUI Membrane Builder 将 S 蛋白置于病毒膜中并进行全原子分子动力学模拟。