Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane.,The Journal of Physical Chemistry B

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Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane.
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-06-19 , DOI: 10.1021/acs.jpcb.0c04553
Hyeonuk Woo ₁ , Sang-Jun Park ₂ , Yeol Kyo Choi ₃ , Taeyong Park ₁ , Maham Tanveer ₃ , Yiwei Cao ₃ , Nathan R Kern ₂ , Jumin Lee ₃ , Min Sun Yeom ₄ , Tristan I Croll ₅ , Chaok Seok ₁ , Wonpil Im _{2,

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Affiliation

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 that 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：

在病毒膜中开发完全糖基化的全长 SARS-CoV-2 刺突蛋白模型。

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 建模套件中基于模板的建模、从头蛋白质结构预测和环建模技术对全长 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 中的糖阅读器和建模器对每个单体的 22 个 N-聚糖和 1 个 O-聚糖进行建模。使用 ISOLDE 评估这些完全糖基化的全长 S 蛋白模型结构，并根据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 蛋白放置在病毒膜中并进行全原子分子动力学模拟。所有结构都可以在 CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19) 中找到，以便研究人员可以使用这些模型来开展创新和新颖的建模和模拟研究。 COVID-19 的预防和治疗。

更新日期：2020-08-20

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