Casalino Lorenzo, Gaieb Zied, Goldsmith Jory A, Hjorth Christy K, Dommer Abigail C, Harbison Aoife M, Fogarty Carl A, Barros Emilia P, Taylor Bryn C, McLellan Jason S, Fadda Elisa, Amaro Rommie E
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States.
ACS Cent Sci. 2020 Oct 28;6(10):1722-1734. doi: 10.1021/acscentsci.0c01056. Epub 2020 Sep 23.
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 deaths worldwide to date. Antibody development efforts mainly revolve around the extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin-converting enzyme 2 (ACE2). Similar to many other viral fusion proteins, the SARS-CoV-2 spike utilizes a glycan shield to thwart the host immune response. Here, we built a full-length model of the glycosylated SARS-CoV-2 S protein, both in the open and closed states, augmenting the available structural and biological data. Multiple microsecond-long, all-atom molecular dynamics simulations were used to provide an atomistic perspective on the roles of glycans and on the protein structure and dynamics. We reveal an essential structural role of -glycans at sites N165 and N234 in modulating the conformational dynamics of the spike's receptor binding domain (RBD), which is responsible for ACE2 recognition. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the "down" state. Additionally, end-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of the SARS-CoV-2 S protein, which may be exploited in the therapeutic efforts targeting this molecular machine. Overall, this work presents hitherto unseen functional and structural insights into the SARS-CoV-2 S protein and its glycan coat, providing a strategy to control the conformational plasticity of the RBD that could be harnessed for vaccine development.
由严重急性呼吸综合征冠状病毒2(SARS-CoV-2)引起的新型冠状病毒肺炎疫情至今已在全球导致超过2800万例感染和90万人死亡。抗体研发工作主要围绕高度糖基化的SARS-CoV-2刺突(S)蛋白展开,该蛋白通过与血管紧张素转换酶2(ACE2)结合介导宿主细胞进入。与许多其他病毒融合蛋白类似,SARS-CoV-2刺突利用聚糖屏蔽来抵御宿主免疫反应。在此,我们构建了处于开放和封闭状态的糖基化SARS-CoV-2 S蛋白的全长模型,补充了现有的结构和生物学数据。通过多个长达微秒级的全原子分子动力学模拟,从原子层面揭示了聚糖的作用以及蛋白质的结构和动力学。我们发现N165和N234位点的聚糖在调节刺突受体结合域(RBD)的构象动力学方面具有重要结构作用,而RBD负责识别ACE2。生物层干涉实验证实了这一发现,该实验表明通过N165A和N234A突变删除这些聚糖会导致RBD构象向“向下”状态转变,从而显著降低与ACE2的结合。此外,端到端可及性分析全面概述了SARS-CoV-2 S蛋白聚糖屏蔽的脆弱性,这可能在针对这一分子机制的治疗研究中加以利用。总体而言,这项工作揭示了SARS-CoV-2 S蛋白及其聚糖外壳前所未见的功能和结构见解,为控制RBD的构象可塑性提供了一种策略,可用于疫苗研发。