Unraveling SARS-CoV-2 spike protein activation pathway reveals unprecedented cryptic pockets
Unraveling SARS-CoV-2 spike protein activation pathway reveals unprecedented cryptic pockets
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DOI：
10.1016/j.bpj.2021.11.491
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发表时间：
2022-02-11
影响因子：
3.4
通讯作者：
Sugita Y
中科院分区：
文献类型：
--
作者：
Dokainish HM;Re S;Mori T;Kobayashi C;Jung J;Sugita Y
严重急性呼吸道综合征冠状病毒2（SARS-CoV-2）是对全球健康的直接威胁。SARS-CoV-2表面的S蛋白被认为是病毒中和和疫苗开发的主要抗原靶点。S-蛋白由高度糖基化的三聚体多肽链组成，并且在活化过程中其受体结合结构域（RBD）经历大的构象变化。结构研究已经显示了300多种S-蛋白构象，包括无活性的down、one-RBD-up（one-up）、two-RBD-up（two-up）和three-RBD-up（three-up）状态，而对结构转变的中间结构和机制知之甚少。在这里，我们进行了原子分子动力学（MD）模拟的基础上，增强的构象采样方法，以探索一个广泛的构象空间的S-蛋白质在溶液中。从向下或向上的冷冻EM结构开始，我们观察到向下、向上、开放和向上两个样构象之间的多个转变，这表明S蛋白的RBD的内在灵活性和动力学，而不管其与人类宿主细胞中的抗体或ACE 2受体的结合。连接在N165、N234、N343处的三个关键聚糖在结构转变中起重要作用。在模拟S蛋白和没有糖基化的单体S蛋白时观察到较大的构象波动，表明聚糖大大减少了S蛋白可用构象的数量。与单分子FRET实验一致，发现了两个在down和one-up之间的中间结构，它们揭示了前所未有的隐蔽口袋，这些口袋可能被靶向以稳定down构象，阻碍ACE 2结合并随后阻碍细胞进入。模拟S-蛋白和不同类别的抗体相互作用表明，聚糖屏蔽是最弱的一个开放的构象。事实上，这种固有的动力学和灵活性的S-蛋白应考虑合理设计的抗病毒药物和疫苗的发展。
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents an immediate threat to global health. Spike (S) protein on the surface of SARS-CoV-2 has been recognized as a primary antigenic target for viral neutralization and vaccine development. S-protein consists of trimeric polypeptide chains heavily glycosylated and undergoes large conformational changes of its receptor binding domain (RBD) during the activation. Structural studies have shown more than 300 S-protein conformations, which include inactive down, one-RBD-up (one-up), two-RBDs-up (two-up), and three-RBDs-up (three-up) states, while little is known about the intermediate structures and mechanisms of the structural transitions. Here, we performed atomistic molecular dynamics (MD) simulations based on an enhanced conformational sampling method to explore a wide conformational space of S-protein in solution. Starting from either down or one-up cryo-EM structures, we observed multiple transitions between down, one-up, one-open, and two-up-like conformations, suggesting the intrinsic flexibility and dynamics of RBDs of S-protein regardless of its binding to antibodies or ACE2 receptor in human host cells. Three key glycans attached at N165, N234, N343 play essential roles in the structural transitions. Larger conformational fluctuations were observed in the simulations of S-protein and a monomeric S-protein without glycosylation, suggesting that the glycans greatly reduce the number of available conformations of S-protein. As consistent with single-molecule FRET experiments, two intermediate structures between down and one-up were found and they reveal unprecedented cryptic pockets that might be targeted to stabilize down conformation, hindering ACE2 binding and subsequently cell entry o. Modelling S-protein and different classes of antibodies interactions shows that glycan shielding is the weakest in one-open conformation. Indeed, such inherent dynamics and flexibility of S-protein shall be considered for rational design of antiviral drugs and vaccine developments.