Saha Prithwidip, Fernandez Ignacio, Sumbul Fidan, Valotteau Claire, Kostrz Dorota, Meola Annalisa, Baquero Eduard, Sharma Arvind, Portman James R, Stransky François, Boudier Thomas, Guardado-Calvo Pablo, Gosse Charlie, Strick Terence, Rey Felix A, Rico Felix
Aix-Marseille Univ., INSERM, DyNaMo, Turing Centre for Living Systems, Marseilles, France.
Institut Pasteur, Université Paris-Cité, Structural Virology Unit, CNRS UMR3569, Paris, France.
Nat Nanotechnol. 2025 Jun 10. doi: 10.1038/s41565-025-01908-1.
The first step of SARS-CoV-2 infection involves the interaction between the viral trimeric spike protein (S) and the host angiotensin-converting enzyme 2 (ACE2). The receptor-binding domain (RBD) of S adopts two conformations: open and closed, respectively accessible and inaccessible to ACE2. Although these changes surely affect ACE2 binding, a quantitative description of the underlying mechanisms has remained elusive. Here we visualize RBD opening and closing using high-speed atomic force microscopy, gaining access to the corresponding transition rates. We also probe the S/ACE2 interaction at the ensemble level with biolayer interferometry and at the single-molecule level with atomic force microscopy and magnetic tweezers, evidencing that RBD dynamics hinder ACE2 binding but have no effect on unbinding. The resulting modulation is quantitatively predicted by a conformational selection model in which each S protomer behaves independently. Our work thus reveals a molecular mechanism by which RBD accessibility and binding strength can be tuned separately, providing hints to better understand the joint evolution of immune evasion and infectivity.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）感染的第一步涉及病毒三聚体刺突蛋白（S）与宿主血管紧张素转换酶2（ACE2）之间的相互作用。S的受体结合域（RBD）呈现两种构象：开放和封闭，分别对应可及和不可及ACE2的状态。尽管这些变化肯定会影响ACE2结合，但对其潜在机制的定量描述仍然难以捉摸。在这里，我们使用高速原子力显微镜观察RBD的开放和关闭，获得相应的转换速率。我们还通过生物层干涉术在整体水平上以及通过原子力显微镜和磁镊在单分子水平上探测S/ACE2相互作用，证明RBD动力学阻碍ACE2结合，但对解离没有影响。通过构象选择模型定量预测了由此产生的调节作用，其中每个S原体独立发挥作用。因此，我们的工作揭示了一种分子机制，通过该机制可以分别调节RBD的可及性和结合强度，为更好地理解免疫逃逸和传染性的联合进化提供了线索。
