Nanopore sensing multivalent ligand-receptor interactions for revealing the infectivity of the omicron variant to ACE2

The protein-protein interactions (PPIs), especially ligand-receptor interactions, are crucial for viral infection. Previous studies have predominantly focused on univalent interactions while overlooking the significance of multivalent interactions. The role of multivalent ligand-receptor interactions in PPI remains unclear, and the dynamic processes of binding and dissociation in multivalent ligand-receptor interactions have yet to be fully elucidated. Thus, it is of significance to study multivalent ligand-receptors interactions to enhance our understanding of the role in PPI. Herein, we introduce the trimeric spike protein and ACE2 as model multivalent ligands and receptors, respectively. We develop a modified nanopore-based SARS-CoV-2 spike protein nanosensor that enables to real-time monitor the multivalent binding and dissociation of various variant spike proteins to ACE2. By effectively confining individual spike proteins and ACE2 within nanopipette orifices, we observe characteristic time-dependent changes in ionic current under applied potentials, providing insights into the dynamic binding and dissociation processes of multivalent ligand-receptor interactions. We propose three different binding models for the interactions between various spike protein variants and ACE2. This method enables real-time monitoring of the formation of three distinct ligand-receptor complexes and their dynamic exchange during multivalent receptor binding reactions. Moreover, we quantify the differences in interaction strength between various spike protein variants and varying numbers of ACE2 receptors, uncovering the reason behind the Omicron variant’s high affinity for ACE2. Remarkably, we provided a new method for virus affinity measurement to understand the interaction mechanism of multivalent ligand-receptors.