Mutation N501Y in RBD of Spike Protein Strengthens the Interaction between COVID-19 and its Receptor ACE2

ABSTRACT

Coronavirus disease-19 (COVID-19) is spreading around the world for the past year. Enormous efforts have been taken to understand its mechanism of transmission. It is well established now that the SARS-CoV-2 receptor-binding domain (RBD) of the spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) as its first step of entry. Being a single-stranded RNA virus, SARS-CoV-2 is evolving rapidly. Recently, two variants, B.1.1.7 and B.1.351, both with a key mutation N501Y on the RBD, appear to be more infectious to humans. To understand its mechanism, we combined kinetics assay, single-molecule technique, and computational method to compare the interaction between these RBD (mutations) and ACE2. Remarkably, RBD with the N501Y mutation exhibited a considerably stronger interaction characterized from all these methodologies, while the other two mutations from B.1.351 contributed to a less effect. Surface plasmon resonance and fluorescence-activated cell scan (FACS) assays found that both RBD mutations are of higher binding affinity to ACE2 than the wild type. In addition, atomic force microscopy-based single-molecule force microscopy quantify their strength on living cells, showing a higher binding probability and unbinding force for both mutations. Finally, Steered Molecular Dynamics (SMD) simulations on the dissociation of RBD-ACE2 complexes revealed the possible structural details for the higher force/interaction. Taking together, we suggested that the stronger interaction from N501Y mutation in RBD should play an essential role in the higher transmission of COVID-19 variants.