Entropic contribution of ACE2 glycans to RBD binding

The spike protein of the SARS-CoV-2 virus (the causative agent of COVID-19) recognizes the host cell by binding to the peptidase domain (PD) of the extracellular receptor angiotensin-converting enzyme 2 (ACE2). A variety of carbohydrates could be attached to the six asparagines in the PD, resulting in a heterogeneous population of ACE2 glycoforms. Experiments have shown that the binding affinity of glycosylated and deglycosylated ACE2 to the virus is virtually identical. In most cases, the reduction in glycan size correlates with stronger binding, which suggests that volume exclusion, and hence entropic forces, determine the binding affinity. Here, we quantitatively test the entropy-based hypothesis by developing a lattice model for the complex between ACE2 and the SARS-CoV-2 spike protein receptor-binding domain (RBD). Glycans are treated as branched polymers with only volume exclusion, which we justify using all-atom molecular dynamics simulations in explicit water. We show that the experimentally measured changes in the ACE2-RBD dissociation constants for a variety of engineered ACE2 glyco-forms are in reasonable agreement with our theory, thus supporting our hypothesis. However, a quantitative recovery of all the experimental data could require weak attractive interactions.

Automated summary

The spike protein of the SARS-CoV-2 virus recognizes the host cell by binding to the peptidase domain (PD) of ACE2. Carbohydrates attached to the PD result in a heterogeneous population of ACE2 glycoforms. Experiments show that glycosylated and deglycosylated ACE2 have virtually identical binding affinity to the virus, and smaller glycans tend to have stronger binding, suggesting that entropic forces play a role in determining the binding affinity.