SARS-CoV-2 infection is mediated by glycosylated spike trimers, which protrude the surface of viral particles and bind to human ACE2 receptors. For a spike to bind ACE2, the receptor binding domain (RBD) must transition from a glycan-shielded ‘down’ to an exposed ‘up’ state. Experimental structures have captured these intermediates, however molecular details of the opening transition have remained elusive. To access the biological timescales of this transition, we used the weighted ensemble (WE) enhanced sampling method to generate unbiased, all-atom molecular dynamics simulations of the glycosylated spike opening. Rather than adding an external biasing force, the WE method relies on running many short simulations in parallel along chosen reaction coordinate(s). The probability, or weight, of each trajectory is rigorously tracked, and there is no statistical bias added to the system. Hence, we are able to directly obtain both thermodynamic and kinetic properties from the WE simulations, which is not possible with most other enhanced sampling methods. From these simulations, we uncovered the primary glycans and residues involved in RBD opening, and obtained extensive sampling of spike conformations, including over 300 continuous pathways and more than 130 µs of simulation data. Together with ManifoldEM and biolayer interferometry, we reveal a gating role for the <i>N</i>-glycan at position N343, which facilitates RBD opening. These simulations represent the largest system ever simulated with the WE method (more than half a million atoms), and provide a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.

Glycan gate: Atomic-level characterization of SARS-CoV-2 spike opening

ACS Spring 2022

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