Using molecular simulation to interpret weak cryo-EM density for the Spike protein post-fusion complex

The Spike protein plays a key role in viral entry during SARS-CoV-2 infection and is central to the Pfizer and Moderna COVID-19 vaccines.  Understanding how the protein works in molecular detail is critical to further optimization of vaccines and therapies. While the structure of many regions of the Spike protein in several conformations has been solved via cryo-EM, the region of the Spike protein that anchors the virus to the host (fusion peptide region) remains elusive. For example, in the cryo-EM reconstruction of the fusion complex, this region has very weak cryo-EM density. Here, we use our cryo_fit method to produce structural ensembles of the spike protein complex, including the fusion peptide, highly consistent with the strong and weak density observed experimentally. Our simulated cryo-EM maps show agreement with the experimentally determined cryo-EM maps for full post-fusion complex (‘fusion state’), including the fusion peptide and fusion peptide proximal regions.