Cryo-EM analysis of cooperative conformational changes in the SARS-CoV-2 spike protein trimer

The entry of SARS-CoV-2 into cells is mediated by a trimeric spike protein that utilizes its receptor-binding domain (RBD) to engage with the cell surface receptor ACE2, with each protomer capable of shuttling between an `up' conformation that can bind ACE2 and a `down' conformation that prevents ACE2 binding. To discover intermediate conformational states during this transition, we applied and refined a recently reported linear subspace method to embed 2D projection cryo-EM images of ACE2-bound spike proteins into a low-dimensional latent space. From this embedding, multiple conformational states were reconstructed followed by an automated masking protocol, leveraging a topology representing network and optimal transport. A surprising result from our analysis is the finding that the dominant trajectory for the transition between conformations that have one-up and two-up RBD states involves an all-down RBD conformational state. The methods we present here could be generally applicable to other dynamic protein assemblies to uncover novel intermediate conformational states.