Fig. 2.

Dynamics of the loop containing the furin cleavage site in SARS-CoV-2 S protein. a Projection of the molecular dynamics simulations into the eigenspace formed by the two first components of a principal component (PC) analysis. Each point represents a conformation of the loop and the color indicates to which protomer and structure it belongs to: tones of orange, closed structure (6VXX) and tones of purple, partially open structure (6VYB). The marginal distributions are obtained using a kernel density estimate. The centroids from a k-means clustering are shown with red stars, and the corresponding structures in b. Representative conformations of the loop for each centroid are colored and labeled according the code defined in panel a. The red sphere indicates the furin cleavage site (Cα of R685).