Fig. 2: HexaPro-SS-Δstalk S2 trimer opening.
From: Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens
a Progress coordinates used in the WE simulation of HexaPro-SS-Δstalk, namely P987Cα triangle area and RMSDCH, are highlighted with yellow shapes (triangle and cylinders, respectively) drawn on top of the molecular structures. The CHs as in the closed conformation of the simulated construct are shown with shades of purple and are overlayed on the open conformation as in the crystal structure (colored in gray, PDB ID: 8U1G32). b Distribution of the conformations sampled in the opening pathways obtained from the WE simulation. Each black point represents a conformation sampled along an opening pathway. The RMSD of the CH to CHOpen-crystal (y-axis) is plotted against the area of the triangle formed by the P987Cα at the CH apex (x-axis). The hexagonal bin color is scaled to the mean interprotomer distance of the black data points within the respective bin. A trace of one of the successful pathways is shown as a black line with white points corresponding to the closed, partially open, and open conformations. c–e Molecular representation of closed (c), partially open (d), and open (e) conformations as highlighted in (b). Chain-A is depicted in light purple, chain-B in purple, and chain-C in dark purple. Residues 900–1030 encompassing HR1 and CH are illustrated with a cartoon representation, whereas the rest of the chain is shown as an opaque surface. Glycans are shown as gray sticks.
