Figure 1 | Scientific Reports

Figure 1

From: Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant

Figure 1

Structural implications of the D614G mutation in the S-protein. (a) Top and side views of the S-protein in the closed and open conformations. D614 in the three protomers is depicted in orange van der Waals spheres. The RBD of protomer A in the down and up state is coloured in light green and dark pink, respectively. Graphical representation of the domain organisation of the S-protein: signal peptide (SP), receptor binding domain (RBD), N-terminal domain (NTD), subdomains 1 and 2 (SD1 and SD2), fusion peptide (FP), heptad repeat 1 (HR1), central helix (CH), connector domain (CD), heptad repeat 2 (HR2), transmembrane domain (TM). (b) Time series of D614 with K835 and P826 at the A–C interface over the course of the simulations initiated from the closed (green) and partially open (pink) conformations. The equivalent interactions of D614 at the B–C interface are given in grey. The probability distribution function (PDF) of the two interactions are displayed on the top of each timeseries. (c) Upper panels: interactions involving D614 for the closed (left) and open (right) conformation at the end of each simulation. The D614 residue of chain A is depicted in pink and green spheres and the interacting residues of chain C are represented in white spheres. Bottom-panels: interactions involving D614, when mutated to glycine, for the closed (left) and open (right) conformation at the end of each simulation. The Cα atom of G614 of chain A is depicted in pink and green spheres and the interacting residues of chain C are represented in white spheres.

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