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. 2023 Apr 12;299(6):104698. doi: 10.1016/j.jbc.2023.104698

Figure 6.

Figure 6

Simulations of the RAC1B conformation for 650 nanoseconds show stability of the loop region relative to the PBR.A, various statistics for the 650 nanosecond (ns) simulation of RAC1B with SmgGDS for 26,000 data points. Shown are the total energy, surface accessible area of all proteins, surface hydrogen bonds with water, Carbon Alpha RMSD, and percent of each secondary structure annotations. All metrics show the equilibrium of the simulation. B–E, representative time points shown in red on panel A for the RAC1B (cyan) interaction with SmgGDS shown as a surface plot. The lipidation site is colored magenta, polar basic residues in blue, and polar acid residues in red. Sampled times include 0 ns (B), 250 ns (C), 500 ns (D), and 650 ns (E). F, average movement of RAC1B loop (red) or polybasic region (PBR, blue) amino acids throughout the entire long simulation. G, dynamic cross-correlation analysis of loop (Top) relative to PBR (Side) amino acids. The numbers are colored on a heatmap of red being highly correlated and blue being negatively correlated. PBR, PBR, polybasic region.