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

Figure 5.

Figure 5

Modeled interaction of RAC1 or RAC1B with SmgGDS-558.A, overlapping modeling approaches used for RAC1-SmgGDS interactions. B, the initial binding of RAC1 places the RAC1B loop (red) within space for SmgGDS (gray) interaction. C, predicted interaction of RAC1 (yellow) or RAC1B (red) with SmgGDS-558 (gray) shown in two orientations separated by a 180-degree rotation of the y-axis. Four variant conformations of RAC1B (light green, blue, cyan, dark green) were generated by sampling, to assess how the RAC1B insert and PBR affect each other’s orientation. The RAC1B_1, RAC1B_2, and RAC1B_3 models depict how different configurations of the insert region affect the position of the C-terminal PBR. The RAC1B_teth model shows the configuration of the insert region when the C terminus is tethered to the RAC1B prenyl group residing in the hydrophobic pocket of SmgGDS-558. D, enlarged view of the region boxed in panel C for each of the conformations. E, molecular dynamic simulations of the global movement as measured by the carbon alpha RMSD in angstroms. Data are shown for 20 nanoseconds (ns). Colors of the line correspond to the initial starting conformations. Amino acid movement of each simulation as measured by the carbon alpha root mean squared fluctuation (RMSF) in angstroms is shown to the right. Legend above the plot shows the proteins corresponding to the plotted data. The RAC1B loop (red) and polybasic region (PBR, blue) are labeled. F, details of the movement of the RAC1B loop (red box) and polybasic region (PBR, blue box). The top plot shows the movement of each amino acid stacked for each conformation as colored in panel C. The bottom plot shows the percent of total movement at the amino acid based on each starting conformation. G, the added movement of the PBR (blue) and loop (red) for each of the starting conformations. They are ranked based on the PBR movement. The lower the value the less the region moves. H, the dynamics cross correlation matrix of all amino acids of both SmgGDS-558 and RAC1B. The yellow color intensity is based on correlation values close to 1 and blue close to −1. I, the correlations above 0.5 from panel H between residues of the RAC1B loop (red) and PBR (blue). J, the correlations above 0.5 from panel H between residues of the RAC1B loop (red) or PBR (blue) relative to SmgGDS-558 (black). PBR, PBR, polybasic region.