Fig. 4: Molecular dynamic simulation of effects of AGO2 mutations.

a Distance between the Cα atom of I365 and the glycosidic N atom of the g7 residue of the guide (I365α-g7(N)). Populations of all core-RISC trajectories were normalized to the same bin number (60). Black and orange dashed vertical lines denote the reference X-ray structures of the int and nonint core-RISC states (4OLA and 4W5N, respectively). The red dashed line denotes the X-ray structure of the helix-7 mutant (5WEA). b Distance between the c.o.m. of the 3′-end of the guide and the c.o.m. of the PAZ domain (g21-PAZ) along the trajectories of all RNA-bound states. Note that the relatively short length of the individual MD trajectories could affect the results. Color code of the states in both a and b panels: apo-Ago2— green, int core-RISC—gray, nonint core-RISC—orange, g2-8 holo-RISC—magenta and g2-7 holo-RISC—blue. cd motion of the helix7 and the PAZ domain along the open-closed mode (left panel, gray scale histogram). The histograms are calculated by concatenating the last 100 ns of non-biased trajectory of each variant with mismatched RNA duplex. Colored circles depict the maximum population density of each trajectory. Black cross denotes the maximum population density of the WT AGO2 with guide RNA. Right panel: population histograms on α7-MID corresponding to the maxima on the left panel. Equivalent analysis of the variants in in complex with a fully matched seed duplex is shown on Fig. S16.