Fig. 6

Structural stability and dynamic behavior of AGO2-siRNA complexes over 100 ns molecular dynamics simulations. Comparative analyses of AGO2 which is complexed with siRNA8 (black) and siRNA12 (red) were performed to evaluate conformational stability, flexibility, and interaction energetics. (a) Radius of gyration (Rg) plots reveal that siRNA12-bound AGO2 maintains a slightly more expanded conformation compared to siRNA8, which exhibits a gradual decrease in Rg, suggesting higher compactness over time. (b) Root mean square deviation (RMSD) profiles indicate that both complexes achieve structural equilibrium, with siRNA8 showing marginally lower deviations, pointing to greater structural stability. (c) Root mean square fluctuation (RMSF) analysis shows comparable residue-level flexibility across both complexes, with elevated fluctuations primarily at terminal regions and surface-exposed loops. (d) Potential energy (PE) plots demonstrate energetically stable trajectories for both systems, with AGO2-siRNA8 maintaining a lower energy state throughout the simulation, indicative of more favorable binding and complex stabilization.