Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
Fig 3
Binary docking models undergo substantial structural re-arrangement towards binary crystal during MD simulations.
(A) Projections of MD trajectories of three representative successful docking models. The rationale behind the choice of representative docked conformations is simply to select conformations that contain different fractions of native contacts (i.e. the lowest: 27.1%; median: 35.4%, and highest: 50.0%). (B) Upper panel: interface-RMSD (iRMSD) of models against binary crystal structure. Lower panel: fraction of native contacts (fnat) between hAgo2 and miRNA of the models. (C) Structural comparison between the binary crystal structure (left) and a representative model from MD (right) with hAgo2 colored in grey and miRNA in red.