Fig. 5: MD simulations of Rrp42-EL in the closed and open state.
From: 4D structural biology–quantitative dynamics in the eukaryotic RNA exosome complex
A Overlay of the representative structures from MD simulations of the completed Exo9 complex comparing the closed and open state of Rrp42-EL. The enlargement illustrates the distinct open (dark green) and closed (cyan) conformation of Rrp42-EL. Rrp41 is in red, Rrp45 in orange and Rrp42 in green. B Local structural dynamics of Rrp42-EL in the closed (cyan) and open (dark green) state revealed by the RMSD of the Cα carbons of only Rrp42-EL within the MD simulation. The RMSD is smoothed by a Bézier curve. C Interaction network analysis between the Exo9 subunits and Rrp42-EL in the closed (left) and open (right) conformation. Shown are the number of hydrogen bonds (HBO, violet) and van-der-Waals contacts (VDW, pink) between Rrp42-EL and the indicated subunits.
