Figure 3.

Structure prediction with mrdna. (A) Comparison of the structural models obtained through an mrdna simulation and cryo-EM reconstruction (EMD-2210) of the ‘pointer’ structure (52). The top row depicts the simulated and experimental structures as isosurfaces of the CG bead (blue, 1 bp/ų isovalue) and electron (white, 0.08 isovalue) densities, respectively. The bottom row compares the simulated (blue) and experimental (red) all-atom models. In the top row, simulated structural fluctuations are visualized using a semi-transparent surface showing the average density of CG beads during the final 600 ns of a 5-bp/bead simulation. Note that some helices along the periphery of the structure were not resolved in the cryo-EM model (52). (B) RMSD of the center of mass of each base pair in the simulated pointer structure from those of the cryo-EM-derived atomic structure (52) at 5 bp/bead (blue) and 2 beads/bp (orange and green) resolutions. For each resolution, an ensemble of sixteen simulations was performed, the RMSD for each trajectory was computed every 2 ns, and the ensemble of RMSD values was averaged at each moment in time to provide the solid line. The shaded regions around each solid line shows the corresponding standard deviation of the RMSD. The dashed lines depict the RMSD between the ensemble’s average structure and the cryo-EM-derived structure. For all RMSD calculations, the splines traced through the instantaneous configurations were used to determine the position of each base pair. The configurations of the 5-bp/bead ensemble after 400-ns were used to initialize an ensemble of 2-beads/bp simulations (green). (C–F) Comparison of the mrdna (blue, 1 bp/ų isovalue) and cryo-EM (white, 0.02 isovalue) models of the objects designed and characterized by the Dietz group (28): v-brick structures without (C; EMD-3828) and with (D; EMD-3828) twist correction, the connector block (E; EMD-3827) and the triangular vertex (F; EMD-3826).