Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
Figure 4
Atomistic DRP folding pathways, projected on the plane selected by the total RMSD to native and by the RMSD to native of the -sheet.
Panels (A) and (B) refer respectively to successful and unsuccessful folding trajectories. The diamonds in panel (A) mark the collective coordinates at the time of knot formation. The scale on the left corresponds to the logarithm of the number of times a given spot is visited by the DRP trajectories, in analogy with free-energy landscape plots.