Figure 3.

In-plane and out-of-plane motions of PCNA. (A) In-plane and (B) out-of-plane order parameters from dimer simulation 1 were calculated at 40-ps intervals. PCNA relaxes in the in-plane direction, while simultaneously diverging from the planar conformation found in the crystal structure of the closed trimer. In panel B, positive values of the order parameter correspond to conformations consistent with a right-handed spiral, while negative values correspond to left-handed spirals. Over the course of the 92-ns simulation, PCNA takes on conformations consistent with both right- and left-handed spirals.