The eukaryotic proliferating cell nuclear antigen (PCNA) is a homotrimeric sliding clamp that encircles DNA and tethers the polymerase at the site of replication. Loading PCNA onto DNA requires that the protein must interconvert between a closed planar ring and an open conformation that permits strand passage into its central channel. We have investigated ring opening using equilibrium and non-equilibrium molecular dynamics simulations. Removal of one subunit relaxes the closure constraint on the ring and allows for fluctuations at the dimer interface. Equilibrium simulations demonstrate that the dimer can relax into conformations consistent with both right- and left-handed spirals. To further investigate the energetics of ring opening, we have begun to map out the minimum free energy path associated with ring opening for the full trimer using the string method in collective variables. The results of these simulations will allow us to predict the conformation of the open ring and trace out the mechanism of ring opening.
University of California, Berkeley