The Mechanical Properties of the Sliding DNA Clamp PCNA

Sliding clamps are toroidal proteins that encircle DNA and act as a mobile platform on which components of the DNA replication and repair machinery bind. While trimeric sliding clamps assemble as stable planar rings, they must disrupt one of their subunit-subunit interfaces in order to thread duplex DNA into their central pore. We have performed molecular dynamics simulations of dimeric PCNA in order to examine the flexibility of the molecule once the closure constraint has been removed. We find that PCNA is able to spontaneously adopt a large ensemble of conformations at equilibrium, and these motions can be described with a simpler coarse-grained elastic model.