Conformational analysis of sliding clamps in solution demonstrates that tertiary structure does not correlate with structural dynamics

Abstract

During DNA replication DNA polymerases are able to catalyze the polymerization of thousands of DNA bases each second without dissociating from DNA. This remarkable processivity is attributed to sliding clamps, which are structurally conserved proteins that encircle DNA and tether the DNA polymerase to the DNA template. Although the three-dimensional structures of these ring-shaped proteins have been well-characterized, less is known about their conformational dynamics in solution. We have probed the dynamics of these proteins in solution using hydrogen exchange mass spectrometry and show that sliding clamps from different species show a wide range of dynamic behavior despite highly similar three-dimensional structures. Several of the clamps undergo local unfolding events with half-lives ranging from five minutes to several hours. We have also analyzed the thermal stability of these proteins and show that sliding clamps with relatively flexible backbones have relatively low thermal stability. Our observations indicate that human proliferating cellular nuclear antigen (PCNA) is less stable and more dynamic than PCNA from yeast, especially in the region of the binding site for interacting protein partners and the subunit interface.