Structural and thermodynamic analysis of human PCNA bound to peptides derived from DNA polymerase-delta p66-subunit and flap endonuclease-1 (FEN1) proteins
Doctor of Philosophy
DNA replication and repair requires the coordination of multiple proteins at the replication fork. Among the proteins found at the replisome, hPCNA (h&barbelow;uman P&barbelow;roliferating C&barbelow;ell N&barbelow;uclear A&barbelow;ntigen) is essential for many of the protein-protein interactions required for replication and repair processes. hPCNA is a member of the sliding clamp family of DNA replication processivity factors. Recent studies have shown that hPCNA is able to make specific protein-protein interactions to a wide range of DNA replication, recombination and repair proteins through a small peptide motif termed the PCNA-Interacting-Protein or "PIP-Box." The structures have been solved of hPCNA bound to PIP-Box containing peptides derived from the p66-subunit of the human replicative DNA polymerase delta at 2.6 A resolution and of the human flap endonuclease (FEN1) at 1.85 A resolution. Both structures indicate that the pol-delta p66 subunit and FEN1 endonuclease peptides bind at a site previously shown to bind a PIP-Box containing peptide from the cdk-inhibitor p21 (CIP1). Both interacting peptides adopt a similar elongated overall conformation with a central 310 helix that plugs into a hydrophobic cavity of hPCNA. Isothermal titration calorimetry studies indicate that PIP-box containing peptides from the p66-subunit of the pol-delta holoenzyme and FEN1 bind hPCNA less tightly, 15.6 muM and 59.9 muM respectively, than p21-derived peptide (82.6 nM). Although it is likely that hPCNA may make additional interactions to the p66 and FEN1 proteins, these structural and calorimetry studies indicate that interactions made through the PIP-box motif can account for much of the hPCNA specificity for these proteins observed in vivo. These studies support a model where hPCNA uses a conserved set of protein-protein contacts made through the PIP-Box to attenuate binding to the proteins of DNA replication, recombination and repair, and that these proteins compete for binding through the same site on hPCNA. The significance of structural studies within the human PCNA system is underscored by the potential antibiotic and cancer drug targets on the PIP-box binding surface.
Molecular biology; Biochemistry; Biophysics