A new insight into protein-protein interactions and the effect of conformational alterations in PCNA

The sliding clamp proteins are present in almost all forms of life and participate in various fundamental processes. Many of these proteins accommodate a conserved sequence that interacts with the hydrophobic groove on sliding clamps. The conserved sequence on proteins is known as the PCNA-interacting protein box, and the hydrophobic groove of PCNA contains regions of the inter-domain connecting loop, the central loop, and amino acids from the C-terminal tail of PCNA. We performed molecular dynamics simulation studies (1.0 μs) to analyze the structural changes at the atomic level in native, C22Y, and C81R mutant PCNA. Our study revealed significant changes at sites responsible for a functional trimeric form of PCNA. This study also unveils the dynamic behavior of IDCL, central loop, and the C-terminal tail, which are essential regions for protein binding with PCNA and also sheds light on the effect of mutations on binding with the Cdc9 peptide. The observation of Cdc9 peptide complexed with native and mutants (C22Y and C81R) structures possibly reveals the mechanism by which PCNA recruits different proteins required for various biological processes and also highlights the importance of dynamic behavior of key regions involved in PCNA protein-protein interactions.