Molecular dynamics simulations reveal R399Q mutation disrupts XRCC1-polβ interaction, potentially impairing DNA base excision repair pathway.

Abstract

Mutations in XRCC1 can disrupt essential protein-protein interactions required for DNA base excision repair, potentially leading to genomic instability and increased cancer risk. This study employs large-scale molecular dynamics simulations to investigate the structural and functional consequences of the R399Q mutation on interactions with DNA ligase IIIα and DNA polymerase β. The results reveal that while the mutant protein retains a stable interaction with DNA ligase IIIα, key residues such as Gly 511, Glu 538, Arg 564, Thr 567 and Ala 568, which form critical hydrogen bonds, exhibit subtle rearrangements. In contrast, binding to DNA polymerase β is significantly destabilized, disrupting key interactions involving Glu 85, Ser 92, Arg 109 and Gly 556. Free energy calculations confirm a substantial reduction in binding affinity between the mutant protein and DNA polymerase β, suggesting an impaired repair efficiency. Unlike previous studies that relied on static structural models or biochemical characterizations, this research provides dynamic, atomic-level insights into how the mutation alters protein stability and interactions over biologically relevant timescales. These findings reconcile conflicting experimental observations and establish a computational framework for understanding mutation-driven defects in DNA repair. Interestingly, the data generated by these extensive simulations resemble empirical findings regarding XRCC1's interactions with BER enzymes. The study thus provides valuable insights into how the R399Q mutation impairs XRCC1's interactions with key DNA repair enzymes, potentially leading to defects in the DNA repair pathway and offering a computational perspective that aligns with experimental observations.