Effects of a cancer-associated mutation and multiple serine phosphorylation on poly(ADP-ribose) polymerase 2

Poly(ADP-ribose) polymerase 2 (PARP2) plays a crucial role in DNA repair. A common single-nucleotide polymorphism (SNP) in the PARP2 gene, rs3093921, has been associated with pancreatic cancer and marginal zone lymphoma. This SNP results in a missense mutation, D235G, in the PARP2 protein. PARP2 is also reported to undergo posttranslational modifications (PTMs), particularly phosphorylation at serine residues 226, 232, and 353. The C-terminal region of PARP2 includes the Trp-Gly-Arg (WGR) domain, the ADP-ribosyl transferase (ART) domain, and the helical subdomain (HD). The latter two, spanning residues 220-583, comprise the catalytic region of PARP2. The DNA-induced enzymatic activation of PARP2 is regulated by local destabilization of the HD domain. We used molecular dynamics simulations to investigate the impact of these three PTMs on both the wild-type (WT) and the mutant (D235G) forms of PARP2. Our simulations suggest that the mutation leads to a change in structure and residual flexibility in specific regions of the HD domain compared with the WT. The presence of the PTMs also shows altered structure of the HD domain, although the residual flexibility remains unchanged compared with the unmodified WT. This is further supported by the destabilizing interactions between the mutation site and the HD domain observed in the presence of both the mutation and the PTMs. Importantly, our results suggest that the three PTMs mitigate the changes in structure and residual flexibility caused by the mutation, helping the PTM-modified mutant protein retain WT-like features. We observe that, while the PTMs alter the dominant mode of motion in the native protein, this shift is not observed in the mutant, further indicating that PTMs mitigate the structural and dynamic consequences of the mutation, preserving WT-like behavior. The mutation and PTMs cause notable changes in correlated motions within the WGR and ART domains, with the PTM-modified mutant structure showing the strongest correlations. Interestingly, a similar trend is observed for anticorrelated motions, particularly between the WGR and ART domains, where the PTM-modified mutant structure again exhibits the highest level of anticorrelation. Additionally the mutation in PARP2 markedly weakens interdomain interactions between the HD and ART domains, as well as between the HD and WGR domains. By contrast, the PTMs alone show no change on the HD-ART interaction, although they weaken the HD-WGR interaction. For the PTM-modified mutant structure the HD-ART interaction remains disrupted compared with the WT, but the extent of disruption is less than that caused by the mutation alone-suggesting a partial compensatory effect of the PTMs. Additionally, the HD-WGR interaction remains consistently weakened in all modified systems.