Molecular insights into PARP1 activation: structural dynamics of DNA, NAD+, and zinc‑mediated allosteric regulation.

Abstract

PARP1 serves as a crucial protein for preserving genomic stability, especially in BRCA1/2-mutant cancers that lack homologous recombination repair. In response to DNA breaks, PARP1 triggers an allosteric response that communicates to its catalytic domain, initiating the synthesis of poly (ADP-ribose) from NAD+. In this study, we used RMSF, hydrogen bond, hydrophobic, and MMPBSA analyses to construct an interface-specific map of PARP1 activation, revealing how DNA, Zn ions, and NAD+ act at each domain interface to drive activation. Our findings show that DNA initiates allosteric signaling, Zn ions and NAD+ strengthen activating interfaces and weaken inhibitory contacts. We found that PARP1 recognizes DNA damage through its ZF1, ZF3, and WGR domains with Zn ions at ZF1 stabilizing DNA binding. Allosteric contacts arose at the ZF1-ZF3 interface strengthened by DNA, ZF3-WGR interface reinforced by Zn ions, and ZF1-WGR interface stabilized by both DNA and Zn ions. This allosteric communication, alongside NAD+, induced a conformational shift in the HD domain enhancing WGR-HD and ZF3-HD interactions and destabilizing HD-ART. This movement, opened the catalytic pocket for NAD+ binding, promoting PARylation. Our study shows that full PARP1 activation requires the PARP1-DNA-Zn-NAD+ complex. These findings advance understanding of PARP1 and may aid development of targeted inhibitors for synthetic lethality-based cancer therapy.