In silico simulations reveal molecular mechanism of uranyl ion toxicity towards DNA-binding domain of PARP-1 protein

The molecular toxicity of uranyl ion (UO22+) in living cells is mainly conditioned by its high affinity to both native and potential metal-binding sites frequently occurring in biomolecules structure. Recent advances in computational and experimental research shed light on the structural properties and functional impacts of uranyl binding to proteins, organic ligands, nucleic acids and their complexes. In the present work, we report the results of the theoretical investigation of the uranyl-mediated loss of DNA-binding activity of PARP-1, eukaryotic enzyme that participates in DNA reparation, cell differentiation, induction of inflammation, etc. Latest experimental studies showed that uranyl ion directly interacts with its DNA-binding subdomains - zinc fingers Zn1 and Zn2, - and changes their tertiary structure. Here, we propose an atomistic mechanism underlying this process and compute the free energy change along the suggested pathway to prove its relevance. According to the results of our QM/MM simulations of Zn2-UO22+ complex, uranyl ion replaces zinc in its native binding site, but the corresponding state is destroyed because of the following spontaneous internal hydrolysis of the U-Cys162 coordination bond. Although the enthalpy of hydrolysis is +2.8 kcal/mol, the final value of the free energy of the reaction constitutes -0.6 kcal/mol, due to structure loosening evidenced by solvation and configuration thermodynamic properties calculated using GIST- and MIST-based trajectory processing techniques. The subsequent reorganization of the binding site includes association of uranyl ion with the Glu190/Asp191 acidic cluster and significant perturbations in the domains tertiary structure, which further decreases the free energy of the non-functional state by 6.8 kcal/mol. The disruption of the DNA-binding interface revealed in our computational simulations is consistent with previous experimental findings and appears to be associated with the loss of the Zn2 affinity for nucleic acids.