Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, Moscow 121205, Russia.
Biomolecules. 2023 Aug 20;13(8):1269. doi: 10.3390/biom13081269.
The molecular toxicity of the uranyl ion (UO) in living cells is primarily determined by its high affinity to both native and potential metal-binding sites that commonly occur in the structure of biomolecules. Recent advances in computational and experimental research have 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 computational investigation of the uranyl-mediated loss of DNA-binding activity of PARP-1, a eukaryotic enzyme that participates in DNA repair, cell differentiation, and the induction of inflammation. The latest experimental studies have shown that the uranyl ion directly interacts with its DNA-binding subdomains, zinc fingers Zn1 and Zn2, and alters their tertiary structure. Here, we propose an atomistic mechanism underlying this process and compute the free energy change along the suggested pathway. Our Quantum Mechanics/Molecular Mechanics (QM/MM) simulations of the Zn2-UO complex indicate that the uranyl ion replaces zinc in its native binding site. However, the resulting state is destroyed due to the spontaneous internal hydrolysis of the U-Cys162 coordination bond. Despite the enthalpy of hydrolysis being +2.8 kcal/mol, the overall reaction free energy change is -0.6 kcal/mol, which is attributed to the loss of domain's native tertiary structure originally maintained by a zinc ion. The subsequent reorganization of the binding site includes the association of the uranyl ion with the Glu190/Asp191 acidic cluster and significant perturbations in the domain's tertiary structure driven by a further decrease in the free energy by 6.8 kcal/mol. The disruption of the DNA-binding interface revealed in our study is consistent with previous experimental findings and explains the loss of PARP-like zinc fingers' affinity for nucleic acids.
铀酰离子（UO）在活细胞中的分子毒性主要取决于其对天然和潜在金属结合位点的高亲和力，这些结合位点通常存在于生物分子的结构中。最近在计算和实验研究方面的进展揭示了铀酰与蛋白质、有机配体、核酸及其复合物结合的结构特性和功能影响。在本工作中，我们报告了计算研究的结果，该研究涉及铀酰介导的 PARP-1 失去 DNA 结合活性，PARP-1 是一种参与 DNA 修复、细胞分化和炎症诱导的真核酶。最新的实验研究表明，铀酰离子直接与它的 DNA 结合亚结构域，锌指 Zn1 和 Zn2 相互作用，并改变它们的三级结构。在这里，我们提出了一个原子机制来解释这个过程，并计算了沿着建议途径的自由能变化。我们对 Zn2-UO 配合物的量子力学/分子力学（QM/MM）模拟表明，铀酰离子取代了其天然结合位点中的锌。然而，由于 U-Cys162 配位键的自发内部水解，导致生成的状态被破坏。尽管水解的焓为+2.8 kcal/mol，但整个反应的自由能变化为-0.6 kcal/mol，这归因于最初由锌离子维持的结构域的天然三级结构的丧失。随后，结合位点的重新组织包括铀酰离子与 Glu190/Asp191 酸性簇的缔合，以及由于自由能进一步降低 6.8 kcal/mol，导致结构域的三级结构发生显著扰动。我们的研究揭示了 DNA 结合界面的破坏与之前的实验发现一致，并解释了 PARP 样锌指对核酸亲和力的丧失。
