Predicting the coordination geometry for Mg2+ in the p53 DNA-binding domain: insights from computational studies

Zn2+ in the tumor-suppressor protein p53 DNA-binding domain (DBD) is essential for its structural stability and DNA-binding specificity. Mg2+ has also been recently reported to bind to the p53DBD and influence its DNA-binding activity. In this contribution, the binding geometry of Mg2+ in the p53DBD and the mechanism of how Mg2+ affects its DNA-binding activity were investigated using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Various possible coordination geometries of Mg2+ binding to histidines (His), cysteines (Cys), and water molecules were studied at the B3LYP/6-311+g** level of theory. The protonation state of Cys and the environment were taken into account to explore the factors governing the coordination geometry. The free energy of the reaction to form the Mg2+ complexes was estimated, suggesting that the favorable binding mode changes from a four- to six-coordinated geometry as the number of the protonated Cys increases. Furthermore, MD simulations were employed to explore the binding modes of Mg2+ in the active site of the p53DBD. The simulation results of the Mg2+ system and the native Zn2+ system show that the binding affinity of Mg2+to the p53DBD is weaker than that of Zn2+, in agreement with the DFT calculation results and experiments. In addition, the two metal ions are found to make a significant contribution to maintain a favorable orientation for Arg248 to interact with putative DNA, which is critically important to the sequence-specific DNA-binding activity of the p53DBD. However, the effect of Mg2+ is less marked. Additionally, analysis of the natural bond orbital (NBO) charge transfer reveals that Mg2+ has a higher net positive charge than Zn2+, leading to a stronger electrostatic attractive interaction between Mg2+ and putative DNA. This may partly explain the higher sequence-independent DNA-binding affinity of p53DBD–Mg2+ compared to p53DBD–Zn2+ observed in experiment.