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

Abstract

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.