The substitutions G245C and G245D in the Zn²⁺-binding pocket of the p53 protein result in differences of conformational flexibility of the DNA-binding domain

Transcription activation of the proapoptotic target genes is a means by which the p53 protein implements its function of tumor suppression. Zn²⁺ is a known regulator of p53 binding to the target genes. We have previously obtained an evidence that amino acid substitutions in the p53 Zn²⁺-binding pocket can presumably exert an influence on Zn²⁺ position in the Zn²⁺-p53 complex and thereby affect p53 binding to DNA. With these background considerations, our aim was to estimate the effect of the putative changes in the Zn²⁺ position in its binding pocket due to the G245C and G245D substitutions on the conformation of the p53 DNA-binding motif. Statistical analysis of the molecular dynamics (MD) trajectories of the mutant p53-Zn²⁺ complexes was used to detect significant deviations in conformation of the mutant p53 forms. MD simulations demonstrated that (1) the two substitutions in the Zn²⁺-binding pocket caused changes in the conformation of the p53 DNA-binding motif, as compared with the wild-type (WT) p53; (2) binding of Zn²⁺ to the p53 mutant forms reduced the effect of the substitutions on conformational change; and (3) Zn²⁺ binding in the normal position compensated the effect of the mutations on the conformation in comparison to the altered Zn²⁺ position.