The substitutions G245C and G245D in the Zn(2+)-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. Zn(2+) is a known regulator of p53 binding to the target genes. We have previously obtained an evidence that amino acid substitutions in the p53 Zn(2+)-binding pocket can presumably exert an influence on Zn(2+) position in the Zn(2+)-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 Zn(2+) 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-Zn(2+) complexes was used to detect significant deviations in conformation of the mutant p53 forms. MD simulations demonstrated that (1) the two substitutions in the Zn(2+)-binding pocket caused changes in the conformation of the p53 DNA-binding motif, as compared with the wild-type (WT) p53; (2) binding of Zn(2+) to the p53 mutant forms reduced the effect of the substitutions on conformational change; and (3) Zn(2+) binding in the normal position compensated the effect of the mutations on the conformation in comparison to the altered Zn(2+) position.

[Phylogenetic analysis of the family of p53].

A relationship between the functional significance of individual amino acid residues of the p53 protein, their positions in the protein structure, and the mode of evolution of the codons corresponding to these residues has been established. A phylogenetic analysis of the coding sequences of the gene of p53 from 32 vertebrate species has been performed. It was found that those codons undergo selection that affect the efficiency of binding of protein p53 as a transcription factor. It was shown that the frequency of occurrence of generative mutations maintaining the normal function of the protein in conservative codons differs statistically significantly from the frequency of occurrence in the same codons of mutations with the effects of loss and acquisition of the function, and the negatively dominant effect. The phylogenetic analysis and molecular dynamics modeling made it possible to obtain evidence for the functional significance of the G245 residue for which the appearance of the binding site for Zn2+ in the case of the substitution G245G has previously been proposed.