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

Abstract

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.

Keywords:

• p53 protein
• molecular dynamics
• conformational flexibility
• DNA binding domain (DBD)
• binding site

Acknowledgments

This work was supported in part by the Ministry of Science and Education of the Russian Federation (Contracts No. P857, No. P721, No. 14.740.11.0001), the program of the basic research of the Presidium of the Russian Academy of Sciences (B.26.29 Biological diversity, A.II.6 Molecular and cell biology), project 29 Bioinformatics of genetic diversity: study of influence of mutations on the molecular-genetic systems of organisms, the program of Russian Academy of Science No. 19. This work was also supported by grants from the Russian Foundation for Basic Research: 11-04-92712-IND; 11-04-01221-a Study of the MD control of the inherited neurosensory forms of hypoacusis/deafness and analysis of their prevalence in populations of Siberia; 11-04-01771 – a Study of the adaptation of the micro-organism proteomes to elevated environmental pressures and EU-FP7 SYSPATHO project No. 260429, Indo-Russia ILTP grant from the Department of Science and Technology, Govt. of India and Russian Academy of Sciences, Russia. The authors are grateful to Anna Fadeeva for translating this manuscript from Russian into English.