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High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds
William C Ho1, Cheng Luo, Kehao Zhao
1The Wistar Institute, Philadelphia, PA 19104, USA.
Abstract:
The p53 transcriptional regulator is the most frequently mutated protein in human cancers and the majority of tumor-derived p53 mutations map to the central DNA-binding core domain, with a subset of these mutations resulting in reduced p53 stability. Here, the 1.55 A crystal structure of the mouse p53 core domain with a molecule of tris(hydroxymethyl)aminomethane (Tris) bound through multiple hydrogen bonds to a region of p53 shown to be important for repair of a subset of tumor-derived p53-stability mutations is reported. Consistent with the hypothesis that Tris binding stabilizes the p53 core domain, equilibrium denaturation experiments are presented that demonstrate that Tris binding increases the thermodynamic stability of the mouse p53 core domain by 3.1 kJ mol(-1) and molecular-dynamic simulations are presented revealing an overall reduction in root-mean-square deviations of the core domain of 0.7 A when Tris is bound. It is also shown that these crystals of the p53 core domain are suitable for the multiple-solvent crystal structure approach to identify other potential binding sites for possible core-domain stabilization compounds. Analysis of the residue-specific temperature factors of the high-resolution core-domain structure, coupled with a comparison with other core-domain structures, also reveals that the L1, H1-S5 and S7-S8 core-domain loops, also shown to mediate various p53 activities, harbor inherent flexibility, suggesting that these regions might be targets for other p53-stabilizing compounds. Together, these studies provide a molecular scaffold for the structure-based design of p53-stabilization compounds for development as possible therapeutic agents.
Insights
Tris binding stabilizes the mouse p53 core domain, increasing its thermodynamic stability. This discovery provides a molecular basis for designing novel p53-stabilizing therapeutic agents for cancer treatment.
Area of Science:
- Structural Biology
- Molecular Biophysics
- Cancer Therapeutics
Background:
- The p53 protein is a critical transcriptional regulator frequently mutated in human cancers.
- Many tumor-derived p53 mutations occur in the DNA-binding core domain, often reducing protein stability.
- Stabilizing the p53 core domain is a potential therapeutic strategy for cancer.
Purpose of the Study:
- To determine the crystal structure of the mouse p53 core domain bound to tris(hydroxymethyl)aminomethane (Tris).
- To investigate the stabilizing effect of Tris on the p53 core domain.
- To identify potential targets for developing p53-stabilizing compounds.
Main Methods:
- 1.55 Å crystal structure determination of the mouse p53 core domain with Tris.
- Equilibrium denaturation experiments to assess thermodynamic stability.
- Molecular-dynamic simulations to analyze structural changes upon Tris binding.
- Analysis of residue-specific temperature factors and comparison with other structures.
Main Results:
- Tris binds to a critical region of the p53 core domain via multiple hydrogen bonds.
- Tris binding increases the thermodynamic stability of the mouse p53 core domain by 3.1 kJ mol⁻¹.
- Molecular-dynamic simulations show a reduction in root-mean-square deviations, indicating increased stability.
- Flexible regions (L1, H1-S5, S7-S8 loops) within the p53 core domain are identified as potential targets for stabilization.
Conclusions:
- Tris binding effectively stabilizes the p53 core domain, offering a molecular basis for therapeutic intervention.
- The study provides a structural scaffold for the rational design of novel p53-stabilizing compounds.
- These findings pave the way for developing new therapeutic agents targeting p53 stabilization in cancer.
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