Structure and Stability Insights into Tumour Suppressor p53 Evolutionary Related Proteins

Abstract

The p53 family of genes and their protein products, namely, p53, p63 and p73, have over one billion years of evolutionary history. Advances in computational biology and genomics are enabling studies of the complexities of the molecular evolution of p53 protein family to decipher the underpinnings of key biological conditions spanning from cancer through to various metabolic and developmental disorders and facilitate the design of personalised medicines. However, a complete understanding of the inherent nature of the thermodynamic and structural stability of the p53 protein family is still lacking. This is due, to a degree, to the lack of comprehensive structural information for a large number of homologous proteins and to an incomplete knowledge of the intrinsic factors responsible for their stability and how these might influence function. Here we investigate the thermal stability, secondary structure and folding properties of the DNA-binding domains (DBDs) of a range of proteins from the p53 family using biophysical methods. While the N- and the C-terminal domains of the p53 family show sequence diversity and are normally targets for post-translational modifications and alternative splicing, the central DBD is highly conserved. Together with data obtained from Molecular Dynamics simulations in solution and with structure based homology modelling, our results provide further insights into the molecular properties of evolutionary related p53 proteins. We identify some marked structural differences within the p53 family, which could account for the divergence in biological functions as well as the subtleties manifested in the oligomerization properties of this family.

Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds

“…The behavior is likely in part due to their DBDs being more stable compared to that of p5318. Consistent with this idea is the lower aggregation tendencies of enhanced stability p53 DBDs.…”

“…In the present study, long timescale MD simulations were employed in combination with experiments to compare the structural and dynamic properties of p53 family DBDs. The simulations are at least 100 times longer than similar comparative studies1842, providing considerably more time for conformational sampling, with all simulations performed in duplicate to verify consistency in the results.…”

Reactivation of mutant p53: Constraints on mechanism highlighted by principal component analysis of the DNA binding domain

“…However, the flexibility of the p53 DBS, and of the L1 loop in particular, has been shown to be essential for DNA binding specificity. Indeed a recent comparison of p53 stability and function in different species showed that the more stable p53 is, the less it interacts (DNA and protein‐protein), and p53‐DNA binding studies showed that p53 scans the DNA before binding specifically to it . First, p53 binds non‐specifically to the DNA, then it drifts along the DNA to find an optimal position on the promoter to which it binds specifically .…”

Intrinsically Disordered Proteins: Where Computation Meets Experiment

“…Tumor suppressor p53 has been dubbed the "guardian of the genome" due to its central role in cell cycle regulation in response to stress [102,103]. Once p53 is activated by cellular stress signals, it binds DNA to regulate transcription of genes involved in stress response pathways, including cell cycle arrest, senescence, apoptosis, and metabolism [104].…”