Water Leakage Pathway Leads to Internal Hydration of the p53 Core Domain

Abstract

The gene encoding the p53 tumor suppressor protein is the most frequently mutated oncogene in cancer patients; yet, generalized strategies for rescuing the function of different p53 mutants remain elusive. This work investigates factors that may contribute to the low inherent stability of the wild-type p53 core domain (p53C) and structurally compromised Y220C mutant. Pressure-induced unfolding of p53C was compared to p63C, the p53 family member with the highest stability, the engineered superstable p53C hexamutant (p53C HM), and lower stability p53C Y220C cancerassociated mutant. The following pressure unfolding values (P50% bar) were obtained: p53C 3346, p53C Y220C 2217, p53C HM 3943, and p63C 4326. Molecular dynamics (MD) simulations revealed that p53C Y220C was most prone to water infiltration, followed by p53C, whereas the interiors of p53C HM and p63C remained comparably dry. A strong correlation (r 2 = 0.92) between P50% and extent of interior hydration was observed. The pathways of individual water molecule entry and exit were mapped and analyzed, revealing a common route preserved across the p53 family involving a previously reported pocket, along with a novel surface cleft, both of which appear to be targetable by small molecules. Potential determinants of propensity to water incursion were assessed, including backbone hydrogen bond protection and combined sequence and structure similarity. Collectively, our results indicate that p53C has an intrinsic susceptibility to water leakage, which is exacerbated in a structural class mutant, suggesting that there may be a common avenue for rescuing p53 function.

Targeting Biomolecular Condensation and Protein Aggregation against Cancer

“…These molecules have progressed to preclinical or clinical trials (CTs). More recent studies using hydrostatic pressure and molecular dynamics simulations have identified dehydrons on the surface of the p53 DBD, i.e., vulnerable sites related to p53 misfolding and aggregation. , These vulnerable regions represent novel targetable sites to stabilize and avoid p53 misfolding.…”

Oncogenic R248W mutation induced conformational perturbation of the p53 core domain and the structural protection by proteomimetic amyloid inhibitor ADH-6

“…100 There are also studies that have underscored the impact of water leakage into the hydrophobic core on p53C. 67 In this context, we tried to investigate how the cavity-enlarging shift of the β-hairpin S2–S2′ affects the hydrophobic core, thereby promoting the reduction in thermal stability and the increase in aggregation propensity of R248W p53C.…”

“…Moreover, ADH-6 inhibits the aggregation of R248W p53 in human cancer cells, restoring the transcriptional activity of p53, leading to cell cycle arrest and apoptosis. 19 Molecular dynamics (MD) simulations have been extensively employed to investigate the conformational properties of different domains of the p53 protein and its mutants, 41,42,[63][64][65][66][67][68][69] as well as the interactions between p53 protein domains and small molecules, 70 short peptides, 71 and other proteins. [72][73][74][75] In spite of experimental and computational studies, it remains mostly unknown how the R248W mutation induces destabilization of R248W p53C and how ADH-6 stabilizes R248W p53C.…”