Full-length p53 tetramer bound to DNA and its quaternary dynamics

Abstract

p53 is a major tumor suppressor that is mutated and inactivated in about 50% of all human cancers. Thus, reactivation of mutant p53 using small-molecules has been a long sought-after anti-cancer therapeutic strategy. Full structural characterization of the full-length oligomeric p53 is challenging because of its complex architecture and multiple highly flexible regions. To explore p53 structural dynamics, here we developed a series of atomistic integrative models with available crystal structures of the full-length p53 (fl-p53) tetramer bound to three different DNA sequences: a p21 response element, a puma response element, and a non-specific DNA sequence. Explicitly solvated, all-atom molecular dynamics simulations of the three complexes (totaling nearly 1 μs of aggregate simulation time) yield final structures consistent with electron microscopy maps and, for the first time, show the direct interactions of the p53 C-terminal with DNA. Through a collective principal component analysis, we identify sequence-dependent differential quaternary binding modes of the p53 tetramer interfacing with DNA. Additionally, L1 loop dynamics of fl-p53 in the presence of DNA is revealed, and druggable pockets of p53 are identified via solvent mapping in order to aid future drug-discovery studies.

Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain

“…sought to probe the full-length protein by solution methods such as fluorescence spectroscopy, cross-linking mass spectrometry, 13 C-methyl NMR, and computational modeling (25,28,36,(38)(39)(40)(41)(42). While these studies have provided important details, they have generally relied on region-specific probes and therefore were resolution-limited.…”

Dynamics of p53: A Master Decider of Cell Fate

“…In addition, the effects of p53 mutants on p53 dynamics can modulate the efficacy of p53-based cancer therapy. It has been found that in tumor cells, most p53 mutant proteins bear a surface cleft that mediates its physical interaction with Mdm2, thereby leading to p53 degradation [ 63 , 64 ]. It appears that for the treatment of such a type of tumors, a therapy that increases the p53 level by extending the half-life of p53 should be a priority before a p53 dynamics-based therapy can be considered.…”

Salvation of the fallen angel: Reactivating mutant p53

“…Phosphorylation of p53 releases it from MDM2, a negative regulator of p53 (Blackford & Jackson, ), and allows p53 to bind to p300 and PCAF (Figure ), the acetyltransferases that acetylate p53, leading to exposure of the DNA‐binding domain (DBD; Jin, Zeng, Dai, Yang, & Lu, ; L. Liu et al, ). After phosphorylation and acetylation, p53 is activated and translocates into the nucleus, assembles into a tetramer through the oligomerization domain (OD), and binds to the target DNA sequence through the DBD (Figure ; Demir, Ieong, & Amaro, ; Friedman, Chen, Bargonetti, & Prives, ; Kitayner et al, ). The protein–protein interaction within the p53 tetramer not only stabilizes the structure of DBD but also supports the p53–DNA interaction, which “locks” the target DNA sequence (Kitayner et al, ).…”

“…Therefore, mutp53 have traditionally been regarded as “undruggable” (Weissmueller et al, ). However, modern techniques, including structural biology, protein engineering, and computational simulation, are gradually revealing the conformation of p53 (Demir et al, ). Recent attempts at reactivation of p53 that combined virtual screening, rational drug design, and cell‐based large‐scale drug screening have produced a number of mutp53 reactivators (Ahire, Das, Mishra, Kulkarni, & Ackland, ; Parrales & Iwakuma, ).…”