The p53 tetramer shows an induced-fit interaction of the C-terminal domain with the DNA-binding domain

Abstract

The Trp53 gene is the most frequently mutated gene in all human cancers. Its protein product p53 is a very powerful transcription factor that can activate different biochemical pathways and affect the regulation of metabolism, senescence, DNA damage response, cell cycle and cell death. The understanding of its function at the molecular level could be of pivotal relevance for therapy. Investigation of long-range intra- and interdomain communications in the p53 tetramer–DNA complex was performed by means of an atomistic model that included the tetramerization helices in the C-terminal domain, the DNA-binding domains and a consensus DNA-binding site of 18 base pairs. Nonsymmetric dynamics are illustrated in the four DNA-binding domains, with loop L1 switching from inward to outward conformations with respect to the DNA major groove. Direct intra- and intermonomeric long-range communications between the tetramerization and DNA-binding domains are noted. These long-distance conformational changes link the C terminus with the DNA-binding domain and provide a biophysical rationale for the reported functional regulation of the p53 C-terminal region. A fine characterization of the DNA deformation caused by p53 binding is obtained, with ‘static' deformations always present and measured by the slide parameter in the central thymine–adenine base pairs; we also detect ‘dynamic' deformations switched on and off by particular p53 tetrameric conformations and measured by the roll and twist parameters in the same base pairs. These different conformations can indeed modulate the electrostatic potential isosurfaces of the whole p53–DNA complex. These results provide a molecular/biophysical understanding of the evident role of the C terminus in post-translational modification that regulates the transcriptional function of p53. Furthermore, the unstructured C terminus is able to facilitate contacts between the core DNA-binding domains of the tetramer.

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

“…2a,b) The best correlation value we obtained was R=0.84 between our ensemble-averaged density map of the p21-RE-bound system and the class III EM map. The closest all-atom model to a full-length p53 tetramer generated in a very recent study included only the residues between 91 and 359 lacking the NTD and CTD regions and was only simulated for approximately 100 ns in total 33 . In our longer and more structurally comprehensive simulations, the TET domains moved about 40 Å toward the DBD center of mass, and the extended CTDs became more compact and approached the DNA, while the NTDs remained mostly in extended form and very dynamic throughout simulations.…”

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

“…p53 structural plasticity can also be exploited to design inhibitory small molecules (92). Conformational changes may occur not only at the interface for DNA binding (40,41,43) but also at distal sites, such as the interface between the p53 DBD core and the disordered N-terminal region (39,74,93) or the C-terminal domain (44). Until now, many MD studies of p53 have focused on conformational changes in the immediate proximity of the DNA binding site (40–43), instead of changes that might potentially occur at distal sites.…”

“…Even though the p53 DBD does not appear to undergo a large conformational change upon binding with cofactors, a slow conformational exchange process in the proximity of the disordered N-terminal region has been identified by NMR experiments on the free protein (39). Previous studies focused mostly on local changes that occur at the DNA-binding interface and L1 loop (40–44), and much less is known about conformational changes at more distal sites (45). …”

The Tail That Wags the Dog: How the Disordered C-Terminal Domain Controls the Transcriptional Activities of the p53 Tumor-Suppressor Protein

“…At least in part, the CTD does this by promoting structural changes within the individual DBDs and increasing cooperative interactions between them when bound to cognate DNA. Correspondingly (and contrary to the results of an early biophysical analysis of full-length and CTD-deleted p53 [51]), new data obtained using molecular dynamics (MD) suggest that the CTD may promote conformational changes within the p53 tetramer through long-range interactions of the DBD of p53 when bound to cognate DNA [52]. …”

“…p53 is an extremely complex protein. While biochemical, structural, and MD studies suggest that interaction of p53 with DNA is accompanied by multiple conformational changes that take place within the individual domains [61], as well as within the tetramer of p53 [44,52], fitting these data into current structural models of the p53-DNA binary complex is daunting. Thus, obtaining molecular insight into the structural details of p53-DNA interactions calls for complex and nontrivial approaches.…”