Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

Abstract

Protein p53 is a transcription factor crucial for cell cycle and genome integrity. It is able to induce both cell arrest when DNA is damaged and the expression of DNA repair machinery. When the damage is irreversible, it triggers apoptosis. Indeed, the protein, which is a homotetramer, is mutated in most human cancers. For instance, the inherited mutation p53-R337H results in destabilization of the tetramer and, consequently, leads to an organism prone to tumor setup. We describe herein a rational designed molecule capable of holding together the four monomers of the mutated p53-R337H protein, recovering the tetramer integrity as in the wild-type structure. Two ligand molecules, based on a conical calix[4]arene with four cationic guanidiniomethyl groups at the wider edge (upper rim) and hydrophobic loops at the narrower edge (lower rim), fit nicely and cooperatively into the hydrophobic clefts between two of the monomers at each side of the protein and keep the tetrameric structure, like molecular templates, by both ion-pair and hydrophobic interactions. We found a good agreement between the structure of the complex and the nature of the interactions involved by a combination of theory (molecular dynamics) and experiments (circular dichroism, differential scanning calorimetry and 1 H saturation transfer difference NMR). molecular recognition ͉ multivalent calix[4]arene ligands ͉ oligoprotein stabilization ͉ protein-protein interactions

First- and second-shell metal binding residues in human proteins are disproportionately associated with disease-related SNPs

“…Once attention is focused on a predicted amino acid/metal-ion interaction destabilized by a dSNP, the metal binding site might be targetable by compounds designed to stabilize the protein and to mimic its native conformation. For example, this general approach has been shown to restore tetramer integrity to the monomers of a variant p53 protein using a compound designed to stabilize the tetrameric structure [Gordo et al, 2008]. Other examples are restabilization of protein structure similar to the function of proenzyme small-molecule activators [Wolan et al, 2009], or engineering conformational changes mimicking those occurring upon metal binding [Axelrod et al, 2010].…”

The Tumor Suppressor p53: From Structures to Drug Discovery

“…Approximately 20% of p53 germline mutations have a mutation at codon 337, whereas the relative frequency of somatic cancer mutations at this site is low (see release R13 of the IARC TP53 Mutation Database at www-p53.iarc.fr) (Petitjean et al 2007). A recent study shows that the structural integrity of the R337H tetramer can be restored by a designed tetraguanidiniomethylcalix[4]arene ligand, which serves as a template for holding together the four monomers of the mutated tetramerization domain (Gordo et al 2008).…”

Molecular dynamics of the full-length p53 monomer

“…[101][102][103][104] MD conformational analyses were also performed for the N-terminal recognition α helix, [105][106][107][108] and for C-terminal fragments. 109,110 In order to study the entire monomeric protein behavior and its inter domain interactions, we have built a model for the full-length p53 (residues 1-393). The structure of unresolved fragments (10%) and disordered links between the domains have been predicted and merged with the experimental data.…”