Insights into the Effect of the G245S Single Point Mutation on the Structure of p53 and the Binding of the Protein to DNA

Abstract

The transcription factor p53 is a potent tumor suppressor dubbed as the “guardian of the genome” because of its ability to orchestrate protective biological outputs in response to a variety of oncogenic stresses. Mutation and thus inactivation of p53 can be found in 50% of human tumors. The majority are missense mutations located in the DNA binding region. Among them, G245S is known to be a structural hotspot mutation. To understand the behaviors and differences between the wild-type and mutant, both a dimer of the wild type p53 (wt-p53) and its G245S mutant (G245S-mp53), complexed with DNA, were simulated using molecular dynamics for more than 1 μs. wt-p53 and G245S-mp53 apo monomers were simulated for 1 μs as well. Conformational analyses and binding energy evaluations performed underline important differences and therefore provide insights to understand the G245S-mp53 loss of function. Our results indicate that the G245S mutation destabilizes several structural regions in the protein that are crucial for DNA binding when found in its apo form and highlight differences in the mutant-DNA complex structure compared to the wt protein. These findings not only provide means that can be applied to other p53 mutants but also serve as structural basis for further studies aimed at the development of cancer therapies based on restoring the function of p53.

Elucidating the role of surface chemistry on cationic phosphorus dendrimer–siRNA complexation

“…Noteworthy, this relationship can hardly be inferred only by biological in vitro and in vivo experiments due to the high number of variables and complexity of the investigated biological system. In this context, a coupled approach based on experimental and computational modelling may provide fruitful information on molecular mechanisms driving interactions of ligand-target systems [40][41][42] , such as a polymer-siRNA complexes 15,33,34,[41][42][43] .…”

Virtual screening using covalent docking to find activators for G245S mutant p53

“…We also used the representative structures from the MD simulations to account for the protein’s flexibility specifically at the binding site. These representative structures were obtained by clustering the equilibrated protein[ 25 ] based on the RMSD of residues 113–124 and 141–146, which constitute the pocket around the reactive C124 residue. Clustering was performed based on the average-linkage algorithm[ 26 ] using the cpptraj utility in Ambertools[ 27 ].…”

“…We created the G245S-mp53 models as described in our previous work[ 25 ]. Briefly, we used the NMR resolved apo wt-p53 with PDB ID: 2FEJ[ 35 ] as well as the X-ray resolved wt p53-DNA complex (PDB ID: 4HJE[ 36 ]) as the starting structures for our models.…”

“…We used PyMol to virtually mutate residue 245 from glycine to serine[ 37 ]. We MD-simulated the mutated models for 1 and 1.5 μs, respectively as described in[ 25 ].…”

Frontiers in Computational Chemistry for Drug Discovery

“…The study by Tuszynski and coworkers is focused on the structural and dynamical alterations triggered by the G245S mutation in transcription factor p53 [ 9 ], which is a protein with mutated variants implicated in more than 50% of human tumours. The majority are missense mutations located in the DNA binding region, and G245S, particularly, is known to be a structural hotspot mutation.…”