p53 R175H hydrophobic patch and H-bond reorganization observed by MD simulation

Network Analysis of Molecular Dynamics Sectors in the p53 Protein

Design of allosteric regulators is an emergent field in the area of drug discovery holding promise for currently untreated diseases. Allosteric regulators bind to a protein in one location and affect a distant site. The ubiquitous presence of allosteric effectors in biology and the success of serendipitously identified allosteric compounds point to the potential they hold. Although the mechanism of transmission of an allosteric signal is not unequivocally determined, one hypothesis suggests that groups of evolutionarily covarying residues within a protein, termed sectors, are conduits. A long-term goal of our lab is to allosterically modulate the activity of proteins by binding small molecules at points of allosteric control. However, methods to consistently identify such points remain unclear. Sector residues on the surfaces of proteins are a promising source of allosteric targets. Recently, we introduced molecular dynamics (MD)-based sectors; MD sectors capitalize on covariance of motion, in place of evolutionary covariance. By focusing on motional covariance, MD sectors tap into the framework of statistical mechanics afforded by the Boltzmann ensemble of structural conformations comprising the underlying data set. We hypothesized that the method of MD sectors can be used to identify a cohesive network of motionally covarying residues capable of transmitting an allosteric signal in a protein. While our initial qualitative results showed promise for the method to predict sectors, that a network of cohesively covarying residues had been produced remained an untested assumption. In this work, we apply network theory to rigorously analyze MD sectors, allowing us to quantitatively assess the biologically relevant property of network cohesiveness of sectors in the context of the tumor suppressor protein, p53. We revised the methodology for assessing and improving MD sectors. Specifically, we introduce a metric to calculate the cohesive properties of the network. Our new approach separates residues into two categories: sector residues and non-sector residues. The relatedness within each respective group is computed with a distance metric. Cohesive sector networks are identified as those that have high relatedness among the sector residues which exceeds the relatedness of the residues to the non-sector residues in terms of the correlation of motions. Our major finding was that the revised means of obtaining sectors was more efficacious than previous iterations, as evidenced by the greater cohesion of the networks. These results are discussed in the context of the development of allosteric regulators of p53 in particular and the expected applicability of the method to the drug design field in general.

Most Probable Druggable Pockets in Mutant p53-Arg175His Clusters Extracted from Gaussian Accelerated Molecular Dynamics Simulations

p53, a tumor suppressor protein, is essential for preventing cancer development. Enhancing our understanding of the human p53 function and its modifications in carcinogenesis will aid in developing more highly effective strategies for cancer prevention and treatment. In this study, we have modeled five human p53 forms, namely, inactive, distal-active, proximal-active, distal-Arg175His mutant, and proximal-Arg175His mutant forms. These forms have been investigated using Gaussian accelerated molecular dynamics (GaMD) simulations in OPC water model at physiological temperature and pH. Our observations, obtained throughout [Formula: see text] of production run, are in good agreement with the relevant results in the classical molecular dynamics (MD) studies. Therefore, GaMD method is more economic and efficient method than the classical MD method for studying biomolecular systems. The featured dynamics of the five human p53-DBD forms include noticeable conformational changes of L1 and [Formula: see text]-[Formula: see text] loops as well as [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] turns. We have identified two clusters that represent two distinct conformational states in each p53-DBD form. The free-energy profiles of these clusters demonstrate the flexibility of the protein to undergo a conformational transition between the two clusters. We have predicted two out of seven possible druggability pockets on the clusters of the Arg175His forms. These two druggability pockets are near the mutation site and are expected to be actual pockets, which will be helpful for the compound clinical progression studies.

Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations

The p53 tumor suppressor is a multifaceted context-dependent protein, which is involved in multiple cellular pathways, with the ability to either keep the cells alive or to kill them through mechanisms such as apoptosis. To complicate this picture, cancer cells that express mutant p53 becomes addicted to the mutant activity, so that the mutant variant features a myriad of gain-of-function activities, opening different venues for therapy. This makes essential to think outside the box and apply new approaches to the study of p53 structure-(mis)function relationship to find new critical components of its pathway or to understand how known parts are interconnected, compete, or cooperate. In this context, I will here illustrate how to integrate different computational methods to the identification of possible allosteric effects transmitted from the DNA binding interface of p53 to regions for cofactor recruitment. The protocol can be extended to any other cases of study. Indeed, it does not necessarily apply only to the study of DNA-induced effects, but more broadly to the investigation of long-range effects induced by a biological partner that binds to a biomolecule of interest.

From mutational inactivation to aberrant gain-of-function: Unraveling the structural basis of mutant p53 oncogenic transition

Various evidence has revealed that mutations in p53 exert activities that go beyond simply inactivation of wildtype functions but rather elicits downstream interactions that promote malignancy described as mutant p53 gain-of-function (GOF). Here we report the first account of the dynamics of mutation-induced structural transition of native p53 to an aberrant gain-of-function state, studying the wildtype (WT) and high incidence contact (R273C) and structural (R175H) mutant p53 (mutp53) through molecular dynamics simulation. Result analysis revealed that both mutants exhibited structural distortion and reduced flexibility, indicative of rigidity and kinetic stability. In addition, surface analysis revealed an increase in the accessible surface area in the p53 mutants. This suggests that the GOF transition involves protein unfolding and exposure of buried hydrophobic surface essential for interaction with HSF-1 oncogenic partner and wildtype p63, and p73 homologs. Further validation revealed binding cavities, similar in the mutants but dissimilar to the WT. Taken together, this study complements experimental findings and reveals the interplay between mutation-induced structural distortion, loss of flexibility, rigidity, enhanced stability, protein unfolding and ultimately, exposure of binding surfaces as conformational attributes that characterize mutP53 structure-GOF activities. This insight is, therefore, of great importance as it opens up a novel therapeutic approach toward the structure based targeting of mutP53 oncogenic involvement beyond wildtype inactivation. Furthermore, "exposed" binding site information obtained from this study can be explored for structure-based design of substances best described as "destabilizers" to disrupt the GOF interaction of mutp53.

Structural Evolution and Dynamics of the p53 Proteins

The family of the p53 tumor suppressive transcription factors includes p73 and p63 in addition to p53 itself. Given the high degree of amino-acid-sequence homology and structural organization shared by the p53 family members, they display some common features (i.e., induction of cell death, cell-cycle arrest, senescence, and metabolic regulation in response to cellular stress) as well as several distinct properties. Here, we describe the structural evolution of the family members with recent advances on the molecular dynamic studies of p53 itself. A crucial role of the carboxy-terminal domain in regulating the properties of the DNA-binding domain (DBD) supports an induced-fit mechanism, in which the binding of p53 on individual promoters is preferentially regulated by the K_OFF over K_ON.