BackgroundThe protein p53 plays an active role in the regulation of cell cycle. In about half of human cancers, the protein is inactivated by mutations located primarily in its DNA-binding domain. Interestingly, a number of these mutations possess temperature-induced DNA-binding characteristics. A striking example is the mutation of Arg248 into glutamine or tryptophan. These mutants are defective for binding to DNA at 310 K although they have been shown to bind specifically to several p53 response elements at sub-physiological temperatures (298–306 K).Methodology/Principal FindingsThis important experimental finding motivated us to examine the effects of temperature on the structure and configuration of R248Q mutant and compare it to the wild type protein. Our aim is to determine how and where structural changes of mutant variants take place due to temperature changes. To answer these questions, we compared the mutant to the wild-type proteins from two different aspects. First, we investigated the systems at the atomistic level through their DNA-binding affinity, hydrogen bond networks and spatial distribution of water molecules. Next, we assessed changes in their long-lived conformational motions at the coarse-grained level through the collective dynamics of their side-chain and backbone atoms separately.ConclusionsThe experimentally observed effect of temperature on the DNA-binding properties of p53 is reproduced. Analysis of atomistic and coarse-grained data reveal that changes in binding are determined by a few key residues and provide a rationale for the mutant-loss of binding at physiological temperatures. The findings can potentially enable a rescue strategy for the mutant structure.

While it has long been known that cholesterol reduces the permeability of biological membranes to water, the exact mechanism by which cholesterol influences transmembrane permeation is still unclear. The thermodynamic and kinetic contributions to the transport of water across mixed DPPC/cholesterol bilayers of different composition are thus examined by molecular dynamics simulations. Our analyses show that cholesterol decreases transmembrane permeability to water mainly by altering the thermodynamics of water transport. In particular, the free-energy barrier to permeation is magnified in the dense bilayer interior and the partitioning of water is significantly lowered. The changes are observed to correlate quantitatively well with the cholesterol-dependent density and thickness of the bilayers. In contrast, diffusion coefficients are relatively insensitive to cholesterol concentration, except in the sparsely populated center of the bilayer. Diffusion of water in cholesterol-containing bilayers appears to be related to changes in the free area in the middle of the bilayer and to the solute cross-sectional area in the denser hydrophobic regions. Overall, cholesterol is found to have an inhibitory effect on the permeation of water at all concentrations investigated, although bilayers containing cholesterol concentrations up to 20 mol % display a more dramatic dependence on cholesterol content than at higher concentrations. Our results show that it is possible to quantitatively reproduce the relative effects of cholesterol on lipid bilayer permeability from molecular dynamics simulations.

Essential collective dynamics is a promising and robust approach for analysing the slow motions of macromolecules from short molecular dynamics trajectories. In this study, an extension of the method to treat a collection of interacting protein molecules is presented. The extension is applied to investigate the effects of dimerization on the collective dynamics of ovine prion protein molecules in two different arrangements. Examination of the structural plasticity shows that aggregation has a restricting effect on the local mobility of the prion protein molecules in the interfacial regions. Domain motions of the two dimeric ovine prion protein conformations are distinctly different and can be related to interatomic correlations at the interface. Correlated motions are among the slow collective modes extensively analysed by considering both main‐chain and side‐chain atoms. Correlation maps reveal the existence of a vast network of dynamically correlated side groups, which extends beyond individual subunits via interfacial interconnections. The network is formed by a core of hydrophobic side chains surrounded by hydrophilic groups at the periphery. The relevance of these findings are discussed in the context of mutations associated with prion diseases. The binding free energy of the dimeric conformations is evaluated to probe their thermodynamic stability. The descriptions afforded by the analysis of the essential collective dynamics of the prion dimers are consistent with their binding free energies. The agreement validates the extension of the methodology and provides a means of interpreting the collective dynamics in terms of the thermodynamic stability of ovine prion proteins. Proteins 2012. © 2012 Wiley Periodicals, Inc.

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