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Mixed MD/MC simulation at fixed difference in chemical potential (Δμ) between two lipid types provides a computational indicator of the relative affinities of the two lipids for different environments. Applying this technique to ternary DPPC/DOPC/cholesterol bilayers yields a DPPC/DOPC ratio that increases with increasing cholesterol content at fixed Δμ,(More)
We have applied a molecular dynamics (MD) method to investigate the aggregation behavior and physicochemical properties of bile salt as well as bile salt/fatty acid mixed micelles. Local atomic density profiles from the center of the micelles confirm that the self-assembly of the trihydroxy bile salt, glycocholate, is largely driven by hydrophobic(More)
The local lipid composition near a transmembrane helical peptide in mixed-lipid bilayers has been studied using a mixed molecular dynamics (MD) and configuration-bias Monte Carlo method that allows the lateral distribution of lipids to equilibrate much more quickly than is possible by diffusive mixing alone. Gramicidin-A peptide was embedded in bilayer(More)
To understand the effects of lipid composition on membrane protein function in a mixture as complex as a biomembrane, one must know whether the lipid composition local to the protein differs from the mean lipid composition. In this study, we simulated the transmembrane domain of a β-barrel protein, OmpA, in mixtures of lipids of different tail lengths under(More)
Conventional molecular dynamics (MD) simulations are seriously limited by the slow rate of diffusive mixing in their ability to predict lateral distributions of different lipid types within mixed-lipid bilayers using atomistic models. A method to overcome this limitation, using configuration-bias Monte Carlo (MC) "mutation" moves to transform lipids from(More)
In this study, a molecular dynamics (MD) method is assessed as a new front-end tool for deriving relevant drug-micelle partitioning rates for use in conjunction with a compartmental-style gastrointestinal absorption model. A refined mechanistic approach for handling micelle-associated vs unbound drug is presented and examined in terms of its utility for(More)
The partitioning of lipids among different microenvironments in a bilayer is of considerable relevance to characterization of composition variations in biomembranes. Atomistic simulation has been ill-suited to model equilibrated lipid mixtures because the time required for diffusive exchange of lipids among microenvironments exceeds typical submicrosecond(More)
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