Abstract
Valinomycin is a potassium specific ionophore used to transport ions down an electrochemical gradient across lipid membranes. Its small size, high selectivity, and strong antibiotic activity make it an interesting target for molecular dynamics simulations. At the same time its conformational flexibility, which strongly depends on the polarity of its environment, poses a challenge. This work was undertaken in order to elucidate the mechanism of valinomycin mediated potassium transport across a lipid bilayer. We have explored several advanced sampling techniques, but chose to perform multi-dimensional free energy calculations that explore conformational space while computing the potential of mean force for membrane translocation. By computing free energy surfaces with and without a bound K+ ion and calculating the free energetics of the ion binding process, we can describe a cycle that reveals the overall permeation mechanism. Our results using implicit and explicit solvent and membrane models will be discussed.
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