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Cell-penetrating peptides (CPPs) have been widely used for drug-deliveryagents; however, it has not been fully understood how they translocate acrosscell membranes. The Weighted Ensemble (WE) method, one of powerful and flexiblepath sampling techniques, can be helpful to reveal translocation paths and freeenergy barriers along those paths. Within the WE approach we show how Arg9(nona-arginine) and Tat interact with a DOPC/DOPG (4:1) model membrane, and wepresent free energy (or potential mean of forces, PMFs) profiles ofpenetration, although a translocation across the membrane has not been observedin the current simulations. Two different compositions of lipid molecules werealso tried and compared. Our approach can be applied to any CPPs interactingwith various model membranes, and it will provide useful information regardingthe transport mechanisms of CPPs.

Free energy analyses of cell-penetrating peptides using the weighted ensemble method