Unassisted Transport of Block Tryptophan through DOPC Membrane: Experiment and Simulation

Abstract

The permeation of a blocked tryptophan through a DOPC bilayer membrane is investigated to probe unassisted or passive transport. The transport rate is measured experimentally and modeled computationally with atomically detailed simulations using the Milestoning algorithm. The time scale measured by PAMPA experiments is ∼8h. Simulations with Milestoning suggest a Mean First Passage Time (MFPT) of ∼4h. A similar calculation with the solubility-diffusion model yields MFPT of ∼15min. Both methods show significant variations for the computed permeation rate from opposing sides of the membrane (a factor of about 100). This underlines the difficulties in sampling membrane conformations even after 50 nanoseconds of umbrella sampling simulations. The permeation rate for this small peptide is very different (nine orders of magnitude slower) from the permeation rate of a tryptophan side chain only that was computed previously. This difference suggests critical dependence of transport time on permeant size and on hydrogen bonding. Analysis of the simulation results suggests that hydrogen bonding of the peptide backbone to water and lipid molecules and the creation of membrane defects are responsible for the exceptionally slow transport rate.