Orientation and interactions of dipolar molecules during transport through OmpF porin

The outer membrane of Gram-negative bacteria contains porins, large sieve-like proteins allowing small molecules to diffuse in and out of the periplasm. We have simulated transport of the dipolar molecules alanine and methylglucose through the OmpF porin from Escherichia coli using non-equilibrium steered molecular dynamics simulations in a realistic bilayer environment. Structural perturbation of the protein is minimal. During the permeation process, both alanine and methylglucose align strongly in the electric field in the eyelet region, where the adhesion force on the permeating molecule has a maximum. Binding of the permeating dipolar molecules in the eyelet region is not observed.