Molecular Dynamics Simulations on the Periplasmic-Open State Lactose Permease

Abstract

Lactose Permease (LacY) is a secondary active transporter (SAT) that belongs to major facilitator superfamily (MFS). LacY structures of the cytoplasmic-open and more recently occluded-like structure have been determined. The structure of periplasmic-open LacY is important for understanding complete proton/sugar transport of LacY as well as other similar transporters. Though the exact structure of periplasmic-open LacY has not been obtained experimentally, a few molecular models have been determined. Previously, Pendse et al. (JMB, 404: 506-521) obtained a periplasmic-open LacY model through a two-step hybrid implicit-explicit (IM-EX) simulation method. Radestock et al. (JMB, 407: 698-715) proposed two new periplasmic-open LacY models by swapping inverted-topology repeats and adopting the outward L-fucose-proton symporter (fucP) crystal structure. The accuracy of these three periplasmic-open state models are tested by performing MD simulations on LacY-apo and LacY-ββ-(Galp)2. The comparison of the calculated pore radii to the data of the crystal structure indicates that the IM-EX model of LacY remains in periplasmic-open state. However, Radestock et al.'s models close on the periplasmic side and partially close on the cytoplasmic side, which indicates these two outward LacY models are unstable. Compared to the DEER experimental data, the selected residue pair distance changes demonstrates that the repeat-swapped LacY seems to be in the occluded state by 100ns. We will run MD simulations with labeled residues to directly compare with DEER for the IM-EX model to verify the effects of the spin label size and orientation on the accuracy of the distance measurement.