(69c) Molecular Dynamics Simulations on the Periplasmic-Open State Lactose Permease

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 and also the mechanism of other substrate transporters. Though the exact structure of periplasmic-open LacY has not been obtained experimentally, a few molecular models of it have been provided. Previously, Pendse et al. (JMB, 404: 506-521) obtained a periplasmic-open LacY model through a two-step hybrid implicit-explicit simulation method (IM-EX MS), in which self-guided Langevin dynamics (SGLD) simulations were performed with LacY in an implicit, from which structures obtained were used in MD simulations in an explicit lipid bilayer. Radestock et al. (JMB, 407: 698–715) proposed a new periplasmic-open LacY model through inverted-topology repeats method. Another periplasmic-open LacY model was based on the available outward crystal structure of L-fucose-proton symporter (fucP). For this presentation, the accuracy of these three periplasmic-open state models is tested using MD simulations. Unprotonated and protonated Glu269 (one of the residues involved in proton translocation) are simulated to compare effects of residue protonation on global structures. Structural changes are described with the root-mean-square deviation (RMSD) and helix-helix distance changes. The RMSD from the three models’ initial states and the RMSD of Radestock et al.’s two models from Pendse et al. coordinate are presented. The helix–helix distances are analyzed through tracking distances of some selected residue pairs. The results show that RMSD’s of C-terminus helices of fucP-based LacY and the structural repeats model in both protonation states are greater than of entire protein, which indicates that instead of rigid conformational change, the C-terminus helices change their packing structure. To search for the reason of this unexpected dynamic behavior, the distance deviation of all helix-helix pairs at helix center of three structures models will be analyzed to determine how helix packing changes in these models and how it differs from the model of Pendse et al. To better verify the accuracy of these models, we will re-compare the simulated structural change data from these three models with the experimental data. Compared to the DEER experimental data, the selected residue pair distance changes indicate that the swapped-repeat LacY seems to be in the occluded state in 100ns, and the fucP-based LacY is more likely to be in periplasmic-open state. The simulated structural change will also be compared to crosslinking, and substrate accessibility experimental data. Moreover, we will calculate and analyze the variation in the radius of protein pore that connecting two pseudo-symmetric domain of LacY during simulation.