Structural Transition between the Inward- and Outward-Facing States of the Glutamate Transporter in Different Lipid Environments

Abstract

Excitatory amino acid transporters (EAATs) are membrane proteins responsible for the reuptake of glutamate from the synaptic cleft in the central nervous system. Crystallographic data of a bacterial EAAT homologue, GltPh, have provided structural information for this trimeric secondary active transporter in different states. Nevertheless, in contrast to other membrane proteins, such as GPCRs, little is known about the structural or functional coupling between EAATs and their membrane environment. In this context, we investigated the effect of lipid environment on the structure and dynamics of GltPh, using all-atom molecular dynamics (MD) simulations of both the outward- and inward-facing conformations of GltPh in either POPC or POPE lipid membranes. The transition between the two states was explored with a variant of targeted MD simulations (sTMD) combining stepwise targeted motion and equilibration. Both the end conformations and the transition pathways were found to be robust to the choice of lipid bilayer type (pairwise trajectory RMSDs<2.5A), implying constant contributions from the energetics of membrane deformation and hydrophobic mismatch computed with 3D-CTMD. The transition pathways connecting the end states agree substantially with the structural intermediates of a path identified recently using the method of motion planning (MP) coupled with MD (minimum RMSDs<3A). Importantly, the agreement includes the prediction that the transport-trimerization domain interface changes continuously during the transition, exhibiting in the middle a significantly reduced contact area and significantly increased solvent-accessibility compared to the end states. This remarkable consistency between simple MP and the new sTMD modeling approaches indicates that the computationally economical MP calculations provide a useful initial modeling tool for major conformational transitions in membrane proteins.