An Atomic-level Model for the Periplasmic Open State of Lactose Permease

Abstract

Membrane transport proteins play significant roles in human physiology, drug transport, bacterial resistance to antibiotics, and diseases. Lactose permease of E. coli (LacY) transports various disaccharides and is a member of the major facilitator superfamily of proteins that exists in a broad range of organisms from archaea to the human central nervous system. Since only the atomic-level structure for the cytoplasmic open state of LacY has been determined, it is our objective to obtain a structure (or set of structures) of LacY open to the periplasm by utilizing a two-step hybrid approach of molecular simulations. In the first step, self-guided Langevin dynamics (SGLD) with an implicit membrane but explicit water is used to enhance conformational sampling. SGLD was found to significantly enhance protein motions compared to identical implicit membrane molecular dynamics (MD) simulations. Significant periplasmic conformational changes are only observed in simulations with Glu269 protonated and a disaccharide in the binding site, which is based on several simulations with different initial structures. LacY helix-helix distances obtained from double electron-electron resonance (DEER) experiments (Smirnova et al., PNAS, 2007) are used to select protein conformations consistent with a periplasmic open state. In the final step, explicit membrane MD simulations with screened structures from the implicit membrane simulations converged to periplasmic open structures. This hybrid implicit/explicit bilayer approach results in LacY structures that transition from a periplasmic closed state (pore radius, Rp, of ∼1A) to one fully open the periplasm (Rp= 3A). The helices on the outside of the protein are the first to fan out (H-III/IV then H-VIII) before there is a concerted motion of the periplasmic half. This two-step simulation approach in conjunction with experiments may be successful in predicting conformational changes of other membrane proteins.