title: Simulations of substrate transport in the multidrug transporter EmrD.
abstract: EmrD is a multidrug resistance (MDR) transporter from Escherichia coli, which is involved in the efflux of amphipathic compounds from the cytoplasm, and the first MDR member of the major facilitator superfamily to be crystallized. Molecular dynamics simulation of EmrD in a phospholipid bilayer was used to characterize the conformational dynamics of the protein. Motions that support a previously proposed lateral diffusion pathway for substrate from the cytoplasmic membrane leaflet into the EmrD central cavity were observed. In addition, the translocation pathway of meta-chloro carbonylcyanide phenylhydrazone (CCCP) was probed using both standard and steered molecular dynamics simulation. In particular, interactions of a few specific residues with CCCP have been identified. Finally, a large motion of two residues, Val 45 and Leu 233, was observed with the passage of CCCP into the periplasmic space, placing a lower bound on the extent of opening required at this end of the protein for substrate transport. Overall, our simulations probe details of the transport pathway, motions of EmrD at an atomic level of detail, and offer new insights into the functioning of MDR transporters.
authors.affiliation: Department of Physics, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Baker
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Wright
authors.forename: Florence
authors.initials: F
authors.lastname: Tama
mesh_terms: D002258:Carbonyl Cyanide m-Chlorophenyl Hydrazone / Q000737:chemistry / Q000378:metabolism; D018432:Drug Resistance, Multiple; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism*; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000378:metabolism*; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D019897:Periplasm
chemical_list: C510268:EmrD protein, E coli; D029968:Escherichia coli Proteins; D008051:Lipid Bilayers; D026901:Membrane Transport Proteins; D002258:Carbonyl Cyanide m-Chlorophenyl Hydrazone