title: Inward open characterization of EmrD transporter with molecular dynamics simulation.
abstract: EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model of rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state.
authors.affiliation: School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Xianwei
authors.initials: X
authors.lastname: Tan
authors.affiliation: Department of Precision Instrument, Tsinghua University, Beijing 100084, China. Electronic address: boxiong_wang@yahoo.com.
authors.forename: Boxiong
authors.initials: B
authors.lastname: Wang
mesh_terms: D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D008051:Lipid Bilayers / Q000737:chemistry*; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D000072417:Protein Domains; D017510:Protein Folding
chemical_list: C510268:EmrD protein, E coli; D029968:Escherichia coli Proteins; D008051:Lipid Bilayers; D026901:Membrane Transport Proteins
keywords: Adaptive tempering; EmrD; Hydrogen bond; Molecular dynamics simulation; Open inward