title: Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter.
abstract: Glutamate transporters are membrane proteins found in neurons and glial cells, which play a critical role in regulating cell signaling by clearing glutamate released from synapses. Although extensive biochemical and structural studies have shed light onto different aspects of glutamate transport, the time-resolved molecular mechanism of substrate (glutamate or aspartate) translocation, that is, the sequence of events occurring at the atomic level after substrate binding and before its release intracellularly remain to be elucidated. We identify an energetically preferred permeation pathway of approximately 23 A between the helix HP1b on the hairpin HP1 and the transmembrane helices TM7 and TM8, using the high resolution structure of the transporter from Pyrococcus horikoshii (Glt(Ph)) in steered molecular dynamics simulations. Detailed potential of mean force calculations along the putative pathway reveal 2 energy barriers encountered by the substrate (aspartate) before it reaches the exit. The first barrier is surmounted with the assistance of 2 conserved residues (S278 and N401) and a sodium ion (Na2); and the second, by the electrostatic interactions with D405 and another sodium ion (Na1). The observed critical interactions and mediating role of conserved residues in the core domain, the accompanying conformational changes (in both substrate and transporter) that relieve local strains, and the unique coupling of aspartate transport to Na(+) dislocation provide insights into methods for modulating substrate transport.
authors.affiliation: Department of Computational Biology and Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Gu
authors.forename: Indira H
authors.initials: IH
authors.lastname: Shrivastava
authors.forename: Susan G
authors.initials: SG
authors.lastname: Amara
authors.forename: Ivet
authors.initials: I
authors.lastname: Bahar
mesh_terms: D000595:Amino Acid Sequence; D027322:Amino Acid Transport System X-AG / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D021381:Protein Transport; D043902:Pyrococcus horikoshii / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D027322:Amino Acid Transport System X-AG