title: Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations.
abstract: A homeostatic concentration of glutamate in the synaptic cleft ensures a correct signal transduction along the neuronal network. An unbalance in this concentration can lead to neuronal death and to severe neurodegenerative diseases such as Alzheimer's or Parkinson's. Glutamate transporters play a crucial role in this respect because they are responsible for the reuptake of the neurotransmitter from the synaptic cleft, thus controlling the glutamate concentration. Understanding the molecular mechanism of this transporter can provide the possibility of an exogenous control. Structural studies have shown that this transporter can assume at least three conformations, thus suggesting a pronounced dynamical behavior. However, some intermediate states that lead to the substrate internalization have not been characterized and many aspects of the transporter mechanism still remain unclear. Here, using metadynamics simulations, we investigate the substrate uptake from the synaptic cleft and its release in the intracellular medium. In addition, we focus on the role of ions and substrate during these processes and on the stability of the different conformations assumed by the transporter. The present dynamical results can complement available X-ray data and provide a thorough description of the entire process of substrate uptake, internalization, and release.
authors.affiliation: Dipartimento di Scienze Farmaceutiche Pietro Pratesi, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Grazioso
authors.forename: Vittorio
authors.initials: V
authors.lastname: Limongelli
authors.forename: Davide
authors.initials: D
authors.lastname: Branduardi
authors.forename: Ettore
authors.initials: E
authors.lastname: Novellino
authors.forename: Carlo
authors.initials: C
authors.lastname: De Micheli
authors.forename: Andrea
authors.initials: A
authors.lastname: Cavalli
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello
mesh_terms: D027322:Amino Acid Transport System X-AG / Q000737:chemistry* / Q000378:metabolism*; D001059:Apoproteins / Q000737:chemistry / Q000378:metabolism; D019843:Archaeal Proteins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D021381:Protein Transport; D043902:Pyrococcus horikoshii; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics
chemical_list: D027322:Amino Acid Transport System X-AG; D001059:Apoproteins; D019843:Archaeal Proteins