Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations. 2012

Mari Gabrielsen, and Aina Westrheim Ravna, and Kurt Kristiansen, and Ingebrigt Sylte
Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway.

The serotonin (5-HT) transporter (SERT) plays an important role in the termination of 5-HT-mediated neurotransmission by transporting 5-HT away from the synaptic cleft and into the presynaptic neuron. In addition, SERT is the main target for antidepressant drugs, including the selective serotonin reuptake inhibitors (SSRIs). The three-dimensional (3D) structure of SERT has not yet been determined, and little is known about the molecular mechanisms of substrate binding and transport, though such information is very important for the development of new antidepressant drugs. In this study, a homology model of SERT was constructed based on the 3D structure of a prokaryotic homologous leucine transporter (LeuT) (PDB id: 2A65). Eleven tryptamine derivates (including 5-HT) and the SSRI (S)-citalopram were docked into the putative substrate binding site, and two possible binding modes of the ligands were found. To study the conformational effect that ligand binding may have on SERT, two SERT-5-HT and two SERT-(S)-citalopram complexes, as well as the SERT apo structure, were embedded in POPC lipid bilayers and comparative molecular dynamics (MD) simulations were performed. Our results show that 5-HT in the SERT-5-HT(B) complex induced larger conformational changes in the cytoplasmic parts of the transmembrane helices of SERT than any of the other ligands. Based on these results, we suggest that the formation and breakage of ionic interactions with amino acids in transmembrane helices 6 and 8 and intracellular loop 1 may be of importance for substrate translocation.

UI MeSH Term Description Entries
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D003198 Computer Simulation Computer-based representation of physical systems and phenomena such as chemical processes. Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D012701 Serotonin A biochemical messenger and regulator, synthesized from the essential amino acid L-TRYPTOPHAN. In humans it is found primarily in the central nervous system, gastrointestinal tract, and blood platelets. Serotonin mediates several important physiological functions including neurotransmission, gastrointestinal motility, hemostasis, and cardiovascular integrity. Multiple receptor families (RECEPTORS, SEROTONIN) explain the broad physiological actions and distribution of this biochemical mediator. 5-HT,5-Hydroxytryptamine,3-(2-Aminoethyl)-1H-indol-5-ol,Enteramine,Hippophaine,Hydroxytryptamine,5 Hydroxytryptamine
D013379 Substrate Specificity A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts. Specificities, Substrate,Specificity, Substrate,Substrate Specificities
D017367 Selective Serotonin Reuptake Inhibitors Compounds that specifically inhibit the reuptake of serotonin in the brain. 5-HT Uptake Inhibitor,5-HT Uptake Inhibitors,5-Hydroxytryptamine Uptake Inhibitor,5-Hydroxytryptamine Uptake Inhibitors,SSRIs,Selective Serotonin Reuptake Inhibitor,Serotonin Reuptake Inhibitor,Serotonin Reuptake Inhibitors,Serotonin Uptake Inhibitor,Serotonin Uptake Inhibitors,Inhibitors, 5-HT Uptake,Inhibitors, 5-Hydroxytryptamine Uptake,Inhibitors, Serotonin Reuptake,Inhibitors, Serotonin Uptake,Reuptake Inhibitors, Serotonin,Uptake Inhibitors, 5-HT,Uptake Inhibitors, 5-Hydroxytryptamine,Uptake Inhibitors, Serotonin,Inhibitor, 5-HT Uptake,Inhibitor, 5-Hydroxytryptamine Uptake,Inhibitor, Serotonin Reuptake,Inhibitor, Serotonin Uptake,Reuptake Inhibitor, Serotonin,Uptake Inhibitor, 5-HT,Uptake Inhibitor, 5-Hydroxytryptamine,Uptake Inhibitor, Serotonin
D050486 Serotonin Plasma Membrane Transport Proteins Sodium chloride-dependent neurotransmitter symporters located primarily on the PLASMA MEMBRANE of serotonergic neurons. They are different than SEROTONIN RECEPTORS, which signal cellular responses to SEROTONIN. They remove SEROTONIN from the EXTRACELLULAR SPACE by high affinity reuptake into PRESYNAPTIC TERMINALS. Regulates signal amplitude and duration at serotonergic synapses and is the site of action of the SELECTIVE SEROTONIN REUPTAKE INHIBITORS. Neurotransmitter Transport Proteins, Serotonin-Specific,Neurotransmitter Transporters, Serotonin-Specific,Serotonin Plasma Membrane Transporter Proteins,5-Hydroxytryptamine Plasma Membrane Transport Protein,5HT Transporter,Platelet Serotonin Transporter,SERT Proteins,SLC6A4 Protein,Serotonectin,Serotonin Transporter,Serotonin Transporter, Platelets,Sodium-Dependent Serotonin Transporter,Solute Carrier Family 6, Member 4 Protein,5 Hydroxytryptamine Plasma Membrane Transport Protein,Neurotransmitter Transport Proteins, Serotonin Specific,Neurotransmitter Transporters, Serotonin Specific,Platelets Serotonin Transporter,Serotonin Transporter, Platelet,Serotonin Transporter, Sodium-Dependent,Serotonin-Specific Neurotransmitter Transporters,Sodium Dependent Serotonin Transporter,Transporter, Sodium-Dependent Serotonin
D056004 Molecular Dynamics Simulation A computer simulation developed to study the motion of molecules over a period of time. Molecular Dynamics Simulations,Molecular Dynamics,Dynamic, Molecular,Dynamics Simulation, Molecular,Dynamics Simulations, Molecular,Dynamics, Molecular,Molecular Dynamic,Simulation, Molecular Dynamics,Simulations, Molecular Dynamics

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