How Dopamine Transporter Interacts with Dopamine: Insights from Molecular Modeling and Simulation

Abstract

By performing homology modeling, molecular docking, and molecular dynamics simulations, we have developed three-dimensional (3D) structural models of both dopamine transporter and dopamine transporter-dopamine complex in the environment of lipid bilayer and solvent water. According to the simulated structure of dopamine transporter-dopamine complex, dopamine was orientated in a hydrophobic pocket at the midpoint of the membrane. The modeled 3D structures provide some detailed structural and mechanistic insights concerning how dopamine transporter (DAT) interacts with dopamine at atomic level, extending our mechanistic understanding of the dopamine reuptake with the help of Na(+) ions. The general features of the modeled 3D structures are consistent with available experimental data. Based on the modeled structures, our calculated binding free energy (DeltaG(bind) = -6.4 kcal/mol) for dopamine binding with DAT is also reasonably close to the experimentally derived DeltaG(bind) value of -7.4 kcal/mol. Finally, a possible dopamine-entry pathway, which involves formation and breaking of the salt bridge between side chains of Arg(85) and Asp(476), is proposed based on the results obtained from the modeling and molecular dynamics simulation. The new structural and mechanistic insights obtained from this computational study are expected to stimulate future, further biochemical and pharmacological studies on the detailed structures and mechanisms of DAT and other homologous transporters.

The binding sites for cocaine and dopamine in the dopamine transporter overlap

“…1 and Table 1). A recent modeling study proposed a similar binding mode for dopamine 20 . The protonated amine of dopamine formed a salt-bridge with the Asp79 side chain (Fig.…”

SLC6 Neurotransmitter Transporters: Structure, Function, and Regulation

“…Structure of the S1 Pocket in Neurotransmitter Transporters and Implications for Substrate Selectivity. For the monoamine transporters, docking 5-HT and dopamine into models of the S1 site in SERT and DAT, respectively, have obtained strikingly similar poses of the substrates (Huang and Zhan, 2007;Beuming et al, 2008;Celik et al, 2008b;Indarte et al, 2008). The aromatic moieties of the substrates are accommodated in a hydrophobic region of the pocket, formed by hydrophobic and aliphatic residues in TM1, TM3, and TM6 (Fig.…”

“…Accordingly, LeuTbased homology modeling is emerging as a valuable tool in studies of the NTT members, both in purely computational studies Huang and Zhan, 2007;Jørgensen et al, 2007a,b;Indarte et al, 2008;Xhaard et al, 2008;Kardos et al, 2010;Wein and Wanner, 2010) and as a complementary tool in functional studies (Dodd and Christie, 2007;Forrest et al, 2007Forrest et al, , 2008Paczkowski et al, 2007;Vandenberg et al, 2007;Zomot et al, 2007;Beuming et al, 2008;Celik et al, 2008b;Kniazeff et al, 2008;Andersen et al, 2009bAndersen et al, , 2010Kaufmann et al, 2009;Tavoulari et al, 2009;Field et al, 2010;Koldsø et al, 2010;Sinning et al, 2010) (section III). Modeling of DAT and SERT have so far received the most attention, which probably reflects the important role of these transporters as drug targets and results in generation of several three-dimensional models of human DAT (Beuming et al, , 2008Ravna, 2006;Indarte et al, 2008) and human SERT Forrest et al, 2007;Jørgensen et al, 2007a,b;Celik et al, 2008b;Forrest et al, 2008).…”

“…The only major difference among these residues is found in the monoamine transporters, which contain an Asp in the position equivalent to Gly24 in LeuT. Homology models of SERT (Henry et al, 2006b;Ravna et al, 2006;Celik et al, 2008b;Forrest et al, 2008;Andersen et al, 2009b) and DAT ( Huang and Zhan, 2007;Beuming et al, 2008;Jin et al, 2008b) suggest that the ␤-carboxyl group of Asp compensates for the inability of the monoamine substrates to interact with Na ϩ in the Na1 site because these lack a negatively charged carboxyl group, in contrast to GABA and glycine as mentioned previously (Figs. 5 and 7).…”

A Second Extracellular Site Is Required for Norepinephrine Transport by the Human Norepinephrine Transporter

“…In addition to helping elucidate the mechanisms of substrate transport, LeuT Aa shares many structural and functional similarities with related monoamine transporters, allowing predictive homology models to be constructed (Rudnick and Wall, 1992;Stephan et al, 1997;Norregaard et al, 1998;Smicun et al, 1999;Mitchell et al, 2004;Beuming et al, 2006Beuming et al, , 2008Zhang and Rudnick, 2006;Forrest et al, 2007Forrest et al, , 2008Huang and Zhan, 2007;Jacobs et al, 2007;Zhou et al, 2007Zhou et al, , 2009Zomot et al, 2007;Erreger et al, 2008;Indarte et al, 2008;Andersen et al, 2009;Tavoulari et al, 2009). For example, homology models built from LeuT Aa have been used to identify putative Cl Ϫ binding sites in serotonin (SERT), dopamine (DAT), and GABA (GAT-1 and GAT-4) transporters (Forrest et al, 2007;Zomot et al, 2007), which predict that Cl Ϫ ions regulate the equilibrium between the open-to-out (substrate binding) and open-to-in (transporting) states (Beuming et al, 2008;Erreger et al, 2008;Forrest et al, 2008;Tavoulari et al, 2009).…”