TY - JOUR

T1 - A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter

A1 - Skovstrup,Soren

A1 - David,Laurent

A1 - Taboureau,Olivier

A1 - Jorgensen,Flemming Steen

AU - Skovstrup,Soren

AU - David,Laurent

AU - Taboureau,Olivier

AU - Jorgensen,Flemming Steen

PB - Public Library of Science

PY - 2012

Y1 - 2012

N2 - The entire substrate translocation pathway in the human GABA transporter (GAT-1) was explored for the endogenous substrate GABA and the anti-convulsive drug tiagabine. Following a steered molecular dynamics (SMD) approach, in which a harmonic restraining potential is applied to the ligand, dissociation and re-association of ligands were simulated revealing events leading to substrate (GABA) translocation and inhibitor (tiagabine) mechanism of action. We succeeded in turning the transporter from the outward facing occluded to the open-to-out conformation, and also to reorient the transporter to the open-to-in conformation. The simulations are validated by literature data and provide a substrate pathway fingerprint in terms of which, how, and in which sequence specific residues are interacted with. They reveal the essential functional roles of specific residues, e.g. the role of charged residues in the extracellular vestibule including two lysines (K76 (TM1) and K448 (TM10)) and a TM6-triad (D281, E283, and D287) in attracting and relocating substrates towards the secondary/interim substrate-binding site (S2). Likewise, E101 is highlighted as essential for the relocation of the substrate from the primary substrate-binding site (S1) towards the cytoplasm.

AB - The entire substrate translocation pathway in the human GABA transporter (GAT-1) was explored for the endogenous substrate GABA and the anti-convulsive drug tiagabine. Following a steered molecular dynamics (SMD) approach, in which a harmonic restraining potential is applied to the ligand, dissociation and re-association of ligands were simulated revealing events leading to substrate (GABA) translocation and inhibitor (tiagabine) mechanism of action. We succeeded in turning the transporter from the outward facing occluded to the open-to-out conformation, and also to reorient the transporter to the open-to-in conformation. The simulations are validated by literature data and provide a substrate pathway fingerprint in terms of which, how, and in which sequence specific residues are interacted with. They reveal the essential functional roles of specific residues, e.g. the role of charged residues in the extracellular vestibule including two lysines (K76 (TM1) and K448 (TM10)) and a TM6-triad (D281, E283, and D287) in attracting and relocating substrates towards the secondary/interim substrate-binding site (S2). Likewise, E101 is highlighted as essential for the relocation of the substrate from the primary substrate-binding site (S1) towards the cytoplasm.

KW - BIOLOGY

KW - AMINOBUTYRIC-ACID TRANSPORTER

KW - TRANSMEMBRANE DOMAIN-I

KW - FREE-ENERGY DIFFERENCES

KW - NEUROTRANSMITTER TRANSPORTERS

KW - BACTERIAL HOMOLOG

KW - HIGH-AFFINITY

KW - RAT-BRAIN

KW - SUBSTRATE-BINDING

KW - DRUG TARGETS

KW - ION-BINDING

U2 - 10.1371/journal.pone.0039360

DO - 10.1371/journal.pone.0039360

JO - P L o S One

JF - P L o S One

SN - 1932-6203

IS - 6

VL - 7

SP - -

ER -