A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter
Figure 6
(a) Graphs following the trajectory of the association of tiagabine (using distance restraints). The individual figures from top to bottom show: the distance of tiagabine relative to the selected point in the bottom of the S1 binding site towards which tiagabine was pulled (I); the biasing potential energy profile (II); the sum of the non-bonded interaction energy profiles between tiagabine and the protein, water, sodium- and chloride ions (III); the electrostatic energy contribution to the non-bonded interaction energies between tiagabine and the protein, water, sodium- and chloride ions (IV); the van der Waals energy contribution to the non-bonded interaction energies between tiagabine and the protein, water, sodium- and chloride ions (V). Tiagabine is moving unhindered with the target movements through the extracellular vestibule until it binds to the S2 site after circa 34 ns. From this point the biasing potential energy is repeatedly accumulating though only by small amounts until tiagabine reaches the S1 site from where it cannot move any further into the protein. Compared to the biasing potential energy accumulated during translocation of GABA to the cytoplasm (Figure 4) the potential energy barriers for tiagabine reaching the S1 site are considerable lower than translocation of a substrate. (b) 2D ligand interaction diagram sketching the binding mode obtained from the association of tiagabine towards the S1 site in GAT-1. Residues are colored according to their properties: charged (pink or purple), polar (blue) and hydrophobic (green). Hydrogen bonds are shown as lines and water molecules as red open circles.