A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter
Figure 2
Dissociation and re-association of GABA.
SMD profiles for GABA dissociation using displacement restraints (a), and GABA re-association using distance restraints (b). For both (a) and (b) the individual figures from top to bottom show the displacement of GABA relative to the center of mass (COM) of the chemical system (I); the biasing potential energy profile (II); non-bonded interaction energy profiles between GABA and the protein, water, sodium ions, and chloride ions (III); non-bonded interaction energy profiles between GABA and residues interacted with during simulation (IV-VII). Figures on the left-hand side share the same time-axis as does figures on the right-hand side. Note, for the displacement restrained simulation depicted in (A) the displacement vector is specified by its components, hence the biasing potential energy is resolved into its x-, y-, and z-components, while the biasing potential energy is given for the vector in space in the distance restrained simulation in (B). Generally, changes in the interaction pattern between GABA and the protein are reflected in e.g. the biasing potential energy profile and vice versa. Most notably is the departure from the primary binding site, S1. During the initial 6 ns of the dissociation simulation (left-hand side) GABA is firmly keeping the initial binding mode (i.e. interactions with particularly Y60, G65, Y140, S396 and Na1), while the biasing potential energy (II) is accumulating. After circa 6 ns the direct ionic or hydrogen bonding interactions to the protein and sodium ion (Na1) are solvated by water molecules (III) thereby facilitating GABA to depart from the binding site, which is visualized by a sudden change in the COM movements depicted in (I) and in the drop in the biasing potential energy in (II). At the S2 site the interactions between GABA and the protein are reinforced due to particularly the interactions to R69 and D451.