A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter
Figure 3
GABA binding upon re-association.
(a) Comparison of the initial binding mode of GABA (from which the dissociation simulation was started) and the binding mode obtained upon re-association to the S1 binding site. The initial binding mode is color-coded with grey carbon atoms, and the binding mode obtained by SMD is color-coded with cyan carbon atoms. Red spheres represent water molecules involved in GABA binding upon re-association (see text), the blue spheres represent the two structural sodium ions, and the green sphere represents the structural chloride ion. Nitrogen and oxygen atoms are color-coded blue and red, respectively. (b) 2D ligand interaction diagram sketching the binding mode obtained from the association simulation (prepared via 2D ligand interaction available through Maestro [55]. Red circles represents water molecules involved in GABA binding, a dashed line represents a hydrogen bond to a protein side chain while a solid line represents an interaction with a protein backbone atom. Protein residues are color-coded as: green – hydrophobic, blue – polar, gray – glycine, pink – metal.