Figure 2.

Glutamate Binding Pathways and Metastable Binding Sites

(A) The PMF calculated from the ligand density using a hard-sphere van der Waals approximation on a grid spacing of 0.5 Å along the x, y, and z axes contoured at 1.89 kcal mol^–1. Data are from the monomeric LBD system with 10 ligands (T_mon2,3). The primary binding pathways for glutamate are depicted by arrows.

(B) The PMF, contoured at 1.16 kcal mol^–1, defines the regions of metastable interaction, sites 0–3. Site 0 is the site of stable binding. Site 1 is shared by Pathways 1 and 2, site 2 is encountered in Pathway 2, and site 3 is encountered in Pathway 3. Site 1 spans the two lobes, involving R453 in Lobe 1 and E657, R660, and R661 in Lobe 2. Site 2 involves E657, R660, and R661 in Lobe 2. Site 3 involves R675 and R684 in Lobe 2. The residues involved in site 0 are shown in Figure 3A. Error analysis is provided in Figure S2.

(C) The PMF, contoured at 0.32 kcal mol^–1, shows the global free energy minimum. This minimum overlaps well with the ligand density derived from crystal structures of the glutamate-bound complex (e.g., PDB: 1FTJ).

(D) The one-dimensional representation of the WT GluA2 ligand-binding PMF was obtained by first computing the three-dimensional PMF (A–C). Values of the three-dimensional PMF were indexed increasing in the z, y, then x directions, from (x_min, y_min, z_min), to produce the one-dimensional representation. The positions of sites 0–3 are indicated. Site 0 is the global free energy minimum and is set to 0 kcal/mol; sites 1–3 form local minima with free energies of 0.29, 0.83, and 0.75 kcal/mol, respectively.

See also Figures S2 and S8.