Figure 1.
(A) Cartoon representation of X-ray structure of hPGK. N-domain, orange; C-domain, blue; interdomain region, green; substrates (BPG and ADP), purple sticks; Mg ion, purple sphere. (B) The hinge bending mechanism of hPGK. Coloring as in (A). Substrate binding triggers a closure of the two domains, thereby bringing the two reaction partners into close proximity.
Figure 2.
Forces exerted by the ligands on the protein.
Absolute value of the averaged residue-wise forces between (A) BPG and hPGK residues, (B) ADP and hPGK residues. Experimentally identified binding residues are marked with vertical lines and labels for BPG (A) and ADP (B), respectively.
Figure 3.
(A) Color coded representation of atomic punctual stresses between apo and complex hPGK. Colors range from blue (minimum value) to red (maximum value). BPG and ADP are denoted by purple sticks, the Mg-ion by a purple sphere. Right: enlarged view of the interdomain region formed by helix 14 and loops L14, 14–15. Spheres show Cα atoms between which the bending angles (denoted by red lines) were calculated (Table 1). Bottom: enlarged view of interdomain region formed by helix 7 and loops F7, 7G. Spheres show Cα atoms between which the bending angles (denoted by red lines) were calculated. (B) Open (cyan) and closed (blue) X-ray structure of hPGK superimposed to the N-domain β-core (yellow). ADP and BPG are marked by sticks, the Mg-ion by a sphere. Enlarged views of the interdomain regions of loop L14 and helix 7. Orange spheres indicate the hinge points.
Table 1.
Angle values in interdomain region.
Figure 4.
Hydrogen-bond network in hinge bending region of apo (A) and complexed (B) hPGK.
Hydrophobic amino acids are shown in red, H-bonds are depicted with dashed lines.
Figure 5.
Network-like representation of significant changes in inter-atomic forces. Red edges connect residue pairs having inter-atomic forces with |ΔFij| >90 pN. Red spheres indicate the substrate binding residues. BPG and ADP are denoted with purple sticks while Mg-ion is marked as a purple sphere. The orange spheres mark the two hinge points Glu192 and Gly394.