Figure 1
From: Fast dynamics perturbation analysis for prediction of protein functional sites
Application of Dynamics Perturbation Analysis (DPA) to predict protein functional sites. Left. In this example, the surface of lysozyme (PDB entry 1JEF [50], yellow cartoon) is decorated with test points (533 spheres at a density of 1 point per Å2), and the degree to which the test points individually perturb the protein conformational distribution is calculated (temperature-coded coloring of the spheres). A tri-NAG molecule (purple wireframe) binds in the active site. Warm-colored spheres indicate where the perturbation is large. Center. Points where the perturbation is largest are selected and clustered (green spheres). Right. Cα atoms within 6 Å of the DPA cluster are selected, and the associated residues define the predicted functional site (16 residues). For comparison, Cα atoms within 6 Å of the tri-NAG are selected; we use the associated residues to define the actual functional site (7 residues). The overlapping residues (6 residues) are shown in orange; there are 10 predicted residues that do not exactly match the functional site (green), and there is 1 functional site residue that is not among the predicted residues (purple, in the helix on the right hand side).