Figure 4.

Representative frames from MD of PPARα–CBM complexes: Panel (A) A ball-and-stick representation is used for the heavy atoms of the ligand, and a stick representation is used for the protein sidechain within 5 Å of the ligand. Protein carbon atoms are colored in dark gray according to ribbon for protein and in magenta for CBM. Hydrogen, nitrogen, oxygen, and sulfur atom are painted white, blue, red, and yellow, respectively. Half-transparency is employed for the ribbon representation of protein regions overlying ligands in the selected view. A “green spring” representation is adopted for H-bonds involving ligand atoms. Panel (B) Stick representation of CBM poses in clust2 (light gray), clust3 (dark gray), and clust1 (magenta) after best fitting of protein backbone. CBM pose in clust1 was translated vertically for clarity.