Figure 2.

Inter-species and inter-isotypes three-dimensional PPAR protein structure comparisons. (a) Three-dimensional surface structure of bovine (residue 202–470; UniProtKB/TrEMBL Q5EA13) and mouse (residue 202–468; UniProtKB/TrEMBL P23204) PPARα ligand binding domain (LBD). The upper and lower panels include two views of the 3D structure of the PPARα protein in bovine and mouse species. The 3D structure is in full alignment between species. From the comparison, the difference in the ligand pocket of the PPARα between the two species is evident, with a larger and more pronounced pocket in bovine compared with mouse. In addition, the bovine PPARα appears to be more neutrally charged compared with the same protein in mouse. (b) Three-dimensional surface structure comparisons between PPARα (residue 202–470; Q5EA13), PPARγ (residue 234–505; O18971), and PPARβ/δ (residue 171–441; A4IFL4) LBD of bovine. Shown is the ligand pocket domain (green arrow) in two diverse views for each of the PPAR isotypes. The comparison highlights the larger and more neutrally charged ligand pocket in PPARα compared with the more negatively charged PPARγ ligand pocket and positively charged and small PPARβ/δ ligand pocket. The images were modified from [28]. Legend: red = negative charge; white = neutral charge; blue = positive charge. The 3D analyses were performed using Swiss-Pdb Viewer software (freely available at http://spdbv.vital-it.ch/).