Modeling and docking of the three-dimensional structure of the human melanocortin 4 receptor

A three-dimensional structure of the human melanocortin 4 receptor (hMC4R) is constructed in this study using a computer-aided molecular modeling approach. Human melanocortin 4 receptor is a G Protein-Coupled Receptor (GPCR). We structurally aligned transmembrane helices with bovine rhodopsin transmembrane domains, simulated both intracellular and extracellular loop domains on homologous loop regions in other proteins of known 3D structure and modeled the C terminus on the corresponding part of bovine rhodopsin. Then tandem minimization and dynamics calculations were run to refine the crude structure. The simulative model was tested by docking with a triplet peptide (RFF) ligand. It was found that the ligand is located among transmembrane regions TM3, TM4, TM5, and TM6 of hMC4R. In consistence with mutational and biochemical data, binding site is mainly formed as a hydrophobic and negatively charged pocket. The model constructed here might provide a structural framework for making rational predictions in relevant fields.