Binding of Natural Peptide Ligands to the Neuropeptide Y₅ Receptor

The binding mode of natural peptide ligands to the Y₅ G protein-coupled receptor (Y₅ R), an attractive therapeutic target for the treatment of obesity, is largely unknown. Here, we apply complementary biochemical and computational approaches, including scanning of the receptor surface with a genetically encoded crosslinker, Ala-scanning of the ligand and double-cycle mutagenesis, to map interactions in the ligand-receptor interface and build a structural model of the NPY-Y₅ R complex guided by the experimental data. In the model, the carboxyl (C)-terminus of bound NPY is placed close to the extracellular loop (ECL) 3, whereas the characteristic α-helical segment of the ligand drapes over ECL1 and is tethered towards ECL2 by a hydrophobic cluster. We further show that the other two natural ligands of Y₅ R, peptide YY (PYY) and pancreatic polypeptide (PP) dock to the receptor in a similar pose.