Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y Receptor.

Understanding the agonist-receptor interactions in the neuropeptide Y (NPY)/peptide YY (PYY) signaling system is fundamental for the design of novel modulators of appetite regulation. We report here the results of a multidisciplinary approach to elucidate the binding mode of the native peptide agonist PYY to the human Y receptor, based on computational modeling, peptide chemistry and in vitro pharmacological analyses. The preserved binding orientation proposed for full-length PYY and five analogs, truncated at the amino terminus, explains our pharmacological results where truncations of the N-terminal proline helix showed little effect on peptide affinity. This was followed by receptor mutagenesis to investigate the roles of several receptor positions suggested by the modeling. As a complement, PYY-(3-36) analogs were synthesized with modifications at different positions in the common PYY/NPY C-terminal fragment (TRQRY-amide). The results were assessed and interpreted by molecular dynamics and Free Energy Perturbation (FEP) simulations of selected mutants, providing a detailed map of the interactions of the PYY/NPY C-terminal fragment with the transmembrane cavity of the Y receptor. The amidated C-terminus would be stabilized by polar interactions with Gln288 and Tyr219, while Gln130 contributes to interactions with Q in the peptide and T is close to the tip of TM7 in the receptor. This leaves the core, -helix of the peptide exposed to make potential interactions with the extracellular loops. This model agrees with most experimental data available for the Y system and can be used as a basis for optimization of Y receptor agonists.