Modeling of the recognition site of the NK₁ receptor

The tachykinin receptor, NK₁, and its native neuropeptide ligand, substance P, are believed to play a major role in the biochemistry of inflammation and in the transmission of pain. The binding of substance P is known to involve extracellular as well as transmembrane regions of the NK₁ receptor. Reported here is the design of a model of the recognition site of the second transmembrane domain of the NK₁ receptor. Molecular mechanics calculations were employed to evaluate the potential of six polypeptides corresponding to the first, second and third transmembrane domains of the NK₁ receptor, to bind with substance P. One of the most promising of these models contained 30 amino acid residues corresponding to part of the first extracellular region coupled to the second transmembrane domain. A model of reduced size (18 amino acid residues) that contains the correct type and location of the amino acid residues predicted to be involved in ligand binding was used to validate the results of the molecular mechanics calculations. One-dimensional proton NMR spectra acquired in DMSO-d₆ indicated that this 18 amino acid residue polypeptide forms a complex with substance P.