Prediction of structure and function of G protein-coupled receptors

Abstract

G protein-coupled receptors (GPCRs) mediate our sense of vision, smell, taste, and pain. They are also involved in cell recognition and communication processes, and hence have emerged as a prominent superfamily for drug targets. Unfortunately, the atomic-level structure is available for only one GPCR (bovine rhodopsin), making it difficult to use structure-based methods to design drugs and mutation experiments. We have recently developed first principles methods (MembStruk and HierDock) for predicting structure of GPCRs, and for predicting the ligand binding sites and relative binding affinities. Comparing to the one case with structural data, bovine rhodopsin, we find good accuracy in both the structure of the protein and of the bound ligand. We report here the application of MembStruk and HierDock to beta1-adrenergic receptor, endothelial differential gene 6, mouse and rat I7 olfactory receptors, and human sweet receptor. We find that the predicted structure of beta1-adrenergic receptor leads to a binding site for epinephrine that agrees well with the mutation experiments. Similarly the predicted binding sites and affinities for endothelial differential gene 6, mouse and rat I7 olfactory receptors, and human sweet receptor are consistent with the available experimental data. These predicted structures and binding sites allow the design of mutation experiments to validate and improve the structure and function prediction methods. As these structures are validated they can be used as targets for the design of new receptor-selective antagonists or agonists for GPCRs.

Figure 1

(A) Comparison of predicted structure for bovine rhodopsin (green) with the x-ray crystal structure (blue). The TM regions have a CRMS of 3.1 Å. (B) Comparison of the HierDock predicted structure of cis-retinal/Rhodopsin to the crystal structure.

Figure 2

(A) Predicted binding site of epinephrine in the predicted structure of β1-adrenergic receptor. (B) Residues within 5 Å of epinephrine bound to β1-adrenergic receptor. Shown in bold are the three residues Asp-138, Ser-229, and Ser-232 (deduced from mutation experiments to be involved in binding).

Figure 3

Residues within 5 Å of the sphingosine-1-phosphate in the predicted structure of EDG6.

Figure 4

Binding site of octanal in rat I7 OR.

Figure 5

Binding site of trehalose in human sweet receptor. This shows residues within 3 Å of trehalose and includes the hydrogen bonds to Ser-798, Ser-646, and Lys-785.

Figure 6

Comparison of the predicted binding sites for GPCRs: white, bovine rhodopsin; green, rat I7 OR; blue, mouse I7 OR; red, β1AR.