Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor

Abstract

The prevailing paradigm for G protein-coupled receptors is that each receptor is narrowly tuned to its ligand and closely related agonists. An outstanding problem is whether this paradigm applies to olfactory receptor (ORs), which is the largest gene family in the genome, in which each of 1,000 different G protein-coupled receptors is believed to interact with a range of different odor molecules from the many thousands that comprise "odor space." Insights into how these interactions occur are essential for understanding the sense of smell. Key questions are: (i) Is there a binding pocket? (ii) Which amino acid residues in the binding pocket contribute to peak affinities? (iii) How do affinities change with changes in agonist structure? To approach these questions, we have combined single-cell PCR results [Malnic, B., Hirono, J., Sato, T. & Buck, L. B. (1999) Cell 96, 713-723] and well-established molecular dynamics methods to model the structure of a specific OR (OR S25) and its interactions with 24 odor compounds. This receptor structure not only points to a likely odor-binding site but also independently predicts the two compounds that experimentally best activate OR S25. The results provide a mechanistic model for olfactory transduction at the molecular level and show how the basic G protein-coupled receptor template is adapted for encoding the enormous odor space. This combined approach can significantly enhance the identification of ligands for the many members of the OR family and also may shed light on other protein families that exhibit broad specificities, such as chemokine receptors and P450 oxidases.

Figure 1

Predicted structure for mouse OR S25 with predicted binding site for hexanol (purple). The membrane is represented by a barrel of dilauroylphosphatidyl choline bilayers (yellow) surrounding the TMs 1–7. The disulfide bonds were assigned between Cys-107 to Cys-209, Cys-132 to Cys-192, Cys-199 to Cys-219, and Cys-157 to Cys-171.

Figure 2

Calculated binding energies for 24 odorants docked to the mouse OR S25. The binding energies were calculated as the difference between the energy of the ligand in protein and in solution. The solvation corrections were calculated by using the Poisson–Boltzmann continuum model for the solvent (22). Binding energy bars are shaded according to the chemical classes indicated above them. The letter “C” followed by a number indicates the number of carbon atoms. Hexanol and heptanol (marked with *) are the only two compounds of the 24 found experimentally to elicit responses (1). These compounds are correctly predicted by our model as having the most favorable binding energies.

Figure 3

Predicted recognition site for hexanol and heptanol in mouse OR S25. Residues within 3 Å of the ligand (hexanol in purple) are displayed as thicker with labels in bold font. Residues within 3–5 Å of the ligand have labels in italics. Lys-302 forms a weak hydrogen bond to the hydroxyl group of the alcohols. Phe-225 and Leu-131 seem to limit the chain length suitable to the binding site. TM 3–7 have residues directly involved in binding. (A) Longitudinal view. (B) Detail view. Hydrogen atoms were suppressed.