Odorant Receptor 7D4 Activation Dynamics

Abstract

Deciphering how an odorant activates an odorant receptor (OR) and how changes in specific OR residues affect its responsiveness are central to understanding our sense of smell. Aj oint approach combining site-directed mutagenesis and functional assays with computational modeling has been used to explore the signaling mechanics of OR7D4. In this OR, ag enetic polymorphism affects our perception of androstenone.M olecular simulations totaling 0.12 ms predicted that, similarly to observations for other G-protein-coupled receptors with knowne xperimental structures,a na ctivation pathway connects the ligand and the G-protein binding site.T he 3D model activation mechanism correlates with in vitro data and notably predicts that the OR7D4 WM variant is not activated. Upon activation, an OR-specific sequence motif is the convergence point of the mechanism. Our study suggests that robust homology modeling can serve as ap owerful tool to capture OR dynamics related to smell perception.Our sense of smell is triggered by the activation of odorant receptors (ORs) expressed on the surface of olfactory sensory neurons.Smelling relies on aso-called combinatorial code of OR activations. [1] Our approximately 400 ORs endow us with spectacular discriminatory power. ORs represent more than 3% of our protein-coding genes and belong to the class AGprotein-coupled receptor (GPCR) family.S tructurally, class AGPCRs are made up of seven transmembrane helices (TMs), named TM1 to TM7, which form abundle within the cell membrane.U pon activation, an allosteric signal is transmitted from the ligand to the G-protein binding site over ad istance of more than 20 (ca. 5h elix turns). [2] The intracellular part of TM6 then tilts outward with respect to its position in the inactive state. [3] Mammalian OR sequences show ah ighly conserved and OR-specific RxKAFSTCxSH motif in the intracellular part of TM6, suggesting acrucial role in the control of OR activation. In non-olfactory class AG PCRs,o nly the second lysine residue is conserved. [4] Odorant-receptor-activation dynamics still remain to be uncovered, but as ignificant body of work has focused on the molecular details of OR activation, especially concerning the interaction between ORs and ligands. [5] Thes trength of molecular-modeling approaches on GPCRs was demonstrated by ag roundbreaking study based on homology modeling and virtual screening, which deorphanized GPR68 and GPR65. [6] By applying this approach to ORs,w er ecently demonstrated how certain mutations alter receptor function or dynamics. [4,7] Human OR7D4, which is narrowly tuned to detect the testosterone metabolites androstadienone and androstenone, is as pectacular example of how natural sequence variations can affect activation and subsequent odor perception. People with two copies of the most common genetic variant (OR7D4-RTorw ild type,w t) tend to describe the androstenone smell as sickening,putrid, foul, or urine-like.However, people who possess the unresponsive R88W/T133M variant (OR7D4-WM) tend to report the smell to...

Copper-mediated thiol potentiation and mutagenesis-guided modeling suggest a highly conserved copper-binding motif in human OR2M3

“…S13, Table 4). A ligand-binding function of position Cys202 5.41 was previously reported for human OR1G1 (Ile201 5.41 ) and OR7D4 (Ala202 5.41 ) [97] and for mouse Olfr544 (MOR42-3) (Thr205 5.41 ) [107] (summarized in Fig. S13 and Table 4).…”

“…For several odorant receptors, tyrosines at positions 252 6.44 and 259 6.51 have been shown to be involved in ligand binding [10,32,50,[94][95][96][97][98][99]. We, therefore, exchanged these tyrosines to alanines and tested the resulting OR2W1 variants against the three agonists 2-phenylethanethiol, 3-mercaptohexyl acetate, and allyl phenyl acetate.…”

Concentration-Dependent Recruitment of Mammalian Odorant Receptors

“…The inactive conformation of an OR is maintained by the ionic interaction, called ionic lock, between D 3.49 belonging to the motif D 3.49 RY common to the GPCR superfamily and R 6.30 belonging to the motif R 6.30 xKAFSTCASH specific to the OR family. During activation, conformational changes in the receptor are associated with a break of this ionic interaction and a switch of the intracellular part of TM6 toward the membrane, opening an intracellular cavity for the G protein coupling (de March et al, 2015b;de March et al, 2018). By observing our multiple molecular dynamics simulations, we noticed that…”

“…Furthermore, it was shown recently that molecular dynamic simulations of ORs can sample active or inactive states of the receptor when bound to an agonist or a non-agonist, respectively (de March et al, 2015b;de March et al, 2018). The most accurate parameter to monitor receptor activation in molecular dynamics simulations is the distance between the intracellular part of TM3 and TM6, particularly between the two protagonists of the ionic lock in GPCR ( Figure 7E) (Altenbach et al, 2008;de March et al, 2015b;de March et al, 2018). The inactive conformation of an OR is maintained by the ionic interaction, called ionic lock, between D 3.49 belonging to the motif D 3.49 RY common to the GPCR superfamily and R 6.30 belonging to the motif R 6.30 xKAFSTCASH specific to the OR family.…”

Agonists of G-Protein-Coupled Odorant Receptors Are Predicted from Chemical Features

“…Other agonists present outside this domain could be discovered using molecular modeling to predict ligand activity based on receptor activation dynamics. 27 Furthermore, to understand the link between the strength of a response and receptor features, a 3D model of OR51E1 was built. We showed how some residues in the cavity can selectively affect efficacy.…”