Correlations between odorant perceptual qualities and odorant receptor agonism show several candidate receptors for a fruity perceptual quality, though no single receptor is fully associated with “fruity” as an odor descriptor. Here we present a hypothesis that fruitiness may be perceived when multiple receptors from a specific group are activated. We further consider the effects […]
Read MoreWhile it is believed that very few real world odors are “primary”, since neary every aroma compound would have multiple human olfactory receptors that are sensitive to it, empirical measurements of receptors’ responses to odors usually identify at most a handful of receptors, often as few as one or even zero. To compound the problem, […]
Read MoreThis dock of d-limonene in OR2B11 shows Tyr256 displaced “down” (i.e. in the cytoplasmic direction) from its pre-dock position (transparent image, lowercase label) near a position of forming a hydrogen bond with Glu115. Tyr256 is in an analogous location to the known highly conserved Trp6.48 important to activation of non-OR GPCRs. Almost all ORs have […]
Read MoreWhile aromas must certainly occupy a perceptual space, the dimensionality of this space remains mired in uncertainty. It has even been argued that the number of dimensions might equal the total number of olfactory receptors themselves! Conceivably, the perceptual space could be less than 400-dimensional, perhaps as little as 30-40 dimensions, if the various receptors […]
Read MoreAstute readers of this website may notice something different: The 3D views for receptors and aroma molecules have been rewritten. Gone is the slow, bulky, buggy JSmol viewer and here to stay is a newer, faster, better 3D renderer, called NGL. Not gonna lie, this 3D engine is impressive in its performance and appearance! You […]
Read MoreSynthesis of 1-octanethiol was attempted by carefully reacting Na2S with sulfamic acid in aqueous solution, beneath a layer of 1-octanol, in a glass vessel that would allow the contents to react under pressure. The odor of hydrogen sulfide was observed. Several hours later the octanol layer was removed and was found to have a definite […]
Read MoreThe Primary Odors docker, or POdock, is an open source molecular docker designed to offer advantages over other dockers. Here we report a successful dock of the aroma compound cadaverine in TAAR8, a known agonist-receptor pair. The change in orientation of the TRP270 side chain is significant. This residue, and the aromatic TYR273 above it, […]
Read MoreHuman TAAR5 may contain an amine-shuttling extracellular α-helix, analogous to a similar structure postulated to exist with a similar function in ORs. TAAR5 is a known receptor for fishy smelling trimethylamine, among other compounds. Like most TAARs, it has an acidic residue inside its ligand binding pocket, located on TMR3 (ASP114) close to a tryptophan […]
Read MoreUsing the new POdock software, we have obtained promising initial results indicating that the changes in binding strengths along a path may be good predictors of which ligands will activate a given receptor. POdock offers a feature not commonly found in docking software, which is the ability to move each generated pose along a path […]
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