This is a dock result of allyl phenylacetate in a predicted active conformation of OR1A1. The active model was generated by applying internal contact changes similar to those known for OR51E2, mTAAR9, and non-olfactory GPCRs. This dock shows the aromatic ring of the ligand in a pi stacking position between two of the receptor’s aromatic […]
Read MoreThe function of the HXXCD/E motif in extracellular loop 2 of many ORs has been debated. One study found that this sequence makes for a strong zinc-coordinating locus, which folds into an alpha helix as it binds the Zn2+ ion. Reasonably, that study postulated that the motif may bind zinc to the extracellular end of […]
Read MoreOR51E2 is a receptor for propionic and acetic acids, and its agonists tend to smell vinegar-like. Other short chain fatty acids (SCFAs) with chains of up to 5 carbon atoms activate this protein progressively less strongly with increasing chain length, and SCFAs of 6 carbons or more are non-agonists and have odors that are more […]
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 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 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 […]
Read MoreFor purposes of researching more accurate computation and prediction of receptor-ligand interactions and receptor activation by agonists, we have created a molecular docker. Like other software packages such as AutoDock and LeDock, our application finds ligand conformers (poses) inside binding pockets of proteins and is available free of charge. But in addition, POdock outputs not […]
Read MoreOlfactory receptors (ORs), being G-protein coupled receptors (GPCRs), exist in an equilibrium between several conformational states. Most of the time, the dominant conformation is the inactive state, which cannot bind a G-protein and signal the cell to the presence of an odorant, while a certain other conformation can bind a G-protein and initiate this signaling, […]
Read MoreAccording to an article by Cheng et al (2010), figure 1, there exist several pathways for GPCR signaling following receptor activation. One of these involves cAMP while another involves Ca²⁺. However, there is the potential for false positives by this method, as well as false negatives because a given receptor or receptor-ligand pair might bind […]
Read MoreAn error was found in the code that was measuring the types and strengths of interactions between odorants and individual binding site residues (BSRs). The gist of the error was that it treated every ligand atom as capable of only van der Waals interactions, the kind that saturated hydrocarbons have, and therefore did not calculate […]
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