Odorant Binding Proteins

[primaryodors]

This is on hold until #263 is complete.

Odorant binding proteins (OBPs) are thought to help odorants, most of which are oil-soluble, disperse into the aqueous mucus layer of the olfactory epithelium. It is also postulated that OBPs might "deliver" odorants to the odor receptors themselves.

This task will be to use the models in the pdbs/OBPs/ directory to investigate whether OBPs have any screening or filtering effect on the absorption of odorants by odor receptors. Specific areas for investigation include:

• Whether the OBP can make contact with the extracellular ends of the receptors;
• If so, whether the exact positioning of the OBP primes the odorant to enter a specific binding pocket, and whether it depends on the OR;
• If the proteins contact, whether the OBP primes the orientation of the odorant for insertion into the OR and its orientation inside the binding pocket;
• Whether the active or inactive form of the OR (or both) is/are involved in any of the above functions;
• Whether involving an OBP in the docking of ligands to receptors improves the prediction accuracy.

The included PDBs are:
hOBP2A: Q9NY56, 4run.pdb
hOBP2B: Q9NPH6

[electronicsbyjulie]

The OBPs have four arginines (R82, R96, R119, R73*) forming almost a right angle, that look like they could span along EXR2 or across EXR2 and EXR3. This could place the "mouth" of the OBP so that it can eject the odorant into the space between TMR5, TMR6, TMR7, and the EXR2 helix.

OBP2B has H119 instead. It also has L123 instead of R, possibly affecting the inter-protein contacts and making it likely that some ORs might prefer one OBP over the other.

Lys127 is important for binding certain aldehydes (source: https://www.sciencedirect.com/science/article/pii/S1631074808002270), and there is a large hydrophobic pocket involving W29, Y30, F66, F112, and several aliphatic residues. Together, this can form a sort of channel that the ligand can pass through in order to get into the receptor's binding site, limiting the possible rotamers of ligands too large to turn around inside the channel.

[primaryodors]

Let's check out some of the high priority Above average priority. issues before we tackle this one.