When the artificial amino acid, Azi, was added to any spot where the CFR1R ligand attached to the receptor, the sticky hand grabbed the ligand, a molecule called urocortin-1, and kept it bound to the receptor. If Azi was integrated into a place where urocortin-1 didn't associate, however, it would have nothing to grab. By detecting whether CFR1R and urocortin-1 become irreversibly attached, the researchers would know whether the Azi had been integrated into part of the binding pocket or not.
Repeating this technique throughout the CFR1R molecule revealed that the receptor's binding pocket consisted of at least 35 amino acids. But that didn't give the researchers the full picture they wanted of the interaction.
"This first, sticky hand probe had given us information about the shape of the binding pocket," says Wang. "But we still didn't know how the ligand is oriented inside that pocket."
So they used a second probe--one which was more selective than the "sticky hand" in the receptor. This time, the probe would only capture one particular amino acid--cysteine. "We inserted cysteines along the ligand to figure out which parts of the receptor were close to precise spots of the ligand", says Wang. It took more than a hundred different combinations to get a perfect match, where the artificial amino acids in the receptor lined up with the cysteines in the urocortin-1.
"We discovered that the ligand lies in the receptor's binding pocket like a too-tall person in a bathtub," Coin says. "One end of the ligand is like the head sticking out, and on the other end, the feet are dangling out."
"This shape makes sense in light of previous data," says Wang. "Because we already knew that you can add a lot of molecules onto the feet of the ligand and it doesn't affect the receptor-li
|Contact: kat Kearney|