IMHO, while explaining binding affinity from a structure is fun, it does not prove anything. Assuming that I understand your situation correctly, you can (relatively) easily find out from experiment which pocket has higher affinity. Just do soaks with different ligand concentrations - the expectation is that the weaker binding site will become partially occupied first.
On Tue, 2013-11-19 at 04:58 +0000, Xiaodi Yu wrote: > Hi Wei: > > Based on the structure, you can calculate the binding surface between > the protein and the ligand. Maybe the two binding pockets will give > you two different numbers. And the larger one usually can have the > higher binding affinity. You also can analyse how the ligand > interacts with the protein though hydrophobic or electrostatic > interaction , etc? the last, you may also compare the b factors of > the ligand or the protein binding pocket regions after you refining > the structure. These things may give you some hints about which > binding site is more strong. > > Dee > > > ______________________________________________________________________ > Date: Mon, 18 Nov 2013 22:45:58 -0500 > From: [email protected] > Subject: Re: [ccp4bb] distinguish ligand binding sites within a > protein > To: [email protected] > > Thank you so much for the suggestions, Tomas! Yes, my ligand is a > small molecule. I have the crystal structure of the ligands bound to > the protein, do I still need to computationally dock the ligand to the > two pockets, can I calculate the parameters of binding directly using > the crystal structure? > > Best, > Wei > > > > On Mon, Nov 18, 2013 at 9:03 PM, Tomas Malinauskas > <[email protected]> wrote: > Dear Wei Shi, > is your ligand a small molecule? If it is a small molecule, I > would > try to computationally dock the small molecule to two pockets > separately using AutoDock, and look at the estimated free > energies of > binding. > Best wishes, > Tomas > > On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi > <[email protected]> wrote: > > Hi all, > > I got the crystal structure of a transcription factor, and > every monomer > > binds two molecules of the same ligand in different binding > pockets. And I > > also did the ITC experiment, titrating the ligand into the > protein, and got > > a U-shaped curve. The binding affinity for the first binding > site is higher > > than the second binding site. > > I am wondering whether I could computationally determine > from the > > protein-ligand complex structure that which binding site has > higher affinity > > for the ligand and correlate the binding sites with the > parameters I got > > from ITC experiment. > > Thank you so much! > > > > Best, > > Wei > > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
