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: wei.shi...@gmail.com
Subject: Re: [ccp4bb] distinguish ligand binding sites within a protein
To: CCP4BB@JISCMAIL.AC.UK
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
<tomas.malinaus...@gmail.com> 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 <wei.shi...@gmail.com> 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
