Gesendet: Donnerstag, 12. Dezember 2013 06:04
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] distinguish ligand binding sites within a protein
Hi Monica,
Yes, I am thinking of doing mutagensis to disrupt binding and do ITC again. Any
suggestions on which and how many residues I should mutate to
Hi Monica,
Yes, I am thinking of doing mutagensis to disrupt binding and do ITC again.
Any suggestions on which and how many residues I should mutate to disrupt
the binding of the ligand?
As I mentioned before that one of the two binding sites, which I am
thinking of mutating first, has the follow
; > 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 +, Xiaodi Yu wrote:
>> > >> >> Hi We
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
o 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
>>
>> __________________
>> 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
>
These things may give you some hints about which
> >> binding site is more strong.
> >>
> >> Dee
> >>
> >>
> >> __
> >> Date: Mon, 18 Nov 2013 22:45:58 -0500
> >>
trong.
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 l
> 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
> t
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
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?
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 wrote:
> Hi al
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 i
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