Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Disordered active sites
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-29

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Subject: Re: How to determine ligand binding from diffraction pattern?
From: "Soisson, Stephen Michael" stephen_soisson {- at -} MERCK {- dot -} COM
Date: 2007-05-29

Subject: Re: How to determine ligand binding from diffraction pattern?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-05-29

Hi Joe

In principle, a FOM-weighted difference Fourier using the known phases
of the apo structure is in essence a comparison of the diffraction
patterns, however in practice it relies on the apo & ligand-bound
crystals being highly isomorphous. The problem is that changes in the
diffraction due to non-isomorphism induced by soaking in the ligand
(e.g. possibly due to changes in the protein structure on ligand binding
or to effects of the DMSO or whatever you're using to solubilise the
compound) and differential effects of crystal freezing can easily swamp
the small differences in the diffraction due to the ligand, so it might
give you a definitive result and then again it might not! We usually
find that even for apparently isomorphous ligand-bound crystals the
degree of non-isomorphism is great enough that it's necessary to
incorporate a Molecular Replacement step using a limited search radius -
often rigid-body refinement alone clearly doesn't have a big enough
convergence radius to 'solve' the structure. If you have significant
non-isomorphism then clearly it makes no sense to compare diffraction
patterns as the molecular transforms are being sampled at different
points.

-- Ian

> -----Original Message-----
> From: owner-ccp4bb@jiscmail.ac.uk
> [mailto:owner-ccp4bb@jiscmail.ac.uk] On Behalf Of Joe Chen
> Sent: 28 May 2007 21:35
> To: ccp4bb@jiscmail.ac.uk
> Subject: How to determine ligand binding from diffraction pattern?
>
> Dear all,
>
>
> Is there a simple way to determine whether ligand is bound or
> not by comparing the diffraction patterns between ligand-free
> (structure known) and ligand-soaked protein crystals? I
> would like to solve the ligand bound protein structure, but
> before I do so, I have to find out if the ligand is actually
> bound. Thank you very much!
>
>
> Best,
>
>
> Joe
>
>

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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Disordered active sites
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-29

Next message:
Subject: Re: How to determine ligand binding from diffraction pattern?
From: "Soisson, Stephen Michael" stephen_soisson {- at -} MERCK {- dot -} COM
Date: 2007-05-29