Yep, just did the calculation - for 2.6 nm looks like it will pretty much
all be bound. Great stuff!!
---------------------------- Original Message ----------------------------
Subject: Re: Binding studies
From: Sébastien Morin <sebastien.mori...@ulaval.ca>
Date: Thu, February 24, 2011 11:01 am
To:
Cc: "Edward d'Auvergne" <edw...@nmr-relax.com>
"Maddy Strickland" <m.strickl...@bristol.ac.uk>
"relax-users@gna.org" <relax-users@gna.org>
Sébastien M <sebast...@nmr-relax.com>
--------------------------------------------------------------------------
Hi again,
One last comment:
Is the KD known ? If yes, than the population of bound complex can be
calculated from the following relation:
Bound = ( [Ligand] ) / ( KD + [Ligand] )
For example, with a KD of 100 uM (0.1 mM), a concentration of ligand of
1 mM (matched with a protein concentration smaller or equal to 1 mM)
would yield a steady-state bound population of ~91% (0.91).
Cheers,
Séb :)
On 11-02-24 11:13 AM, Sébastien Morin wrote:
> Hi,
>
> I have not worked with this situation.
>
> However, I agree that binding kinetics should be known (on and off
> rates) and a majority of bound complex should exist over time,
> otherwise the situation might be tricky since some contribution from
> unbound protein might arise (with a shorter correlation time, and
> potentially different dynamics). Also, contribution from potential
> conformational exchange caused by binding and unbinding of the ligand
> (depending on the exchange rate, i.e. on and off rates), rather than
> 'real' changes in dynamics on the protein, could complicate analysis
> and give a false impression of changes in the protein dynamics.
>
> I hope this helps.
>
> Best regards,
>
>
> Séb :)
>
>
> On 11-02-24 10:45 AM, Edward d'Auvergne wrote:
>> Hi,
>>
>> This can be tricky. Can you estimate the percentage of monomer verses
>> dimer? Can you also estimate the amount of time the peptide binds to
>> the receptor? Do you have binding data for the NMR sample conditions?
>> If the more than 90% of the receptor is bound to the peptide and the
>> time bound to the receptor is significant, then you should be able to
>> handle this with standard model-free analysis using a single diffusion
>> tensor. This will likely require data at 2 or more field strengths.
>> Seb, have you worked with this situation?
>>
>> Regards,
>>
>> Edward
>>
>>
>> On 23 February 2011 11:04, Maddy
>> Strickland<m.strickl...@bristol.ac.uk> wrote:
>>> Hi everyone,
>>>
>>> I'm moving on to looking at dynamics of binding to a receptor which
>>> I've
>>> already studied using Relax for Lipari-Szabo data. I was wondering
>>> if I
>>> added some unlabelled peptide to the 15n receptor how I could study the
>>> new relaxation data? Can I still use Relax and the same pulse
>>> sequences
>>> etc. or do I need a program specific to binding? It's a fairly strong
>>> binder, but it would render the receptor more of a cylinder than a
>>> sphere... What do you all think?
>>>
>>>
>>> Madeleine Strickland
>>>
>>>
>>>
>>> _______________________________________________
>>> relax (http://nmr-relax.com)
>>>
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>
--
Sébastien Morin, Ph.D.
Postdoctoral fellow
S. Grzesiek NMR Laboratory
Biozentrum, Universität Basel
Basel, Switzerland
Madeleine Strickland
MCJC Group
N317, School of Chemistry, Bristol University
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