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.morin.1@xxxxxxxxx>
Date: Thu, February 24, 2011 11:01 am
To:
Cc: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
"Maddy Strickland" <M.Strickland@xxxxxxxxxxxxx>
"relax-users@xxxxxxx" <relax-users@xxxxxxx>
Sébastien M <sebastien@xxxxxxxxxxxxx>
--------------------------------------------------------------------------
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.Strickland@xxxxxxxxxxxxx> 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
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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
[Fwd: Re: Binding studies]