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Dear Nikola.<br>
<br>
to make it perfectly clear, thermodynamic affinities and kinetic rate
constants are two different things and you cannot calculate kinetic
constants from affinities (while you may try to calculate an affinity
from known kinetic constants). The affinity may be calculated as the
ratio of on- and off rate constants (Guldberg Wage law) and any
combination of these two can result in a given affinity. You need to
know one of the rate constants to calculate the other.<br>
<br>
Thus, don't be bothered by your Kd, but use the Debye Smoluchowsky
theory of
diffusion controlled reactions instead. With this you can estimate the
diffusion controlled dissociation rate constant as beeing roughly the
reciprocal of the time it takes for the dissociating molecule to
diffuse across the
diameter of the reaction sphere (which to me sounds reasonable). This
will give you the rate of the two molecules separating after all
interactions have been destroyed and does most probably not represent
the lifetime of the associated state (which would be the 1/k_off you
might want to know)<br>
Anyhow, the equation is<br>
<br>
k(21)=4 Pi() R(0) N(L) D(A)D(B)⋅B<br>
<br>
with <br>
R(0) : reaction distance of the two molecules (this distance must be
the distance of their cenetrs of gravity)<br>
D(A),D(B) : diffusion coefficient of the two molecules<br>
N(L) Avogadro number<br>
B : 1000 m^3/L<br>
k(21) : dissociation rate constant<br>
Pi(): 3.14......<br>
<br>
<br>
but be very careful in interpreting the results.<br>
<br>
With heavy "Bauchschmerzen" and best wishes<br>
<br>
Claus<br>
<br>
Wenta Nikola schrieb:
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<p><font size="2">Dear Colleagues!<br>
Does anyone know how to calculate the k_off rate of a given dimer from
it's kD? As the kD was found from Sedimentation Equilibrium, there are
no kinetic information within. But there exists a crystal structure of
that dimer, and with HydroPro, I obrained a diffusion coefficient for
the dimer as well as for the monomer. Does anyone has any suggestions
how to calculate my protein's k_off rate?<br>
I am grateful for any suggestions.<br>
Niko<br>
<br>
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<pre class="moz-signature" cols="72">--
Prof. Dr. Claus Urbanke
Medizinische Hochschule
Abtlg. Strukturanalyse OE 8830
Carl-Neuberg Str. 1
D-30625 Hannover
Tel.: +49 511 532 9372
FAX: +49 511 532 5966
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