[RASMB] k_off rate

[Claus Urbanke]

Dear Nikola.

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.

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)
Anyhow, the equation is

k(21)=4 Pi() R(0) N(L) ?D(A)?D(B)??B

with
R(0) : reaction distance of the two molecules (this distance must be the 
distance of their cenetrs of gravity)
D(A),D(B) : diffusion coefficient of the two molecules
N(L) Avogadro number
B : 1000 m^3/L
k(21) : dissociation rate constant
Pi(): 3.14......


but be very careful in interpreting the results.

With heavy "Bauchschmerzen" and best wishes

Claus

Wenta Nikola schrieb:
>
> Dear Colleagues!
> 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?
> I am grateful for any suggestions.
> Niko
>
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-- 
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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