[RASMB] k_off rate

[Dmitry Veprintsev]

Dear Niko,
Although Kd =k_on/k_off, as Claus has suggested, you have to know one of 
the constants to determine the other. Calculating diffusion-limited 
on_rates may be helpful but can also be very misleading if there are any 
electrostatic interactions involved, and for proteins thay almost always 
are. If you really on/off rates, you will have to measure them. There 
are lots of methods available, starting with stopped-flow or dilution 
followed by fluorescence, CD or absorbance.  NMR - based techniques may 
also be useful. Calculating based on structure unfortunately has not 
matured enough to give this answer with any accuracy.
best regards, Dmitry

Wenta Nikola wrote:
>
> Dear Colleagues!
> In order to make my question more precise, I want to to calculate the 
> theoretically diffusion-controlled maximum possible k_off rate of a 
> given dimer based it's kD (from SE run), in combination with a 
> calculated diffusion coefficient for monomer and dimer by HydroPro.
> If anyone had any suggestions how to calculate that k_off rate, I 
> would be very grateful.
> Niko
>
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Dr. Dmitry Veprintsev
MRC Laboratory of Molecular Biology
Hills Road, Cambridge CB2 0QH, UK