Kd semantics

ChenHA via methods%40net.bio.net (by hzhen from freeuk.com)
Tue Feb 12 16:51:19 EST 2008


DK wrote:
> In article <1202849253.8712.0 from proxy01.news.clara.net>, ChenHA <hzhen from freeuk.com> wrote:
>> DK wrote:
>>> There can never be a strict threshold but for protein-protein 
>>> interaction the fuzzy boundary between real and not, specific 
>>> and not lies somewhere around tens of microM Kd. 
>> The bane of my life, trying to find out whether the binding of a protein 
>> or peptide is real or has any significance.  BTW, I had done experiments 
>> where I showed that a binding in the low mM range is real and specific 
>> (by NMR - you can show specific binding by the effect on particular 
>> cluster of residues).  Whether it has any significance is another matter 
>> entirely.
> 
> Thanks for joining my club :-)
> 
> My reasoning about tens of uM follows simply from the fact that few 
> proteins have intracellular concentration exceeding that. (Calmodulin, 
> which is pretty abundant, is estimated to be around 30 uM; actin  
> is not much higher, I think). So, unless the process is exlusively under 
> kinetic control (I think this is rather rare), it would have to work at
> this concentrations - which places a high limit on the Kd. 

That particular protein I worked on (years ago) is a membrane surface 
protein which has a tendency to cluster (there's other bane of my life, 
trying to stop protein aggregation messing up true binding), so the 
local concentration at the interaction site may be very high.  Doubtful 
it has any real significance, but you never know.


> 
> (Then, of course, there is always a possibility of molecule C 
> significantly affecting interaction between A and B, so people 
> tend to always assume some C really does exist...)
> 
> DK


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