Kd semantics

ChenHA via methods%40net.bio.net (by hzhen from freeuk.com)
Tue Feb 12 15:42:38 EST 2008

DK wrote:
> In article <foounk$dd9$1 from oravannahka.helsinki.fi>, kaj.stenberg from helsinki.fi.invalid wrote:
>> DK <dk from no.email.thankstospam.net> wrote:
>>> In article <fomluv$bge$3 from oravannahka.helsinki.fi>,
>> kaj.stenberg from helsinki.fi.invalid wrote:
>>>> This is probably trivial, but it confuces me:
>>>> If the Kd for a ligand is mM it binds poorly, if the Kd is nM it binds
>>>> well. But in which case does one refer to the Kd as being "higher" or
>>>> "lower"?
>>> mM is "higher" than nM. However, sometimes people switch from 
>>> talking about Kd to talking about "affinity". Affinity is "higher" when
>>> Kd ~ nM. 

Yes, people tend to say "X has a high affinity binding with a Kd of 
...", the reason probably being that affinity is easily understood 
semantically, while the number from Kd is easily understood 
scientifically.  No problem if you know what affinity is, but many 
student don't.

>> Thank you, "affinity" is of course unambigious, I did just not come to 
>> think of it. 
>> Just another thing: when can you start talking about a "real" (as in
>> specific) affinity? I am reading papers with a Kd in the ballpark of
>> tens of millimolar and find it hard to repeat the work so that I truly
>> believe in the results, since every random event seems to affect the 
>> curves fairly much.
> AFAIK, for proteins > mM affinities are usually derived indirectly 
> from some other data (such as Km) rather than measured. 
> 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 


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