Gating functions in protein networks

Gordon D. Pusch gdpusch at NO.xnet.SPAM.com
Fri Aug 1 14:39:34 EST 2003


Dan <dmb at mrc-dunn.cam.ac.uk> writes:

> Lord Snooty wrote:
>>  "Gordon D. Pusch" wrote:
>>> Dan <dmb at mrc-dunn.cam.ac.uk> writes:
>>> 
>>>> I think you can generate all logical functions using
>>>> just a simple combination of lesser functions, but I
>>>> forget which.
>>> 
>>> NAND (NOT(a AND b)) will work. Also NOR (NOT(A OR b)).  Also the
>>> "Sheffer stroke," <http://www.wikipedia.org/wiki/Sheffer_stroke>.
>>> There are several other possibilities. To build a NOR gate,
>>> insert two or more dissimilar repressor binding sites in between
>>> its promotor binding site and the gene; if a repressor protein
>>> binds to any of them, it shuts off transcription of the gene.
>>> (Of course, the boolean response will be "softened" due to chemical
>>> kinetics, but that's just a fact of life --- in both senses of the phrase! :-/)
>>
>> Thanks! This is exactly the kind of information I'm looking for. 
>> You've described a plausible physical model for implementation 
>> of a NOR gate. My only follow-up question would be whether we 
>> in fact observe this in specific instances, for any known genes?

Sort of. The "LAC operon" (lactose operon) in E. coli is _almost_ an
example of this, since the RNA polymerase won't transcribe the genes
downstream of the LAC repressor site unless the CAP site is occupied
and the LAC repressor site is NOT occupied. So the "logic" for the LAC
operon is (CAP AND (NOT LAC)): 
<http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/LacOperon.html>.


> Do you mean one gene with two separate negative control mechanisms?

Correct.


> (sorry I am not sure what NOR is)

"NOR" is a contraction of "NOT OR," as in "NOT (a OR b)," as I wrote above.
A "NOR" gate is "on" only when _neither_ of its inputs are "on," and "off"
if either of its inputs are on. In the case of a gene, it is "on" if it can
be transcribed to mRNA, and "off" if it is blocked from being transcribed;
this could in principle be achieve by putting two "repressor" binding sites
between it and its promoter.


-- Gordon D. Pusch   

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