[transport] defs needed

[Jennifer Deegan (nee Clark)]

Thanks :-)

Jen

Midori Harris wrote:

> Hi,
> 
> Some ideas  ...
> 
>> dihydropyridine-sensitive calcium channel activity GO:0015270
> 
> 
> PMID:15486420 leaves me a little unsure whether dihydropyridine 
> sensitivity is relevant in vivo, but if the transport group wants to 
> keep the term, a def could be based on the original identification 
> criteria:
> 
>   1.Activation by strong depolarizations (high-voltage-activated [HVA]).
>   2.High sensitivity to dihydropyridine agonists and antagonists.
>   3.Relatively slow activation kinetics.
>   4.Calcium-dependent inactivation with little voltage-dependent
>     inactivation (long-lasting).
>   5.Large single-channel conductance.
> 
> (note, however, that one of the points the review makes is that there 
> isn't a nice neat correlation between being an L-type channel and having 
> one set of specific functional features)
> 
>> store-operated calcium channel activity GO:0015279
> 
> 
> Catalysis of the transmembrane transfer of an ion by a channel that 
> opens in response to a reduction in calcium ion concentration in the ER. 
> PMID:17361175
> 
>> volume sensitive anion channel GO:0005225
> 
> 
> Catalysis of the transmembrane transfer of an anion by a channel that 
> opens in response to changes in cell volume. (rest of std def here)
> PMID:8638650
> 
>> excitatory extracellular ligand-gated ion channel activity GO:0005231
>> Note:  Although there is only one direct annotation (Drosophila ISS) 
>> this term has children used for many annotations 
>> (mouse/rat/zfish/worm) which DO NOT appear to specify 'excitatory' 
>> ....should they?
> 
> 
> According to Alberts et al. (ISBN:0815316194), "excitatory" and 
> "inhibitory" refer to neurotransmitters, specifically whether they would 
> open cation channels (excitatory) or close anion channels (inhibitory) 
> when they bind. So GO:005231 can be interpreted as "channel gated by an 
> extracellular ligand that is an excitatory neurotransmitter" ... and 
> this brings us up against the same problems that David is trying to 
> resolve (see SFs 1695781 and 1695784) of whether a substance is ALWAYS a 
> neurotransmitter. Ugh.
> 
> Oh, and no, as far as I know, ATP is not an excitatory neurotransmitter.
> 
> https://sourceforge.net/tracker/index.php?func=detail&aid=1695781&group_id=36855&atid=440764 
> 
> https://sourceforge.net/tracker/index.php?func=detail&aid=1695784&group_id=36855&atid=440764 
> 
> 
>> amiloride-sensitive sodium channel activity GO:0015280<br>
> 
> 
> Again, not sure whether amiloride sensitivity is a real aspect of the 
> activity or just a handy identification tool in the lab; the wikipedia 
> entry is pretty molecule(s)-specific:
> 
>   http://en.wikipedia.org/wiki/Amiloride-sensitive_Sodium_channels
> 
> The string might work as a narrow or related synonym for something more 
> descriptive of an activity, e.g. "ligand-gated sodium ion channel 
> activity," which could then get a standard def.
> 
> have fun!
> m

-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium