[transport] defs needed

[Midori Harris]

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