transporter activity def

[gocentral]

Is the definition of transporter narrow enough?

I would tend not to annotate things to transpoter activity unless they are actually 'transporters' of some sort, not just if they have been shown to be involved in the transport process in some way (like a nuclear pore complex protein)

not sure if this is correct or not.....

see SF1229677 & 1224076 on the annotation tracker

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/2661":https://sourceforge.net/p/geneontology/ontology-requests/2661

[gocentral]

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Also see main transporter ontology item, 703326

more from closed duplicate item (1305954):

A couple of items on the annotation tracker (SF 1229677 & 1304683) are making me wonder if the def for transporter activity is a bit misleading.

"Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells"

This could be misleading as it seems as though it could apply also to molecules which are involved in the process of transport, but do not themselves have 'transporter activity'.

One of the examples from the Interpro mappings was a nuclear pore protein......

Original comment by: mah11

[gocentral]

• summary: transproter activity def --> transporter activity def

Original comment by: mah11

[gocentral]

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I think it's nice and straightforward to have a term:

transmembrane transporter activity def: 'Catalysis of the transport of a solute across a membrane.'

but I'm not sure if transporter activity is meant to include something else in addition to this.

I think a nuclear pore protein belongs in process since transport of a substance through a nucler pore is a multi-step business.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

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Also... When I was reading about nuclear pore transport it seemed to me that those proteins all had an activity like 'binding such-and-such' or 'folding-such-and- such' and that that's what the proteins would be annotated to in function, but that they'd be annotated to a transport term in process. Is that right?

Jen

Original comment by: jenclark

[gocentral]

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Hi Jen

Not all transporters involve catalysis, if they are purely transporting along a concentration gradient.

For the nuclear pore, I didn't think of the pore itself as a transporter so i just annotate the pore complex t term . I have, however annotated the karyopherins which bind and chaperone the proteins/mRNAs between the nucleus and the cytoplasm to 'transporter activity'. Actually to be precise I have annotated them to 'carrier activity' because they are sometimes described as 'protein carriers'. I just read the def of carrier and reilised this doesn't work so I'll move them up to 'transporter activity'. I think this annotation is O.K, (unless they should be annotated to a term like transport chaperone, or transport receptor) but I'm not sure how the definition should be worded.......

Original comment by: ValWood

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a bit of that got deleted. It should have said I didn't think of the pore itself as a transporter so i just annotate the pore complex to the appropriote binding terms and the process term for transport.

I'm not sure that what I have done is correct.....

Original comment by: ValWood

[gocentral]

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Hi Val,

I see what you mean. It sounds as if we have a number of concepts that we need to capture and we could at least straighten those out and then try to get a structure and some definitions.

Concepts:

1) There are gene products that are embedded in a membrane and catalyse transport of a solute across the membrane.

2) There are gene products embedded in a membrane that are just there to keep the pore open and allow things to diffuse across.

3) There are gene products that bind things and guide them through holes in membranes.

4) Maybe there are also gene products that bind things and guide them to where they want to go without crossing a membrane.

All these could be called transporter activity but they're not a single function. It seems to me that the current transporter activity term is kind of a grouping term and that's really not ideal.

I've got an idea but the wording is not going to be great. How about a better worded version of this:

[i]molecular_function ---[i]being-a-doorway-in-the-membrane transporter activity ---[i]carrying-things-along transporter activity

We could get rid of the tranporter activity grouping term altogether that way and still have the two sets of terms we need.

Is that kind of what you're looking for?

Jen

Original comment by: jenclark

[gocentral]

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You are right. Some of these things are not functionally related at all.

One suggestion for the term 'carrying-things-along transporter activity' is 'transport chaperone' which I believe was one term suggested to resolve the 'different kinds of chaperone activity issue'.

your being-a-doorway-in-the-membrane transporter activity is most similar to 'channel or pore class transporter activity'

Good luck with this!

val

Original comment by: ValWood

[gocentral]

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Hi Val,

Thanks, I'm glad I'm on the right track. Your transport chaperone sounds like a good name. I think the doorway term may need a less specific name since it will have child terms including channels, pores and lots of other things.

I'll have a think.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

• assigned_to: nobody --> jenclark

Original comment by: mah11

[gocentral]

• priority: 5 --> 3

Original comment by: jenclark

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Don't forget about this item when you tackle transporters!

m :)

Original comment by: mah11

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Logged In: YES user_id=516865 Originator: YES

I think this can be closed.

Original comment by: ValWood

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OK

(you know I love closing these)

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> TermGenie
• status: open --> closed-fixed

Original comment by: mah11