#11407 Channel activity defined too strictly?

[Valerie Wood]

I raised an issue with SGD about the use of "protein channel activity" to describe the Tim23 complex.

channel activity is defined

"Catalysis of energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules."

(also all of the children, I was particularly concerned with protein channel in this instance).

It is a child of "passive transmembrane transporter activity"

Rama pointed out
Tom40 forms the channel in the outer membrane, while Tim23 does the same in the inner membrane.
Channels operate in many ways (during facilitated diffusion or passive transport) and change in membrane potential is one of them.
Definition could be better.

So it seems our use of "channel" is quite strictly defined (certainly many things which are annotated to 'channel' do not fit this def).

[Valerie Wood]

We should probably avoid the use of the word "channel" in the primary term names if we want to include the mechanism here.

[David Osumi-Sutherland]

AFAIK - The distinction between transporter activity (active transport via ATP dependent pumps or powered directly by PD) and channel activity (passive diffusion - which can be down a concentration gradient) works well for ion channels.

Looks like the term channel may be used more broadly in the case of protein transport. The TOM/TIM example looks informative. Can you sketch out some more details - emphasising which steps are active and which (if any passive)? Also wondering if the disinction here is between subunit on its own been channel forming (Tom40) but functioning in the context of active transport (HSP90 / coupling with TIM?).

[Valerie Wood]

Will ask SGD to comment, if they aren't monitoring.
Val

[Maria C. Costanzo]

Transport through the TOM and TIM complexes is definitely energy-dependent, so Val is right that we shouldn't be using the term as defined. However, they are always referred to as channels. PMID: 23912355 has a nice review of the mechanism.

Maria

[Rama balakrishnan]

Yes, there are both energy dependent (ATP hydrolysis) and energy independent (passive, diffusion, change in membrane potential based channels). So the definition of protein channel should include both aspects.
In the case of Tim23 in yeast, its channel activity is based on potential difference across the membrane.

Rama