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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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difficult to describe MF: microtubule sliding brake #18152

Closed ValWood closed 5 years ago

ValWood commented 5 years ago

I want to describe the activity of acting as a brake to microtubule sliding. The mechanism is like this:

sliding

As overlapping microtubules start to slide apart, Ase1 molecules become compacted in the shrinking overlap and the sliding velocity gradually decreases in a dose-dependent manner. Compaction is driven by moving microtubule ends that act as barriers to Ase1 diffusion.

any suggestions?

I can't see anything suitable under https://www.ebi.ac.uk/QuickGO/term/GO:0003674

ukemi commented 5 years ago

microtubule lateral binding negatively_regulates 'plus end directed microtubule sliding'? I think the direction is correct. 'regulation of microtubule-based movement'

ValWood commented 5 years ago

OK I wondered if to do that, but I thought that we wanted to have "non-binding" only molecular functions if we knew more about the mechanism than "microtubule binding"? @pgaudet was that correct?

Anyway I can do it like this for now.

So in this case are we no longer using "positive" and "negative" regulation of process terms? I would like to be consistent with what we have done previously and request

'negative regulation of plus end directed microtubule sliding'

If we are using "negatively_regulates" to link functions to processes rather than have "regulation" process terms we should do it across all the annotation consistently?

ukemi commented 5 years ago

I think adding the negative regulation term would be ok if it is still within scope. I didn't list it because we didn't have it. That's why I made the GO-CAMesque expression in the second line. With respect to the binding function, I thought about the desire not to use them and the only other thing I could think of was the 'protein binding, bridging term' and then having an input of a tubulin or microtubule. It's not inhibiting the kinesin and it's not really cross-linking. It's just kind of getting in the way. That's why I went with lateral binding.

ukemi commented 5 years ago

Do you want me to add ''negative regulation of plus end directed microtubule sliding'?

ValWood commented 5 years ago

Yes I don't think there is any obvious way to describe this activity. I will do as you suggest, yes please can I have

negative regulation of plus-end directed microtubule sliding

ukemi commented 5 years ago

It is plus-end right, because the kinesin moves to the minus end?

ukemi commented 5 years ago

Do you have a PMID?

ValWood commented 5 years ago 
PMID:21892183

yes the sliding is plus-end directed.