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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Change label 'GO:0044183 protein binding involved in protein folding' and move as a direct child of molecular function #16649

Closed pgaudet closed 5 years ago

pgaudet commented 5 years ago

I propose to change the label of 'protein binding involved in protein folding' to a label more easy to find: 'protein folding chaperone'.

As well, I'd like to make it a direct child of molecular function, as this is a true 'molecular activity', not just a binding.

ValWood commented 5 years ago

Also in the ticket I just closed as "duplicate" what about: unfolded protein binding (GO:0051082)

does that mean something slightly different?

pgaudet commented 5 years ago

I dont think these are different. I think the unfolded protein is just how you test protein folding (ie you denature it and look at it unfold). See http://science.sciencemag.org/content/353/6294/aac4354?casa_token=x0P-xac5lWQAAAAA:fi7awS-rnamIvw7KN9PU3LpLl9Szx8SVreXjkfFni97c8XtdBNlTJyhqrPMPHaI4aKFTdUhtjkHI1a8

What do you think ? (I think there is another ticker somwehere else).

ValWood commented 5 years ago

I can't think of any immediate difference but it might be good to ask more widely...

Maybe there are instances of binding to an unfolded protein to catabolise it, not to fold it? I don't really know....

pgaudet commented 5 years ago

I'll go ahead and do that. Just pinging a few people for comments: @thomaspd @vanaukenk @RLovering @hattrill

Pascale

pgaudet commented 5 years ago

@ValWood The new name will be 'protein folding chaperone'. If there is a need for 'protein degradation chaperone' we can create that later.

ValWood commented 5 years ago

good point!

pgaudet commented 5 years ago

Changing the logical definition to

molecular_function and 'has part' some 'protein binding' and ('part of' some 'protein folding')

@ukemi does that seem OK to you ?

hattrill commented 5 years ago

With regard to "unfolded protein binding", there are chaperones/co-chaperones/small HSPs that bind unfolded proteins to keep them unfolded so that they can be correctly folded by ATP-dep. chaperones or stop them from making big, nasty aggregates under cell stress.

ukemi commented 5 years ago

Correct. I'm not sure all of these refold the proteins. Sometimes they target them for destruction. That was part of the confusion with the original chaperone term.

pgaudet commented 5 years ago

@hattrill @ukemi This term specifically describes a protein folding activity - the definition "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding."

We can discuss terms for unfolded protein binding separately if needed.

Pascale

RLovering commented 5 years ago

sounds good to me