protein maturation by protein folding (GO:0022417) parentage and other issues

[ValWood]

protein maturation by protein folding (GO:0022417) but currently, ALL protein folding is_a "protein maturation"

protein folding is "protein maturation" is incorrect (only de novo protein folding is maturation)

SUGGEST 1) obsolete protein maturation by protein folding (GO:0022417) direct replacement 'de novo' protein folding (GO:0006458)

2) remove parent 'protein maturation' from protein folding add instead to 'de novo' protein folding (GO:0006458)

[ValWood]

Maybe, based on this definition Any process leading to the attainment of the full functional capacity of a protein.

All folding it maturation, but that doesn't seem quite right. Will check.

[pgaudet]

Hi @ValWood

I am not sure we need the distinction between de novo protein folding and protein refolding. AFAIK these are mediated by the same proteins. (I thought there was a ticket about this but I cannot find it right now).

Protein folding is now a MF, 'GO:0044183 protein folding chaperone'

I suggest we obsolete the entire branch, as describing MFs:

• GO:0006457 protein folding
  • • GO:0006458 'de novo' protein folding
  • • GO:0061077 chaperone-mediated protein folding
  • • GO:0007023 post-chaperonin tubulin folding pathway
  • • GO:0042026 protein refolding

as well as the regulation terms:

• GO:1903332 regulation of protein folding
  • GO:1903333 negative regulation of protein folding
  • GO:1903334 positive regulation of protein folding

and 'consider' by MF GO:0044183 protein folding chaperone' and BP either 'GO:0051604 protein maturation or by 'GO:0034605 cellular response to heat'

The protein folding terms are not clear about the 'biological purpose' of the activity.

Nice review here: PMID: 27365453

Thanks, Pascale

[ValWood]

Your solution might be OK but some pathways operate only cotranslationally as the proteins are formed.

This includes, for example, the TTT complex (an adaptor between the hsp chaperone and or Rvb1 and 2) and the protein being translated. This particular pathway is specific for the PIKK kinase proteins. e.g. The Hsp90 cochaperone TTT promotes the cotranslational maturation of PIKKs prior to complex assembly.

Presumably, there are different setups for other proteins which need to be folded during translation. This is part of gene expression, and occurs after translation and before complex assembly.

There are other processes that occur after maturation during various stresses when proteins need to be refolded (I.e after ER stress, or other proteotoxic).

I guess I could annotate these to maturation, but it loses a lot of information, especially if you aren't annotating the chaperone.

Right now I have

MF protein-macromolecule adaptor activity

 tti1 connects tor1 to hsp90, part of 'de novo' cotranslational protein folding tti1 connects tra1 to hsp90, part of 'de novo' cotranslational protein folding

I think it is important that we don't lump all of the refolding of proteins after stress with protein maturation.

[ValWood]

I guess my issue is that the chaperones require adaptors ( co-chaperones), and it isn't so clear how to annotate these if you cannot annotate to "cotranslational protein folding"

[pgaudet]

ok - we can keep cotranslational and post-translational protein folding, if we decide these are processes. Or we can annotate both to protein maturation...?