query protein folding

[gocentral]

This query has a risen from teh spkw mapping enquiry mapping chaperone to protein folding.

The def of protein folding is

The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.

Doe this term therefore apply to any protein complex assembly? or is there somthing else more subtly?

Is it does, presumable 'protein complex assembly' should be a child??? (although instinctively this doesn't seem correct perhaps there is a problem with the def?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/3476":https://sourceforge.net/p/geneontology/ontology-requests/3476

[gocentral]

Logged In: YES user_id=554736

Val,

Protein complex assembly should be a child of protein folding because currently protein folding includes covalent and non-covalent changes.

But then, we have to make all the protein modification terms as children too because they are covalent modifications.

I am thinking the covalent and noncovalent parts should be separated out of the protein folding node.

I will read some more/consult an expert and make a proposal. Thanks,

Rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=554736 Originator: NO

Val,

I think protein complex assembly should be on its own and not be a child of protein folding because Protein complex assembly is more like bringing the various components of the complex together, not so much folding involved. Does that help?

Rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=516865 Originator: YES

OK, thats what I originally thought. I think I'm being a bit dense here but its the definition that is confusing me.

"assembly** of single chain polypeptides or multisubunit complexes***** into the correct tertiary structure"

It dosn't mean any muti-subunit complex does it.....?

or is it just that the def doesn't capture the 'folding' aspect

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=554736 Originator: NO

Val,

Sorry, you lost me there. Definition of protein complex assembly is- The aggregation and bonding together of a set of components to form a protein complex.

Which one are you talking about?

rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Hi Rama,

Sorry, its the definition of protein folding that I have a problem with.

Cheers

Val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=554736 Originator: NO

Hi,

I would leave the definition of protein folding as is. Some Protein complex assembly processes do not require any folding or chaperones to assist them to arrive at the final quaternary structure, while there are some processes that require assembly and some assistance with folding into the corerct final structure.

chaperone-mediated protein complex assmebly (51131) should hence be a child of protein folding.

In addition, I think the definition of protein complex assembly needs some clarification. I will work on that.

Rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Sorry I didn't explain my problem clearly.

The current def of protein folding is

"The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure."

..but then here we are referring to more than one subunit...so do we mean quaterny structure? (i.e dosn't tertiary structure refer only to the fold?)

The use of "assembly of multisubunit complexes"

implies that any protein complex assembly term could be annotated to protein folding?

I guess I don't understand the use of multisubunit complex/tertiary structure in the protein folding definition.

also from what you say below, should the protein folding definition be extended to explicitly cover the chaperone mediated protein complex assembly? although I am still unclear what it includes/excludes?

Sorry, am I being dense here?

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=554736 Originator: NO

I will update the definition for both terms. Hopefully that will clear some of your issues.

Rama

Original comment by: rbalakri

[gocentral]

• assigned_to: nobody --> ramab

Original comment by: mah11

[gocentral]

Logged In: YES user_id=554736 Originator: NO

Val,

Sorry for going back and forth on this.

We should separate protein complex assembly and protein folding. Protein folding is mostly for single polypeptides to fold to a stable tertiary structure and protein complex assembly process brings well folded individual polypeptides together. Definition of protein folding should be-

The process of assisting in the covalent and noncovalent assembly of single chain polypeptides into the correct tertiary structure."

Definition of protein assembly shoud be- The aggregation and bonding together of a set of components to form a protein complex or a quarternary strucutre.

Consequence- tubulin folding should be removed from under protein folding and made a child of protein complex assembly

thoughts? let me know if I overlooked something.

rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Hi Rama,

Thats clearer, if that is the distinction. Still confused about moving tubulin folding though. This may because I'm not exactly sure what the chaperonin-containing T-complex does.

This is its def:

A multisubunit ring-shaped complex that mediates protein folding in the cytosol without a cofactor.

also chaperonin-mediated tubulin folding Partial folding of alpha- or beta-tubulin into a non-native folding intermediate, mediated by cytosolic chaperonin CCT.

neither of these defs mention complex assembly, but perhaps these need rewording?

but the term tubulin folding does look like a complex assembly term......

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=554736 Originator: NO

ugghhh...I just read some of the papers used to annotate to these terms. Moving GO:7021-tubulin folding as child of protein complex assembly will fix this problem. Children of tubulin folding are also protein complex assembly processes. The definitions are useless. I will work on them.

Let me know your thoughts.

Thanks,

Rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=516865 Originator: YES

OK! will the term names also be reworded to something related to 'tubulin assembly' ? the 'folding' is misleading

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=554736 Originator: NO

Val,

Sure. we can rename the term names.

Rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=516865 Originator: YES

do you think that 'tubulin folding/tubulin comple assembly' should also be a part of child of microtubule organization and biogenesis?

Val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Hi Rama,

Can this be done, it looks fairly straightforward? Midori is going to purge unassigned SF items shortly,

Thanks

Val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=554736 Originator: NO

Hi,

Sure. It can be closed.

rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=436423 Originator: NO

It looks like there are still a couple of things to do for this item:

- rename GO:0007021 (currently 'tubulin folding'; to become 'tubulin complex assembly')

• move GO:7021 to is_a protein complex assembly (GO:
• rephrase definitions for GO:7021 and its children

Note: two of the children, 'alpha-tubulin folding' GO:7024 and abeta-tubulin folding GO:7025 seem to apply to single gene products. Should they stay under protein folding?

Rama - let me know if you want to finish this off or have me take over. m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=554736 Originator: NO

Sorry for the tardy response. Tubulin folding fits better under protein complex assembly. Grouping term should be tubulin assembly and make tubulin folding a synonym.

Can you please finish this off? Please let me know if there are any more outstanding questions.

Rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=436423 Originator: NO

renamed GO:0007021 to 'tubulin complex assembly'; rephrased def to use assembly standard wording moved 7021 to is_a protein complex assembly GO:0006461 moved 7021's children to be directly is_a protein folding GO:0006457

thanks for comments and patience! m

Original comment by: mah11

[gocentral]

• milestone: --> 224410
• assigned_to: ramab --> gomidori
• labels: --> Other term-related request
• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11