[go] Protein domain GO annotation

[Harold Drabkin]

This sounds more like an interpro to GO translation table,.

E Dimmer wrote:
> Hi,
>
> Could I please ask people's opinion on the functional annotation of 
> protein domains/regions to the GO?
>
> I have been contacted by a group who would like to annotate GO 
> functions to identified disordered regions in proteins.
>
> The thought so far is that they would annotate to a 
> 'disordered_region' SO term, along with sequence co-ordinates, and 
> then also attach a GO term with a reference and evidence code.
> (I have spoken with Gabby Reeves from BioSapiens, who would be happy 
> to add 'disordered_region' terms to the BioSapiens protein feature 
> ontology section of SO).
>
> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered 
> region corresponding to residues 296 - 397. This domain has been found 
> to act to bend DNA, as reported in a experiment in PMID: 7651541.
> In the normal course of GO annotation I would of course happily to 
> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA 
> bending activity, GO:0008301), and while I might read about the 
> discrete region in the protein that is responsible for this function I 
> would not capture this data.
> However the IUP(Intrinsically Unstructured Protein) curators would 
> include the aa residue information in their annotations and want to 
> describe the individual functions that a protein's multiple domains 
> might have.
>
> So I assume that for these kinds of annotations, where an equivalent 
> GO term exists, a GOC annotation group could integrate this group's 
> annotations and relate it up to the whole protein/gene product (and 
> possibly being able to keep the SO term in the new cross-reference 
> column 16? but not the aa residue location?).
>
> While the majority of the function terms that the IUP community are 
> interested in applying to their domains do map quite 
> straight-forwardly to GO terms, there are some new ones which would 
> need to be requested. And some of these new terms seem to describe 
> more domain-specific, intra-protein function. For example, for some of 
> the function terms used in the DisProt database:
>
> flexible linker/spacer
> Provides separation and permits movement between adjacent domains
>
> entropic brisle
> A disordered region that creates a zone of exclusion by its entropic 
> movement
>
> entropic spring
> Provides a restoring force resulting from randomization of bond 
> torsion angles that become restricted upon stretching.
>
> (see: http://www.disprot.org/view_function_subclass.php)
>
> So, would GO be willing to add these types of terms? And how much of 
> the IUP communities annotation data would GOC groups be happy to 
> incorporate into their own annotation sets?
>
> Thanks,
> Emily
>
>