[go] Protein domain GO annotation

[E Dimmer]

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


-- 
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    Emily Dimmer
    GOA Coordinator
    EMBL-EBI
    Wellcome Trust Genome Campus
    Hinxton
    Cambridge CB10 1SD, U.K.
    Tel:     +44 1223 494654
    Fax:    +44 1223 494468
    email:  edimmer at ebi.ac.uk
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