[go] Protein domain GO annotation

[Alexander Diehl]

Emily,

I am not entirely happy with the idea of adding "sub-molecular" 
functions for protein domains to the GO that refer functions that occur 
between parts of the same protein such as "entropic spring" as these 
would not map neatly to the whole protein were we to import IUP 
(Intrinsically Unstructured Protein) annotations into the GO.

-- Alex

Harold Drabkin wrote:
> 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
>>
>>
>


-- 
Alexander Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131