Are lipoprotein particles complexes?

[gocentral]

Hi with the QC that all contributes_to MF annotations should have a protein complex annotation please could you advise about the annotation of P02647 APOA1 (and P02652 APOA2) contributes to cholesterol transporter activity which is also annotated to a variety of lipoprotein particles, eg high-density lipoprotein particle.

Assuming this is the correct interpretation of cholesterol transporter activity, would it be possible to include GO:0032994 protein-lipid complex within the QC so that these annotations are accepted as providing a complex along with the contributes_to MF annotation.

Thanks

Ruth

Reported by: RLovering

Original Ticket: geneontology/ontology-requests/11279

[gocentral]

Hi Ruth,

I generally think of protein complexes as having a defined stoichiometry and structure. Is that true for lipoprotein particles? If that is not true, then I don't think lipoprotein particles should be classified as protein complexes.

Possibly, they could be considered a "protein aggregate". GO does not currently have a general term for "protein aggregate", though personally I think it might be good if we did. We have some other terms like "keratohyalin granule" that is basically a non-structured accumulation of the precursor proteins and molecules that will form the cornified envelope and "protein aggregate" would be an appropriate parent term for this. The PRO group has discussed this some, but we should check with Alex Diehl on this.

-Karen

Original comment by: krchristie

[gocentral]

Hi Karen,

"Protein aggregate" sounds a like an artifact; if that solution is chosen, we need to make sure there is a clear note that advises against using the term for overexpression and pathological overexpression.

Maybe a simpler solution would be to change the QC check to all contributes_to MF annotations should have CC annotations to 'GO:0034364 macromolecular complex' instead of whatever it is now (I assume GO:0043234 protein complex?)

Thanks, Pascale

Original comment by: pgaudet

[gocentral]

Human lipoprotein particles start out with defined structures, as they assemble through the association of specific kinds of lipids around a core protein (different protein and assembly site for different lipoproteins). I don't think that even in this initial form any of them has an exact stoichiometry - more like a limited range, like the protein oligomers recently discussed here. As they circulate, they can gain additional proteins (specific kinds for each kind of particle, and in limited but probably not exact stoichiometries), and they lose or exchange lipids, definitely not with exact stoichiometries (an individual loss or exchange affects one lipid molecule but the number of each can vary).

The different forms that a lipoprotein particle takes on in its life cycle don't look like a problem: each transition is sufficiently well-defined to be used as a differentia so a parent term can have terms for the successive life cycle forms as children.

Opinion: the earlier argument that oligomers could be treated as complexes without corrupting the MF ontology looks like it would work here too.

Original comment by: deustp01

[gocentral]

• assigned_to: Paola Roncaglia

Original comment by: paolaroncaglia

[gocentral]

Hi All

Pascale's suggestion sounds the best to me.

http://lipidlibrary.aocs.org/Lipids/lipoprot/index.htm states that APOA2 is a homodimer but that the physical properties of apoproteins enable them to bind readily at the interface between water and phospholipids, and specifically they bind to the phospholipids on the surface of the lipoproteins. So I don't think that they are necessarily involved in protein-protein interactions.

Ruth

Original comment by: RLovering

[gocentral]

Thanks all for your feedback.

Ruth, may I close this ticket then? Or do we need an action item to change the QC script to accept 'macromolecular complex' rather than the more specific 'protein complex'?

Thanks,

Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Ruth,

Do you think I could close this ticket now, please? Or do we need an action item to change the QC script to accept 'macromolecular complex' rather than the more specific 'protein complex'?

Thank you, Paola

Original comment by: paolaroncaglia

[gocentral]

HI Paola

Please could we have an action item to change the QC script to accept 'macromolecular complex' rather than the more specific 'protein complex'

Do I need to do this or is this something you do?

Sorry

Ruth

From: Paola Roncaglia paolaroncaglia@users.sf.net<mailto:paolaroncaglia@users.sf.net> Reply-To: "[geneontology:ontology-requests]" 11279@ontology-requests.geneontology.p.re.sf.net<mailto:11279@ontology-requests.geneontology.p.re.sf.net> Date: Wednesday, 12 November 2014 17:07 To: "[geneontology:ontology-requests]" 11279@ontology-requests.geneontology.p.re.sf.net<mailto:11279@ontology-requests.geneontology.p.re.sf.net> Subject: [geneontology:ontology-requests] #11279 Are lipoprotein particles complexes?

Hi Ruth,

Do you think I could close this ticket now, please? Or do we need an action item to change the QC script to accept 'macromolecular complex' rather than the more specific 'protein complex'?

Thank you, Paola

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[ontology-requests:#11279]http://sourceforge.net/p/geneontology/ontology-requests/11279 Are lipoprotein particles complexes?

Status: open Group: BHF-UCL Labels: QC query Created: Fri Oct 31, 2014 04:36 PM UTC by Ruth Last Updated: Tue Nov 04, 2014 01:56 PM UTC Owner: Paola Roncaglia

Hi with the QC that all contributes_to MF annotations should have a protein complex annotation please could you advise about the annotation of P02647 APOA1 (and P02652 APOA2) contributes to cholesterol transporter activity which is also annotated to a variety of lipoprotein particles, eg high-density lipoprotein particle.

Assuming this is the correct interpretation of cholesterol transporter activity, would it be possible to include GO:0032994 protein-lipid complex within the QC so that these annotations are accepted as providing a complex along with the contributes_to MF annotation.

Thanks

Ruth

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Original comment by: RLovering

[gocentral]

Hi Ruth,

I'd need you to take care of this one please, as it goes beyond ontology changes. For a change in a QC script, I'm assuming you may want to ping Rama and Prudence, and then instruct the relevant software people (Tony; anyone else?) to implement the change. Should be straightforward once there is a consensus.

(Note that Prudence is at a course all week. Rachael could probably confirm details of strategy here...)

Please confirm that you're ok to take care of this, and I'll close the ticket, thanks!

Paola

Original comment by: paolaroncaglia

[gocentral]

ok will do thanks Ruth

Original comment by: RLovering

[gocentral]

Thanks Ruth. Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-accepted

Original comment by: paolaroncaglia