definition of amino acid chain
Brought to you by:
darren_natale
Menu
▾
▴
#89 definition of amino acid chain
proteins can have other than amino acids or amino acid residue parts - e.g. sugars. However proteins are amino acid chains, and amino acid chains are defined "A molecular entity that is a polymer of amino acids linked by peptide bonds" which might be interpreted to mean that it doesn't have such parts.
In addition, should the definition read (ignoring the above issue) A molecular entity that is a polymer of amino acid residues linked by peptide bonds. I don't know enough chemistry to know if one end has an amino acid vs a residue.
Related
**Term Requests** DEPRECATED: use purl.obolibrary.org/obo/pr/tracker: #89
A protein is, at a minimum, an amino acid chain. Furthermore, no protein exists that lacks such a component. The definition provided for amino acid chain gives the necessary and sufficient conditions. Thus, anything else that is part of a protein is in addition to this basic component.
However, your concern about needing the word 'residue' is valid. Saying an amino acid chain is composed of linked amino acids is biologist jargon and should be changed to 'amino acid residue'. There are no amino acids in an amino acid chain. For reference, see the source of the definition for amino acid residue in CHEBI:
http://goldbook.iupac.org/A00279.html
Then protein has_part amino acid chain, not protein is_a amino acid chain.
Based on the definition and/or use of has_part then your statement is correct, since every independent continuant has_part itself (unless this changed with BFO2?). If we reorganize the top part of PRO (as we plan to do) then has_part will actually become the necessary relation anyway (which would allow us to say that a protein complex is_a protein instead of has_part protein). Currently, however, a 'Protein' in PRO will always be a type of amino acid chain, as would a polypeptide, oligopeptide, dipeptide, etc.
Wait a sec. My statement is correct independent of whether has part is reflexive. And we don't want to say protein complex is a protein. And we don't want to say, as I understand it now, protein is a amino acid chain.
This shouldn't wait for a reorganization.
Unfortunately you have biologists that disagree with you about what a protein complex is (based on a Consortium meeting a few years ago). I believe Alex is among them (though he is far more concerned with cleavage products).
I am still failing to see how a protein as currently defined in PRO is NOT an amino acid chain.
an amino acid chain is molecular entity that is a polymer of amino acids linked by peptide bonds"
Every protein is an amino acid chain
Every protein is a molecular entity that is a polymer of amino acids linked by peptide bonds.
A protein can have a covalently bound part that is a sugar.
A sugar can't be part of a molecular entity that is a polymer of amino acids
BANG!
There are biologists who would consider a ribosome a protein?
Ah, I see your confusion. The sugar (or any other modification) is never a part of the chain itself:
A-A-A-A-A < this is the chain
|
sugar
not
A-A-A-sugar-A-A
Right. So:
A chain can't have a sugar as part.
A protein is a chain
=>A protein can't have a sugar as part.
Ribosome is more commonly considered a ribonucleoprotein since it also has nucleic acid parts. But even amino-acid-chain-only complexes are often considered 'protein' (which is why PRO very strictly defined protein as the product of a ribosome).
On Mon, Jul 28, 2014 at 4:04 PM, Darren Natale darren_natale@users.sf.net
wrote:
Related
**Term Requests** DEPRECATED: use purl.obolibrary.org/obo/pr/tracker:
#89An amino acid chain can't have a sugar as part of the chain (what we call the backbone). There are no claims made about the side chains (those things that are not part of the backbone, but instead is attached to the main amino acid). There is no discrepancy.
In that case I would request that the definition of amino acid chain be clarified to admit that possibility explicitly. As it reads it is easy to understand it as something made only of residues.
Regarding amino acid chain, are you of the opinion that a modified amino acid residue is not an amino acid residue? That is the only way there is a problem with the current definition.
Regarding complexes, our definition of protein complex is the one that GO uses. It allows the possibility of other (non-amino acid chain) components. The GO definition of protein complex would include ribosomes as either child or grandchild. As for "every protein complex is a protein" I think, yes, old-school biologists would say that. I personally don't agree with it, and have crafted our definitions to make clear what we mean, but we encountered resistance to this.
On Mon, Jul 28, 2014 at 4:42 PM, Darren Natale darren_natale@users.sf.net
wrote:
Related
**Term Requests** DEPRECATED: use purl.obolibrary.org/obo/pr/tracker:
#89I would interpret 'crosslinked residue' as referring to one half of the linked residues, so yes, a crosslinked residue is_a residue. (this without looking up how RESID or MOD handles it)
DN:
Regarding amino acid chain, are you of the opinion that a modified amino acid residue is not an amino acid residue? That is the only way there is a problem with the current definition.
AR:
I think that should probably be discussed with a chemist. I would expect there would be some degree of modification that left it of the type and other not.
One of the issues with resid is that there are entries for cross-linked residues. Is a cross-linked residue a residue?
DN:
I would interpret 'crosslinked residue' as referring to one half of the linked residues, so yes, a crosslinked residue is_a residue. (this without looking up how RESID or MOD handles it)
AR:
RESID and MOD have these as the combined molecule - check the mass
http://pir.georgetown.edu/cgi-bin/resid?id=AA0108
http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:00117
CHEBI has these
On Tue, Jul 29, 2014 at 1:28 AM, Alan Ruttenberg alanr@users.sf.net wrote:
Don't know if I sent you a response on this, but at least RESID represents
the whole.
Sorry for this late notification; I'm going through tickets marked open that should actually have been closed long ago. To summarize the action taken: I had very lengthy discussion with John Garavelli (of RESID fame) regarding the nature of amino acid residues, modifications thereof, and how to define amino acid chain so that it fits under the appropriate ChEBI term. The final version of amino acid chain is this:
"An organic amino compound that is a polymer of amino acid chain components (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds."
http://purl.obolibrary.org/obo/PR_000018263