It would be useful to have some commonly encountered entity composition terms such as dimer, homodimer, trimer etc., for BioModels annotation purposes.
created sbo:0000607 and 608 (dimer/homodimer respectively) under macromolecular complex (sbo:0000296). Other can be added as necessary (trimer. tetramer, oligomer, etc).
ChEBI has polymer: purl.obolibrary.org/obo/CHEBI_60027
Nicolas Le Novère
Dimer, homodimer, trimer etc. are not polymers. I do not know who curated this ChEBI entry, but it is very odd. The definition corresponds to "multimer" or "oligomer" not "polymer". The Wikipedia entries displayed is correct though! See http://en.wikipedia.org/wiki/Multimer for what Nick is looking for.
I did have a search around but did not find anything to use for homodimer for example. I haven't created more than I needed right now, and of course i will cross reference if I do find something down the line.
Based on my reading of wikipedia:
- oligomers (or multimers) are macromolecular complexes composed of only a few monomers (up to 4?)
- polymers are macromolecular complexes composed of more than 4 monomers
Is that correct? Is that "4" limit specified somewhere - i.e., is a pentamer an oligomer or a multimer?
Nicolas, would you mind submitting a ticket to ChEBI, https://sourceforge.net/p/chebi/curator-requests/?
No, the difference is not in the number of units, but their linkage. A polymer is a covalently bound set of identical units. The units react to provide the polymer and they actually disappear. Contrarily to what we abusively say, a polypeptide is not "made up of amino-acids", because the amines and acids have been consumed in the polymerisation.
In biochemistry, a multimer is a non-covalent assembly of subunits. The subunits are generally not modified chemically by the assembly (well there are the disufide bonds ...)
While the wikipedia page on polymer is clear, the one on oligomer is not very good. Something to do there.