Re: protein entities

Darren Natale wrote:
> 
> Protein, in this scheme, is the amino acid polymer produced by a 
> translation process using an mRNA as a template.  

This fits about any polypeptide produced by a ribosome.
I'd think that the term 'protein' is reserved for some, but not all 
polypeptides (even if we talk only about those produced by ribosomes).

Interestingly, Lodish et al. [1] say, "we reserve the term protein for a 
polypeptide (or a complex of polypeptides) that has a three-dimensional 
structure".  I just can't imagine a polypeptide that does not have a 
three-dimensional structure -- even if it is ideally linearly stretched 
(which is rarely the case in a cell).  I guess they mean tertiary structure.

Lots of nice problems lurking here.

> I suppose this 
> excludes peptides (also amino acid polymers) that are produced 
> non-ribosomally, but perhaps that is okay for the time being.  The 
> precise definition will be constructed with input from the Sequence 
> Ontology curators.

Do you consider SO a source of precise definitions?

vQ

[1] Lodish et al. (2000). Molecular Cell Biology. Freeman and Co.