Regarding Fluorescent Protein research, GFP alone refers to the 1st described GFP. A lot of other biochemically identical proteins have been identified since then, and they all belong to the family of GFP, but nomenclature got a little crazy in my opinion.
With this question in particular, I'm wondering if there is any type of "rule" as to how to name a protein when it is named after a similar one... And if not, then why would fluorescent proteins with very similar characteristics be named "GFP-like" and "GFP-type" in different situations?
If someone finds it useful to be able to answer my questions, here's an example of such results:
http://www.uniprot.org/uniprot/?query=gfp%20taxonomy:cnidaria+taxonomy:44298
Thanks a lot in advance!
It exists only one GFP. Variants and other autofluorescing proteins have their own names e.g.YFP or mCherry and should be cited according to thei first desciption. ´GFP-lke or GFP-type , for my opoinion, should not be used.
Best,
Guenther
Even more complications: the term "related protein" is also used in naming proteins and there is no rule as yet to standardize the nomenclature as with IUPAC or in enzymology. For now it seems function is used for "like" ; IGF-1 for example is called insulin like growth factor 1 but doesn't have the amino acid homology to insulin. I think "type may refer more to amino acid homology. Terminology dilemmas exists everywhere in biology and biochemistry, paralogue and orthologue for example, but for now people will need to define their terms and editors/reviewers will need to enforce it.
The original green-fluorescent protein was isolated from Aequorea victoria, a homologous red fluorescent protein was found in Discosoma corals. Natural homologs are likely to be found in related organisms. Since the discovery of the original GFP, protein engineering has been used to improve the stability, folding properties, fluorescence quantum yield and spectrum of both GFP and RFP. Other natural homologs share the fold of GFP but have other functions. http://mbe.oxfordjournals.org/content/21/5/841.full . GFP-like molecules are sequence and structural homologs of GFP, both natural and artificial.
Grant Shimamoto: Insulin-like growth factors IGFI and IGFII both not only have marked sequence homology to insulin, but also crossreact with the insulin receptor. Upon discovery, they were called "NSILA", non-supressable insulin-like activity, since they did elicit insulin like effects in cells and animals that could not be blocked by neutralizing antibodies against insulin. After the proteins had been characterized, they were renamed insulin-like growth factors since they are members of the insulin family, but their primary physiological role was found to be growth regulation (somatomedin) rather than metabolic regulation.
XXX-like is often used to describe genes/proteins that have clear sequence homology to gene XXX, but have not yet been characterized well enough to tell whether they are orthologs of XXX, or paralogs that may have a similar structure but a different function.
Sorry for cut/paste error. Should read "and does have". The "but doesn't have" referred to the cleavage site between chains. A reference which seems to help with the orthologue - paralogue explanation could be helpful: Genome Biol. 2001; 2(8): interactions1002.1–interactions1002.3.
Published online 2001 Aug 3.
PMCID: PMC138949
Orthologs and paralogs - we need to get it right
Roy A Jensencorresponding author1
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