Presumably you need the rest of the structure of the GFP to make the cyclization reaction possible,
In the patent there is also a claim that the patent a peptide from 64 to 69, so *perhaps* you really would just need this oligopeptide?
But there is a very big question:
The pre-czn-peptide is based on this
http://www.bio.davidson.edu/courses/molbio/restricted/02gfpseq/GFPseqfig2.GIF
Nucleotide 736-739 (in frame!) is TAA so the jellyfish polymerase will stop and fall of the mRNA. Then it goes on with ATG TCC ..... That is junk DNA? I would expect it to be an apo-protein or something alike. But jellyfish machinery doesn't support operons, so this wouldn't be expresssed.
Or is this a compilation, and before the ATG there was another promoter?
On Wed, Dec 26, 2012 at 4:45 PM, Patrik D'haeseleer <patrikd@gmail.com> wrote:
On Monday, December 24, 2012 11:31:19 PM UTC-8, Nathan McCorkle wrote:Is there possibly a way to search for protein motifs based on the structure of Coelenterazine or Coelenteramide?
Not much of one. The chromophore core in GFP is Serine-Tyrosine-Glycine, which becomes Tyrosine-Tyrosine-Glycine in the patent Mega dug up. You also need a phenylalanine in position 64 that becomes part of the coelenterazine. So the core motif you're looking for is FYYG, but that doesn't narrow it down by much.
Presumably you need the rest of the structure of the GFP to make the cyclization reaction possible, so you're better off looking for a GFP homolog, with FYYG where you'd expect to see FSYG.--To view this discussion on the web visit https://groups.google.com/d/msg/diybio/-/nYvvS6WXGNAJ.
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