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.
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