I recently heard a presentation on this crazy guy, Peter Schultz, who has engineered bacteria to use para-aminophenylalanine instead of amber codons. The bacteria synthesize para-phenylalanine, have a para-phenylalanine tRNA synthetase, and and insert it with very high fidelity whenever the amber codon is found. The amber codon, which causes the ribosome to stop reading the mRNA when it’s found, is apparently quite rare, and because bacterial mRNAs aren’t as processed as eukaryotic ones, the bacteria get along quite well. I was thinking it would be really keen to make a series of mutants, each of which incorporated a different D-amino acid instead of the L version. Then, analysis of the structures of the D tRNA synthetases, of the ribosome translating the codon, and of the resulting protein could contribute a little information towards answering why we use all L amino acids.
Coincidentally, while I was googling a good link for this story, I found Lagniappe, who just blogged this story about the same time I heard the presentation.
Here’s Schultz’s PDF in JACS.
Derek, if you’re reading this, you’re the number one link at google for para-aminophenylalanine. Kinda funny that I find a blogspot blog as the number one search result for something right after google buys pyra. However, there were only 2 results total, so I only mention this to be funny, not to suggest anything conspiratorial.