Welcome to the Alanine World! Computational design takes over! Painting protein translation blue

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Let me introduce you one curious species. This is a little microorganism (archea), which lives in hot hydrotermal sources, and converts carbon dioxide into methane, with a remarkably lengthy name Methanocaldococcus jannaschii.

Same as we’re doing it, M jannaschii makes proteins by decoding RNA sequence into proteins. However, this is a fairly complex process overall. First an amino acid is recognized by a special enzyme, aminoacyl-tRNA-synthetase (AARS), the enzyme attaches the amino acid to a corresponding adaptor, the transfer RNA molecule (tRNA), and resulting conjugate, aminoacyl-tRNA then travels to the ribosome, where the amino acid will be incorporated in place of a correct codon. The identity of the amino acid is only checked by the the enzyme, AARS, and not checked thereafter. When you need to have tyrosine in a protein,special AARS will link tyrosine to corresponding tRNA, and this tRNA will then place the amino acid at the place of the tyrosine codons.

What’s so special about M. jannaschii though? Special is the fact that the tRNA for tyrosine in this organism is different to the tRNA of tyrosine in our best friend Escherichia coli. If we’d take this tRNA from M. jannaschii and transfer this to E. coli, the AARS from E. coli will not charge it with an amino acid. At this point we can make a good use of it. For example, we can charge this tRNA with something else, and E. coli will place this amino acid into a protein where we want to have it.

In the pair of AARS and tRNA, we can modify the amino acid recognition pocket of AARS such that it will accept another amino acid of interest, and then charge it on the tRNA, which will incorporate it into a protein on a position of a free codon (stop codon). Nether the synthethse, AARS, nor the tRNA from the M. jannschii is known for E. coli, and there will be no cross reactivity between different synthetases and tRNAs. The M. jannaschii pair of AARS and tRNA will act in parallel to the common cellular apparatus, therefore it is also called an orthogonal pair.

There is a number of orthogonal pairs originally used by different organisms for some amino acids. The system from the metanogenic microorganism M. jannaschii, is among the most common and reliable. To date, it has been used for incorporation of a huge set of chemically diverse structures into proteins in addition to the common set of 20 amino acids. Of course, most of these diverse structures are in some way resembling tyrosine or phenylalanine, because the original enzyme was for tyrosine. With O-propargoxy-tyrosine or para-azido-phenylalanine we will have a handle for click-chemistry, with para-cyano-phenylalanine we have a probe for infrared spectroscopy, with para-trifluoromethyl-phenylalanine - a probe for fluorine NMR, with O-ortho-nitrobenzyl-tyrosine (photocaged tyrosine) we will have a masked tyrosine residue, which can be set free by sheding light on it etc.

Why is tyrosine so useful in the protein structures? Well, it is reasonably hydrophobic, therefore it can be placed in the hydrophobic core. Nonetheless, even in the hydrophobic environments, it can make additional hydrogen bonds. There is an additional acid-base transition in the Tyr residue, the pKa of the phenolic group in Tyr is about 10, and this may be used for catalysis. The hydroxyl-group of Tyr can be phosphorylated and dephosphorylated for regulation purposes. As you can see, there are many reasons to have tyrosine in the genetic code.

One more fact should not be omitted. Tyrosine is a precursor for dopamine in our neurons. We all need it very much.

Interesting readings:
  • Hubbard, S. R. and Till, J. H. Protein Tyrosine Kinase Structure and Function. Annu. Rev. Biochem., 69, 2000, 373-398, doi: 10.1146/annurev.biochem.69.1.373
  • Wang, L. et al. Expanding the Genetic Code of Escherichia coli. Science, 292, 2001, 498-500, doi: 10.1126/science.1060077
  • Radi, R. Nitric oxide, oxidants, and protein tyrosine nitration. Proc. Natl. Acad. Sci. USA, 101, 2004, 4003-4008, doi: 10.1073/pnas.0307446101

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