A recent study by Ruben L. Gonzalez Jr. and coworkers  provides insight into how to improve the incorporation of D-α-amino acids into proteins. It has already been shown that D-α-amino acids can be incorporated at the C-terminus of a growing peptide chain by wild type E. coli ribosomes  but at a cost: they halt translation in a fraction of the incorporating ribosomes. The proportion of ribosomes that stall out during translation depends on the identity of the D-α-amino acid at the C-terminus of the peptidyl-D-aminoacyl-tRNA.
This study reveals that translation arrest is mediated not only by the D-aminoacyl-tRNA donor in the ribosomal P site, but also by the identity of the aminoacyl-tRNA acceptor in the A site. In other words, the identity of the amino acid that directly follows the D-amino acid influences ribosomal stalling.
The effect of the aa-tRNA acceptor in the A site involves both the tRNA and amino acid identity. Charged amino acids such as arginine and glutamate lead to high levels of translation arrest, while valine and phenylalanine allow translation to continue almost unimpeded even after incorporation of a D-amino acid. Scientists who wish to incorporate D-amino acids into proteins could take advantage of this effect by ensuring that the D-α-amino acids is always followed by valine or phenylalanine.
- Rachel C. Fleisher, Virginia W. Cornish, and Ruben L. Gonzalez, Jr. (2018) “D-Amino Acid-Mediated Translation Arrest Is Modulated by the Identity of the Incoming Aminoacyl-tRNA”. Biochemistry, 57 (29), pp 4241–4246 doi:10.1021/acs.biochem.8b00595
- Englander MT, Avins JL, Fleisher RC, Liu B, Effraim PR, Wang J, Schulten K, Levh TS, Gonzales RL Jr, Cornish VW. (2015) “The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center.” Proc. Natl. Acad. Sci. USA., 112 (19), pp 6038-6043. doi:10.1073/pnas.1424712112