Talk:CH391L/S12/Unnatural Amino Acids

• James L. Bachman 12:54, 29 March 2012 (EDT): Has it been shown that incorporation of UAAs can confer an advantageous phenotype in engineered cells? If not, what a promising example of an engineered cell using UAAs in a way that it is more beneficial than using natural AA's?
  • Jeffrey E. Barrick 17:30, 1 April 2012 (EDT):Are there any studies that use UAA in directed evolution to show an advantage to having the UAA? I know that there are various studies that introduce new chemical functionalities into RNAs during in vitro selection and that they are able to show that they get better function with things like histidines incorporated into the RNA.
    • Michael Hammerling 20:55, 1 April 2012 (EDT) It seems to me that Logan and Jeff are asking related but different questions. There are certainly situations where incorporating UAAs confers an advantageous phenotype in engineered cells - at least one of the RF1 knockouts requires UAA incorporation for growth. In this case, the engineering of the cell itself creates a phenotype in which UAA incorporation is a necessity. What I think he really meant, however, was whether there are any examples of situations where UAA incorporating strains have higher fitness than wild-type cells in the same environment. I don't know of any strains/environments where this is the case.

Jeff's question more directly addresses whether specific proteins have been evolved which require a UAA for a particular function. This question is related to Logan's, since such a protein could potentially confer a fitness advantage on UAA incorporating strains in a particular environment. For example, the evolution of an antibiotic resistance gene which requires the UAA to function would render UAA incorporating strains more fit than wild-type strains in media containing the antibiotic. The discipline of evolving proteins that require a UAA to function or function better than wild-type when evolved to use UAAs is still in its infancy. Antibodies which require sulfation of a tyrosine as a post-translational modification for function have been evolved using phage display in the presence of sulfotyrosine as a UAA. These proteins rapidly evolve to incorporate sulfotyrosine at the location of the post-translationally modified tyrosine in wild-type.[1] This result is not particularly surprising or interesting, but it proves the principle that UAAs can be used to confer unique properties on the proteins in which they reside. More promisingly, the same group evolved glycan-binding proteins containing p-boronophenylalanine by correctly predicting that boron-containing proteins would have a special affinity for diols. [2] In this case, a unique protein is evolved for a task, rather than an already-existing protein with known function being evolved from biased sequences.

• Yi Kou 12:26, 1 April 2012 (EDT):why is that the 6 red of GFP (presence of amber codon) is dimmer than that of the counter part?
• Michael Hammerling 18:51, 1 April 2012 (EDT) I'm not sure you can make the conclusion that Red 6 is dimmer than Black 6 in that figure. It doesn't look dimmer to me. They do not indicate in the paper that this is the case.

• Jeffrey E. Barrick 17:30, 1 April 2012 (EDT):Add a note about why only 50 aa peptides can be synthesized, when oligos of > 100 nt can be synthesized?
• Michael Hammerling 18:51, 1 April 2012 (EDT) Done

• Jeffrey E. Barrick 17:30, 1 April 2012 (EDT):Add citation for native chemical ligation figure.
• Michael Hammerling 18:51, 1 April 2012 (EDT) Done

<biblio>

1. Liu2008 pmid=2584696
2. Liu2009 pmid=2745334