[ubiquitination]

I think the key advantage here is adding synthetic amino acids to key sites (e.g., a binding interface). It'll be easier to modify surface chemistry that way, rather than modifying the structure of the entire protein to try and subtly alter a reaction site of interest. But yes, we are a long from adding new amino acids and DNA bases to the natural alphabet - all the molecular machines we currently have are optimised for 4 bases and 20 amino acids, it's not trivial to do it better than nature!