The fluorescent molecule at the center is not actually a nucleic acid, but is formed several hours after the protein has folded after a secondary reaction between some of the atoms at the center of the protein find a lower energy state. This seems to me (not a protein engineer) to be virtually impossible to design a-priori.
[1] Meta-Meta-Article: https://www.bakerlab.org/index.php/2019/01/02/nature-article...
[2] Actual paper: https://www.nature.com/articles/s41586-018-0509-0
From the paper: "Synthetic genes encoding the 56 designs were obtained and the proteins were expressed in E. coli. Thirty-eight of the proteins were wellexpressed and soluble; SEC and far-ultraviolet CD spectroscopy showed that 20 were monomeric β-sheet proteins (Supplementary Table 3). Four of the oligomer-forming designs became monomeric upon incorporation of a disulfide bond between the N-terminal 3–10 helix and the barrel β-strands. The crystal structure of one of the monomeric designs (b10) was solved to 2.1 Å, and was found to be very close to the design model (0.57 Å backbone r.m.s.d., Fig. 3c)."
"Two of the 20 monomeric designs—b11 and b32—were found to activate DFHBI fluorescence by 12- and 8-fold with binding dissociation constants (KD) values of 12.8 and 49.8 μM, respectively (Extended Data Fig. 6f)"
As a side note, this is why I appreciate HN, never would have seen this paper otherwise.
De novo Design of Potent and Selective Mimics of IL-2 and IL-15: https://www.nature.com/articles/s41586-018-0830-7
Lab's accompanying media post: https://www.bakerlab.org/index.php/2019/01/09/potent-anti-ca...
" Potent anti-cancer proteins with fewer side effects. Today we report in Nature the first de novo designed proteins with anti-cancer activity. These compact molecules were designed to stimulate the same receptors as IL-2, a powerful immunotherapeutic drug, while avoiding unwanted off-target receptor interactions. ..."
A remarkable and powerful achievement.