Generation of small molecule ribosome sensors

The general goal of this project is to generate biological sensors for small molecules using the translating ribosome that contains the nascent TnaC peptide as a template. Our recent cryoEM structure shows a unique binding site for L-Trp generated by residues of the nascent TnaC peptide and nucleotide residues located in the narrowest (constriction) region of the ribosome exit tunnel, where the nascent peptide travels out of the ribosome during synthesis. Preliminary structural and biochemical analysis suggest that the presence of L-Trp within the exit tunnel narrows the constriction region of the exit tunnel perhaps blocking any movement of the nascent TnaC peptide and that maintaining its helical structures necessary for blocking translation termination. It seems possible using the information obtained from the new cryoEM structure to design changes in both TnaC peptide and ribosome that can produce new binding sites for small molecules at the constriction region of the tunnel without affecting the regulatory function of the TnaC peptide.

van der Stel AX et al. 2021. Nat. Comm. 12(1):5340