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Project Progress

One of our primary interests is to elucidate the nature of the interaction between the ribosome peptide exit tunnel and the nascent peptide before breeching the extraribosomal interface. In doing so, we will be able to gain a better understanding of the molecular basis for the choice of nucleic acid as exit tunnel construction materials. Using molecular probes – peptolides – that we have developed, we have characterized the interaction between varied peptide sequences and key residues within the exit tunnel and the space adjoining the entrance to the exit tunnel and the peptidyl transferase site. This was accomplished by cell-free translation inhibition assays (Table 1), footprinting experiments of the ribosomal RNA (rRNA) through dimethyl sulfate (DMS) and 1-cyclohexyl-(2-morpholino-ethyl)carbodiimide metho-p-toluene sulfonate (CMCT) modification in the presence of the peptolides (Figs. 1 & 2). Our footprinting data strongly suggest that the peptide moieties of all the peptolide studied preferred a path of travel where they are oriented back to the peptidyl transferase site. This observation is consistent with crystallographic data on telithromycin (ketek), the ketolide template for all our peptolides, showing that it could adopt a conformation which has its flag-pole moiety oriented toward the peptidyl transferase site.^1-3

In continuation of our study, we have designed and commenced the synthesis of a series of oxazolidinone-peptide conjugates (Zyvotides) (Table 2) that places nascent peptide at a different window to the exit tunnel, thereby affording a path to the tunnel that is quite different from the peptolides’. We will characterize the interaction of these Zyvotides with the ribosome exit tunnel using the tools we have developed during our investigation of the peptolides. Additionally, we are designing another generation of peptolides to address the deficiency of the 1^st generation pepolides which were built off of telithromycin flag-pole moiety. We had anticipated that the flexibility of the flag-pole moiety would afford an easy placement of the peptides down the exit tunnel, mimicking a growing peptide. As stated earlier, it seems flipping the peptide back to the peptidyl transferase site is preferred. By replacing the telithromycin scaffold with that of azithromycin, an azalide, the flexibility of the flag-pole moiety is removed. Crystal structures of both H. marismortui and T. thermophilus with azithromycin bound show that the proposed site of peptide attachment, N10, has an expansive space that would easily permit modification (Figs. 3-6). The loss of the flexibility afforded by telithromycin will allow the peptide probe to be guided down the exit tunnel.
 
References
1) Berisio, R.; Harms, J.; Schluenzen, F.; Zarivach, R.; Hansen, H. A.; Fucini, P.; Yonath, A. J. Bacteriol. 2003, 185, 4276-4279.
2) Tu, D.; Blaha, G.; Moore, P. B.; Steitz, T. A. Cell 2005, 121, 257–270.
3) Dunkle, J. A.; Xiong, L.; Mankin, A. S.; Cate, J. H. D. PNAS, 2010, 107, 17152-17157.