Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site

Tetracyclines (Tc) are important antibiotics that inhibit bacterial ribosomes. Two and six Tc binding sites, respectively, were seen in two X-ray structures of the Thermus thermophilus 30S ribosome subunit; the exact functional role of the various sites remains unclear. We study the two consensus sites, seen in both structures: a primary site, which is positioned to block tRNA A-site binding, and a secondary site, which has a weaker electron density. We combine molecular dynamics simulations and continuum electrostatic calculations to estimate the relative affinities of the two sites. The dielectric constant of the ribosome is set to 8, to reproduce the experimental binding free energy differences between Tc and its analogues minocycline and doxycycline, as well as more rigorous free energy simulations of Mg2+ binding. We find that both sites include a prebound Mg2+ ion, present before Tc binds. Using long simulations and comparing eight structural models for each site, we then show that primary site Tc binding is stronger by 1-4 kcal/mol; this range appears consistent with the crystallographically observed occupancies of the two sites. With this free energy range, TET5 is largely unoccupied under physiological conditions. Thus, we propose that the primary site is the inhibitory site and that allosteric effects may not be essential for tetracycline function.