Aminoglycoside Association Pathways with the 30S Ribosomal Subunit

Many aminoglycoside antibiotics target bacterial ribosomes and alter their proper functioning as translational machinery leading to bacterial death. To better understand their several inhibitory mechanisms we applied Brownian dynamics and investigated the kinetics and association of paromomycin, an aminoglycoside representative, with the entire 30S ribosomal subunit. We determined that aminoglycoside specific binding at the ribosomal aminoacyl-tRNA site (A-site) begins with antibiotic diffusion toward any point on the 30S subunit and is followed by exploration of the 30S surface. Surprisingly, there is no direct electrostatic steering of the antibiotic to the A-site. Furthermore, we discovered two possible entrances to the A-site around which the mobility of paromomycin is high. The antibiotic also visits binding sites for other drugs targeting the 30S subunit. We found that paromomycin interacts with different sites located along the helix 44 of 16S rRNA, which might explain the recent experimental findings that paromomycin's other inhibitory role arises from overstabilizing the ribosomal 70S complex. In addition, our simulations revealed an alternate binding cleft in the 30S subunit that may be important for paromomycin's inhibitory effect on translocation. The diffusion limited rate of association was estimated of the order of 10(9) (M.s)(-1) with no dependence on the ionic strength of the solution; the physical origins of this result are explained.