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Updated: Jun 24, 2026

Single Molecule Fluorescence Energy Transfer Study of Ribosome Protein Synthesis
Published on: July 6, 2021
Association of aminoglycosidic antibiotics with the ribosomal A-site studied with Brownian dynamics
Maciej Długosz1, Jan M Antosiewicz, Joanna Trylska
1Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Żwirki i Wigury 93, Warsaw 02-089, Poland.
Abstract:
Brownian dynamics methodology was applied to simulate the encounter of aminoglycosidic antibiotics with the ribosomal A-site RNA. Studied antibiotics included neamine, neomycin, ribostamycin and paromomycin which differ in chemical structure, the number of pseudo-sugar rings and the net charge. The influence of structural, electrostatic and hydrodynamic properties of antibiotics on the kinetics of their association with the ribosomal A-site was analyzed. The computed diffusion limited rates of association are of the order of 10(10)[Formula: see text] and they weakly depend on ionic strength. Prior to binding antibiotics often slide along the RNA groove with the time scale of approximately 10 ns per base pair in case of neamine. We observed that upon forming the encounter complex aminoglycosides displace from the binding pocket up to two Mg(2+) ions.
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