Influence of thiostrepton binding on the ribosomal GTPase associated region characterized by molecular dynamics simulation.

The thiostrepton antibiotic inhibits bacterial protein synthesis by binding to a cleft formed by the ribosomal protein L11 and 23S's rRNA helices 43-44 on the 70S ribosome. It was proposed from crystal structures that the ligand restricts L11's N-terminal movement and thus prevents proper translation factor binding. An exact understanding of thiostrepton's impact on the binding site's dynamics at atomistic resolution is still missing. Here we report an all-atom molecular dynamics simulations of the binary L11·rRNA and the ternary L11·rRNA·thiostrepton complex (rRNA = helices 43-44). We demonstrate that thiostrepton directly impacts the binding site's atomic and biomacromolecular dynamics.