title: Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site.
abstract: Paromomycin is an aminoglycosidic antibiotic that targets the RNA of the bacterial small ribosomal subunit. It binds in the A-site, which is one of the three tRNA binding sites, and affects translational fidelity by stabilizing two adenines (A1492 and A1493) in the flipped-out state. Experiments have shown that various mutations in the A-site result in bacterial resistance to aminoglycosides. In this study, we performed multiple molecular dynamics simulations of the mutated A-site RNA fragment in explicit solvent to analyze changes in the physicochemical features of the A-site that were introduced by substitutions of specific bases. The simulations were conducted for free RNA and in complex with paromomycin. We found that the specific mutations affect the shape and dynamics of the binding cleft as well as significantly alter its electrostatic properties. The most pronounced changes were observed in the U1406C∶U1495A mutant, where important hydrogen bonds between the RNA and paromomycin were disrupted. The present study aims to clarify the underlying physicochemical mechanisms of bacterial resistance to aminoglycosides due to target mutations.
authors.affiliation: Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw Poland. jrom@icm.edu.pl
authors.forename: Julia
authors.initials: J
authors.lastname: Romanowska
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000187:drug effects* / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009154:Mutation; D010303:Paromomycin / Q000494:pharmacology*; D011485:Protein Binding; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism*; D054680:Ribosome Subunits, Small, Bacterial / Q000235:genetics / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D012336:RNA, Ribosomal, 16S; D010303:Paromomycin