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Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site.

Romanowska J, McCammon JA, Trylska J - PLoS Comput. Biol. (2011)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw Poland. jrom@icm.edu.pl

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.

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Related in: MedlinePlus

The number of hydrogen bonds formed between subsequent base pairs plotted versus simulation time.Data from simulations: (a) G1491A and (b) U1406C/U1495A. Asterisks (*) indicate the mutated bases.
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pcbi-1002099-g006: The number of hydrogen bonds formed between subsequent base pairs plotted versus simulation time.Data from simulations: (a) G1491A and (b) U1406C/U1495A. Asterisks (*) indicate the mutated bases.

Mentions: We found that the single mutants G1491U and G1491A did not affect the stability of the U1406·U1495 pair and that the pair was predominantly formed by two hydrogen bonds (Figure 6a and Table S2). In contrast, the resulting 1406C∶1495A pair from the U1406C/U1495A simulation formed one hydrogen bond and was only moderately stable (Figures 6b, 7b, and Table S2). Occasionally, 1406C was observed rotating to a position that was almost perpendicular to the base pair plane (Figure 7c). Nevertheless, the 1406C∶1495A pair often adopted an experimentally observed pattern(http://bps.rutgers.edu/atlas/bppattern/ac_5 [41]; Figure 7b).


Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site.

Romanowska J, McCammon JA, Trylska J - PLoS Comput. Biol. (2011)

The number of hydrogen bonds formed between subsequent base pairs plotted versus simulation time.Data from simulations: (a) G1491A and (b) U1406C/U1495A. Asterisks (*) indicate the mutated bases.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3140962&req=5

pcbi-1002099-g006: The number of hydrogen bonds formed between subsequent base pairs plotted versus simulation time.Data from simulations: (a) G1491A and (b) U1406C/U1495A. Asterisks (*) indicate the mutated bases.
Mentions: We found that the single mutants G1491U and G1491A did not affect the stability of the U1406·U1495 pair and that the pair was predominantly formed by two hydrogen bonds (Figure 6a and Table S2). In contrast, the resulting 1406C∶1495A pair from the U1406C/U1495A simulation formed one hydrogen bond and was only moderately stable (Figures 6b, 7b, and Table S2). Occasionally, 1406C was observed rotating to a position that was almost perpendicular to the base pair plane (Figure 7c). Nevertheless, the 1406C∶1495A pair often adopted an experimentally observed pattern(http://bps.rutgers.edu/atlas/bppattern/ac_5 [41]; Figure 7b).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw Poland. jrom@icm.edu.pl

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.

Show MeSH
Related in: MedlinePlus