ArticleThe journal of physical chemistry. B2008
Molecular dynamics study of the ribosomal A-site.
Article in The journal of physical chemistry. B, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site.PloS one · 2018Article
- Electrostatic interactions in aminoglycoside-RNA complexes.Biophysical journal · 2015Article
- Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.Journal of molecular biology · 2014Article
- Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study.PloS one · 2014Article
- Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.PLoS computational biology · 2013Article
- Article
- Novel insights of structure-based modeling for RNA-targeted drug discovery.Journal of chemical information and modeling · 2012Article
- Computational studies of molecular machines: the ribosome.Current opinion in structural biology · 2012Review
- A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.PLoS computational biology · 2012Article
- Nanopore analysis of individual RNA/antibiotic complexes.ACS nano · 2011Article
- Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome.RNA (New York, N.Y.) · 2011Article
- Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site.PLoS computational biology · 2011Article
- Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome.Journal of the American Chemical Society · 2010Article
- Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.The journal of physical chemistry. B · 2010Article
- Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.Nucleic acids research · 2010Article
- An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods.Journal of chemical theory and computation · 2010Article
- Search for novel aminoglycosides by combining fragment-based virtual screening and 3D-QSAR scoring.Journal of chemical information and modeling · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Many aminoglycosidic antibiotics target the A-site of 16S RNA in the small ribosomal subunit and affect the fidelity of protein translation in bacteria. Upon binding, aminoglycosides displace two adenines (A1492 and A1493 for E. coli numbering) that are involved in tRNA anticodon loop recognition. The major difference in the aminoglycosidic binding site between the prokaryota and eukaryota is an adenine into guanine substitution in the position 1408. This mutation likely affects the dynamics of near A1492 and A1493 and hinders the binding of aminoglycosides to eukaryotic ribosomes. With multiple 20 ns long all-atom molecular dynamics simulations, we study the flexibility of a 22 nucleotide RNA fragment which mimics the aminoglycosidic binding site. Simulations are carried out for both native and A1408G mutated RNA as well as for their complexes with aminoglycosidic representative paromomycin. We observe intra- and extrahelical configurations of A1492 and A1493, which differ between the prokaryotic and the mutated structure. We obtain configurations of the A-site that are also observed in the NMR and crystal structures. Our studies show the differences in the internal mobility of the A-site, as well as that in ion and water density distributions inside of the binding cleft, between the prokaryotic and mutated RNA. We also compare the performance of two force field parameters for RNA, Amber and Charmm.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.