ArticlePloS one2012
A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- In Silico Investigation against Inhibitors of Alpha-Amylase Using Structure-based Screening, Molecular Docking, and Molecular Simulations Studies.Cell biochemistry and biophysics · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- Folding@home: Achievements from over 20 years of citizen science herald the exascale era.Biophysical journal · 2023Review
- Repurposing Amphotericin B: anti-microbial, molecular docking and molecular dynamics simulation studies suggest inhibition potential of Amphotericin B against MRSA.BMC chemistry · 2023Article
- Folding@home: achievements from over twenty years of citizen science herald the exascale era.ArXiv · 2023Article
- Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease.Journal of biomolecular structure & dynamics · 2022Article
- Identification of Novel Cannabinoid CB2 Receptor Agonists from Botanical Compounds and Preliminary Evaluation of Their Anti-Osteoporotic Effects.Molecules (Basel, Switzerland) · 2022Article
- Dielectric dispersion characteristics of the phospholipid bilayer with subnanometer resolution from terahertz to mid-infrared.Frontiers in bioengineering and biotechnology · 2022Article
- Modelling and targeting mitochondrial protein tyrosine phosphatase 1: a computational approach.In silico pharmacology · 2022Article
- Protobiotic Systems Chemistry Analyzed by Molecular Dynamics.Life (Basel, Switzerland) · 2019Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance.Bioinformatics (Oxford, England) · 2016Article
- A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.Nature communications · 2016Article
- Molecular dynamics simulations of large macromolecular complexes.Current opinion in structural biology · 2015Review
- Molecular dynamics simulations: advances and applications.Advances and applications in bioinformatics and chemistry : AABC · 2015Review
- Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.Structure (London, England : 1993) · 2014Article
- Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study.PloS one · 2014Article
- A nonredundant structure dataset for benchmarking protein-RNA computational docking.Journal of computational chemistry · 2013Article
- Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.PLoS computational biology · 2013Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ribosome is a large macromolecular machine, and correlated motion between residues is necessary for coordinating function across multiple protein and RNA chains. We ran two all-atom, explicit solvent molecular dynamics simulations of the bacterial ribosome and calculated correlated motion between residue pairs by using mutual information. Because of the short timescales of our simulation (ns), we expect that dynamics are largely local fluctuations around the crystal structure. We hypothesize that residues that show coupled dynamics are functionally related, even on longer timescales. We validate our model by showing that crystallographic B-factors correlate well with the entropy calculated as part of our mutual information calculations. We reveal that A-site residues move relatively independently from P-site residues, effectively insulating A-site functions from P-site functions during translation.
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