ArticleNucleic acids research2010
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops.RNA (New York, N.Y.) · 2026Article
- Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping.The Journal of cell biology · 2025Article
- Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments.Journal of chemical theory and computation · 2023Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Article
- Screening Collagenase Activity in Bacterial Lysate for Directed Enzyme Applications.International journal of molecular sciences · 2021Article
- 2'-Chemical science · 2020Article
- Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer.ACS omega · 2020Article
- Structural Basis of Teneurin-Latrophilin Interaction in Repulsive Guidance of Migrating Neurons.Cell · 2020Article
- Mutagenesis of α-Conotoxins for Enhancing Activity and Selectivity for Nicotinic Acetylcholine Receptors.Toxins · 2019Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Three-dimensional Modelling of the Voltage-gated Sodium Ion Channel from Anopheles gambiae Reveals Spatial Clustering of Evolutionarily Conserved Acidic Residues at the Extracellular Sites.Current neuropharmacology · 2017Article
- Structural similarities in the CPC clip motif explain peptide-binding promiscuity between glycosaminoglycans and lipopolysaccharides.Journal of the Royal Society, Interface · 2017Article
- Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation.Journal of molecular modeling · 2017Article
- Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot.Nucleic acids research · 2017Article
- Adaptation of a Genetic Screen Reveals an Inhibitor for Mitochondrial Protein Import Component Tim44.The Journal of biological chemistry · 2017Article
- Genetic Algorithm Managed Peptide Mutant Screening: Optimizing Peptide Ligands for Targeted Receptor Binding.Journal of chemical information and modeling · 2016Article
- A benchmark for reaction coordinates in the transition path ensemble.The Journal of chemical physics · 2016Article
- Reaction mechanism and reaction coordinates from the viewpoint of energy flow.The Journal of chemical physics · 2016Article
- Markov state models of protein misfolding.The Journal of chemical physics · 2016Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Conformational equilibrium within the ubiquitous GNRA tetraloop motif was simulated at the ensemble level, including 10 000 independent all-atom molecular dynamics trajectories totaling over 110 micros of simulation time. This robust sampling reveals a highly dynamic structure comprised of 15 conformational microstates. We assemble a Markov model that includes transitions ranging from the nanosecond to microsecond timescales and is dominated by six key loop conformations that contribute to fluctuations around the native state. Mining of the Protein Data Bank provides an abundance of structures in which GNRA tetraloops participate in tertiary contact formation. Most predominantly observed in the experimental data are interactions of the native loop structure within the minor groove of adjacent helical regions. Additionally, a second trend is observed in which the tetraloop assumes non-native conformations while participating in multiple tertiary contacts, in some cases involving multiple possible loop conformations. This tetraloop flexibility can act to counterbalance the energetic penalty associated with assuming non-native loop structures in forming tertiary contacts. The GNRA motif has thus evolved not only to readily participate in simple tertiary interactions involving native loop structure, but also to easily adapt tetraloop secondary conformation in order to participate in larger, more complex tertiary interactions.
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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.