ArticleNucleic acids research2008
NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Article
- Insights into the A-C Mismatch Conformational Ensemble in Duplex DNA and its Role in Genetic Processes through a Structure-based Review.Journal of molecular biology · 2024Review
- Article
- Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop.Journal of the American Chemical Society · 2023Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
- The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development.Advanced drug delivery reviews · 2022Review
- RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics.Nucleic acids research · 2022Article
- Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions.Computational and structural biotechnology journal · 2022Review
- Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties.Journal of chemical theory and computation · 2021Article
- Integrating NMR and simulations reveals motions in the UUCG tetraloop.Nucleic acids research · 2020Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints.Communications biology · 2018Article
- Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.Physical chemistry chemical physics : PCCP · 2017Article
- The structure of the SOLE element of oskar mRNA.RNA (New York, N.Y.) · 2015Article
- Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin.RNA (New York, N.Y.) · 2015Article
- Mutational robustness and resilience of a replicative cis-element of RNA virus: Promiscuity, limitations, relevance.RNA biology · 2015Article
- Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.Proteins · 2014Article
- Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.Journal of biomolecular NMR · 2013Article
- Temperature dependence of molecular interactions involved in defining stability of glutamine binding protein and its complex with L-glutamine.Biochemistry · 2012Article
- Synergistic applications of MD and NMR for the study of biological systems.Journal of biomedicine & biotechnology · 2012Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In a combined NMR/MD study, the temperature-dependent changes in the conformation of two members of the RNA YNMG-tetraloop motif (cUUCGg and uCACGg) have been investigated at temperatures of 298, 317 and 325 K. The two members have considerable different thermal stability and biological functions. In order to address these differences, the combined NMR/MD study was performed. The large temperature range represents a challenge for both, NMR relaxation analysis (consistent choice of effective bond length and CSA parameter) and all-atom MD simulation with explicit solvent (necessity to rescale the temperature). A convincing agreement of experiment and theory is found. Employing a principle component analysis of the MD trajectories, the conformational distribution of both hairpins at various temperatures is investigated. The ground state conformation and dynamics of the two tetraloops are indeed found to be very similar. Furthermore, both systems are initially destabilized by a loss of the stacking interactions between the first and the third nucleobase in the loop region. While the global fold is still preserved, this initiation of unfolding is already observed at 317 K for the uCACGg hairpin but at a significantly higher temperature for the cUUCGg hairpin.
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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.