ArticleJournal of chemical theory and computation2010
Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed, 169 citations in OpenAlex.
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- Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set.Journal of chemical theory and computation · 2025Article
- Experimental and computational investigations of RNA duplexes containing N7-regioisomers of adenosine and LNA-adenosine.Nucleic acids research · 2025Article
- NMR structures of small molecules bound to a model of a CUG RNA repeat expansion.Bioorganic & medicinal chemistry letters · 2024Review
- NMR structures and magnetic force spectroscopy studies of small molecules binding to models of an RNA CAG repeat expansion.bioRxiv : the preprint server for biology · 2024Article
- NMR structures of small molecules bound to a model of an RNA CUG repeat expansion.bioRxiv : the preprint server for biology · 2024Article
- Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent.Biophysical reviews · 2024Review
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 2024Article
- Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design.Nature communications · 2024Article
- Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies.Nucleic acids research · 2023Article
- Red light-emitting short Mango-based system enables tracking a mycobacterial small noncoding RNA in infected macrophages.Nucleic acids research · 2023Article
- Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.RNA (New York, N.Y.) · 2023Article
- Dynamic docking of small molecules targeting RNA CUG repeats causing myotonic dystrophy type 1.Biophysical journal · 2023Article
- CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs.The journal of physical chemistry. B · 2022Article
- Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations.Journal of chemical theory and computation · 2022Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
- Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.Journal of computational biophysics and chemistry · 2022Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.
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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.