ArticleBiophysical journal1999
Molecular dynamics simulations of solvated yeast tRNA(Asp).
Article in Biophysical journal, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 73 citations in OpenAlex.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- Structural basis of MALAT1 RNA maturation and mascRNA biogenesis.Nature structural & molecular biology · 2024Article
- RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics.Nucleic acids research · 2022Article
- Structure and Dynamics of tRNAACS omega · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Structural Insights into tRNA Dynamics on the Ribosome.International journal of molecular sciences · 2015Review
- Article
- Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics.Journal of chemical theory and computation · 2014Article
- The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.Journal of chemical theory and computation · 2012Article
- Dynamics of tRNA at different levels of hydration.Biophysical journal · 2009Article
- Analyzing the flexibility of RNA structures by constraint counting.Biophysical journal · 2008Article
- Dynamics of Recognition between tRNA and elongation factor Tu.Journal of molecular biology · 2008Article
- High performance computing in biology: multimillion atom simulations of nanoscale systems.Journal of structural biology · 2007Review
- Review
- Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop.Biophysical journal · 2007Article
- Simulating movement of tRNA into the ribosome during decoding.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.Biophysical journal · 2005Article
- Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.Nucleic acids research · 2005Article
- Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets.Nucleic acids research · 2003Article
- Biopolymer Chain Elasticity: A novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances.Nucleic acids research · 2003Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transfer RNA molecules are involved in a variety of biological processes, implying complex recognition events with proteins and other RNAs. From a structural point of view, tRNAs constitute a reference system for studying RNA folding and architecture. A deeper understanding of their structural and functional properties will derive from our ability to model accurately their dynamical behavior. We present the first dynamical model of a fully neutralized and solvated tRNA molecule over a 500-ps time scale. Starting from the crystallographic structure of yeast tRNA(Asp), the 75-nucleotide molecule was modeled with 8055 water molecules and 74 NH4+ counterions, using the AMBER4.1 program and the particle mesh Ewald (PME) method for the treatment of long-range electrostatic interactions. The calculations led to a dynamically stable model of the tRNA molecule. During the simulation, all secondary and tertiary base pairs are maintained while a certain lability of base triples in the tRNA core is observed. This lability was interpreted as resulting from intrinsic factors associated with the "weaker" hydrogen bonding patterns seen in these base triples and from an altered ionic environment of the tRNA molecule. Calculated thermal factors are used to compare the dynamics of the tRNA in solution and in the crystal. The present molecular dynamics simulation of a complex and highly charged nucleic acid molecule attests to the fact that simulation methods are now able to investigate not only the dynamics of proteins, but also that of large RNA molecules. Thus they also provide a basis for further investigations on the structural and functional effects of chemical and posttranscriptionally modified nucleotides as well as on ionic environmental effects.
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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.