ArticleNucleic acids research2006
Molecular dynamics simulations of sarcin-ricin rRNA motif.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 79 citations in OpenAlex.
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- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.Methods (San Diego, Calif.) · 2016Review
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Nucleic acids research · 2015Article
- Platinum-RNA modifications following drug treatment in S. cerevisiae identified by click chemistry and enzymatic mapping.ACS chemical biology · 2014Article
- Computational identification of RNA functional determinants by three-dimensional quantitative structure-activity relationships.Nucleic acids research · 2014Article
- Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.The journal of physical chemistry. B · 2013Article
- A novel implicit solvent model for simulating the molecular dynamics of RNA.Biophysical journal · 2013Article
- Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.The journal of physical chemistry. B · 2012Article
- Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.Journal of chemical theory and computation · 2012Article
- Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.Nucleic acids research · 2012Article
- Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform.Journal of chemical theory and computation · 2012Article
- Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.Journal of biophysics (Hindawi Publishing Corporation : Online) · 2011Article
- Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.Journal of chemical theory and computation · 2010Article
- Effect of high hydrostatic pressure on hydration and activity of ribozymes.Molecular biology reports · 2010Article
- RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.Nucleic acids research · 2010Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other SRD features is presented. The SRD is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean square deviation (r.m.s.d.) values between averaged MD and high-resolution X-ray structures of 1-1.4 A. Modest dynamics is observed in the tetraloop, namely, rotation of adenine in its apex and subtle reversible shift of the tetraloop with respect to the adjacent base pair. The deformed flexible region in low-resolution rat X-ray structure is repaired by simulations. The simulations reveal few backbone flips, which do not affect positions of bases and do not indicate a force field imbalance. Non-Watson-Crick base pairs are rigid and mediated by long-residency water molecules while there are several modest cation-binding sites around SRD. In summary, SRD is an unusually stiff rRNA building block. Its intrinsic structural and dynamical signatures seen in simulations are strikingly distinct from other rRNA motifs such as Loop E and Kink-turns.
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