ArticleBiophysical journal2008
Analyzing the flexibility of RNA structures by constraint counting.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.Biophysics and physicobiology · 2025Article
- Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs.RNA (New York, N.Y.) · 2020Article
- Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser.Journal of biomolecular NMR · 2019Article
- Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion.Journal of chemical information and modeling · 2018Article
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Nucleic acids research · 2015Article
- Structural Insights into tRNA Dynamics on the Ribosome.International journal of molecular sciences · 2015Review
- Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis.PloS one · 2015Article
- Solving nucleic acid structures by molecular replacement: examples from group II intron studies.Acta crystallographica. Section D, Biological crystallography · 2013Review
- Article
- Towards accurate modeling of noncovalent interactions for protein rigidity analysis.BMC bioinformatics · 2013Article
- Voronoia4RNA--a database of atomic packing densities of RNA structures and their complexes.Nucleic acids research · 2013Article
- Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids.ACS medicinal chemistry letters · 2011Article
- Computational approaches to RNA structure prediction, analysis, and design.Current opinion in structural biology · 2011Review
- Free state conformational sampling of the SAM-I riboswitch aptamer domain.Structure (London, England : 1993) · 2010Article
- Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch.Nucleic acids research · 2009Article
- Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome.BMC structural biology · 2009Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA requires conformational dynamics to undergo its diverse functional roles. Here, a new topological network representation of RNA structures is presented that allows analyzing RNA flexibility/rigidity based on constraint counting. The method extends the FIRST approach, which identifies flexible and rigid regions in atomic detail in a single, static, three-dimensional molecular framework. Initially, the network rigidity of a canonical A-form RNA is analyzed by counting on constraints of network elements of increasing size. These considerations demonstrate that it is the inclusion of hydrophobic contacts into the RNA topological network that is crucial for an accurate flexibility prediction. The counting also explains why a protein-based parameterization results in overly rigid RNA structures. The new network representation is then validated on a tRNA(ASP) structure and all NMR-derived ensembles of RNA structures currently available in the Protein Data Bank (with chain length >/=40). The flexibility predictions demonstrate good agreement with experimental mobility data, and the results are superior compared to predictions based on two previously used network representations. Encouragingly, this holds for flexibility predictions as well as mobility predictions obtained by constrained geometric simulations on these networks. Potential applications of the approach to analyzing the flexibility of DNA and RNA/protein complexes are discussed.
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