ArticleNature protocols2011
3D maps of RNA interhelical junctions.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.Nature communications · 2025Article
- Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble.Journal of the American Chemical Society · 2023Article
- Spherical frame projections for visualising joint range of motion, and a complementary method to capture mobility data.Journal of anatomy · 2022Article
- RNAloops: a database of RNA multiloops.Bioinformatics (Oxford, England) · 2022Article
- Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.The journal of physical chemistry letters · 2022Article
- Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.Nature communications · 2020Article
- Article
- A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation.Nucleic acids research · 2019Article
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 2018Article
- High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble.Nature structural & molecular biology · 2018Article
- Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.Nucleic acids research · 2017Article
- Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.Physical chemistry chemical physics : PCCP · 2016Article
- Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.Nucleic acids research · 2016Article
- Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.Cell reports · 2015Article
- Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.The journal of physical chemistry. B · 2015Article
- Slowdown of Interhelical Motions Induces a Glass Transition in RNA.Biophysical journal · 2015Article
- Predicting RNA 3D structure using a coarse-grain helix-centered model.RNA (New York, N.Y.) · 2015Article
- New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.Nucleic acids research · 2015Review
- Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.Journal of the American Chemical Society · 2015Article
- From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function.Current opinion in structural biology · 2015Review
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Authors and funding
4 authors.
Funding
Abstract
More than 50% of RNA secondary structure is estimated to be A-form helices, which are linked together by various junctions. Here we describe a protocol for computing three interhelical Euler angles describing the relative orientation of helices across RNA junctions. 5' and 3' helices, H1 and H2, respectively, are assigned based on the junction topology. A reference canonical helix is constructed using an appropriate molecular builder software consisting of two continuous idealized A-form helices (iH1 and iH2) with helix axis oriented along the molecular Z-direction running toward the positive direction from iH1 to iH2. The phosphate groups and the carbon and oxygen atoms of the sugars are used to superimpose helix H1 of a target interhelical junction onto the corresponding iH1 of the reference helix. A copy of iH2 is then superimposed onto the resulting H2 helix to generate iH2'. A rotation matrix R is computed, which rotates iH2' into iH2 and expresses the rotation parameters in terms of three Euler angles α(h), β(h) and γ(h). The angles are processed to resolve a twofold degeneracy and to select an overall rotation around the axis of the reference helix. The three interhelical Euler angles define clockwise rotations around the 5' (-γ(h)) and 3' (α(h)) helices and an interhelical bend angle (β(h)). The angles can be depicted graphically to provide a 'Ramachandran'-type view of RNA global structure that can be used to identify unusual conformations as well as to understand variations due to changes in sequence, junction topology and other parameters.
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