ArticleRNA (New York, N.Y.)2010
Predicting loop-helix tertiary structural contacts in RNA pseudoknots.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics.Journal of computer-aided molecular design · 2025Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model.Journal of biological physics · 2022Article
- VfoldMCPX: predicting multistrand RNA complexes.RNA (New York, N.Y.) · 2022Article
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions.Computational and structural biotechnology journal · 2022Review
- Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding.The journal of physical chemistry. B · 2021Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity.Nucleic acids research · 2021Article
- Graph, pseudoknot, and SARS-CoV-2 genomic RNA: A biophysical synthesis.Biophysical journal · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.PLoS computational biology · 2018Article
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot.Nucleic acids research · 2017Article
- Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel.Journal of the American Chemical Society · 2015Article
- RNAssess--a web server for quality assessment of RNA 3D structures.Nucleic acids research · 2015Article
- Article
- Conjoined use of EM and NMR in RNA structure refinement.PloS one · 2015Article
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3 authors.
Funding
Abstract
Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop-stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop-stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop-stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the energy parameters for the tertiary contacts as inserted parameters, we can then predict the RNA folding thermodynamics, from which we can extract the tertiary contact thermodynamic parameters from theory-experimental comparisons. These comparisons reveal a contact enthalpy (DeltaH) of -14 kcal/mol and a contact entropy (DeltaS) of -38 cal/mol/K for a protonated C(+)*(G-C) base triple at pH 7.0, and (DeltaH = -7 kcal/mol, DeltaS = -19 cal/mol/K) for an unprotonated base triple. Tests of the model for a series of pseudoknots show good theory-experiment agreement. Based on the extracted energy parameters for the tertiary structural contacts, the model enables predictions for the structure, stability, and folding pathways for RNA pseudoknots with known or postulated loop-stem tertiary contacts from the nucleotide sequence alone.
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