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Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functio...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007934/ https://www.ncbi.nlm.nih.gov/pubmed/29879103 http://dx.doi.org/10.1371/journal.pcbi.1006222 |
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author | Shi, Ya-Zhou Jin, Lei Feng, Chen-Jie Tan, Ya-Lan Tan, Zhi-Jie |
author_facet | Shi, Ya-Zhou Jin, Lei Feng, Chen-Jie Tan, Ya-Lan Tan, Zhi-Jie |
author_sort | Shi, Ya-Zhou |
collection | PubMed |
description | RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions. |
format | Online Article Text |
id | pubmed-6007934 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-60079342018-06-21 Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions Shi, Ya-Zhou Jin, Lei Feng, Chen-Jie Tan, Ya-Lan Tan, Zhi-Jie PLoS Comput Biol Research Article RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions. Public Library of Science 2018-06-07 /pmc/articles/PMC6007934/ /pubmed/29879103 http://dx.doi.org/10.1371/journal.pcbi.1006222 Text en © 2018 Shi et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Shi, Ya-Zhou Jin, Lei Feng, Chen-Jie Tan, Ya-Lan Tan, Zhi-Jie Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions |
title | Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions |
title_full | Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions |
title_fullStr | Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions |
title_full_unstemmed | Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions |
title_short | Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions |
title_sort | predicting 3d structure and stability of rna pseudoknots in monovalent and divalent ion solutions |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007934/ https://www.ncbi.nlm.nih.gov/pubmed/29879103 http://dx.doi.org/10.1371/journal.pcbi.1006222 |
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