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Molecular dynamics simulation of RNA pseudoknot unfolding pathway

Many biological functions of RNA molecules are related to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus (M...

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Autores principales: Guo, Yun, Zhang, Wenbing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Wuhan University 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149040/
http://dx.doi.org/10.1007/s11859-013-0905-0
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author Guo, Yun
Zhang, Wenbing
author_facet Guo, Yun
Zhang, Wenbing
author_sort Guo, Yun
collection PubMed
description Many biological functions of RNA molecules are related to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus (MMTV) RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynamics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hairpin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after formation of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure’s unfolding process, which means that both are the unzipping process.
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spelling pubmed-71490402020-04-13 Molecular dynamics simulation of RNA pseudoknot unfolding pathway Guo, Yun Zhang, Wenbing Wuhan University Journal of Natural Sciences Article Many biological functions of RNA molecules are related to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus (MMTV) RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynamics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hairpin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after formation of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure’s unfolding process, which means that both are the unzipping process. Wuhan University 2013-03-12 2013 /pmc/articles/PMC7149040/ http://dx.doi.org/10.1007/s11859-013-0905-0 Text en © Wuhan University and Springer-Verlag Berlin Heidelberg 2013 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Article
Guo, Yun
Zhang, Wenbing
Molecular dynamics simulation of RNA pseudoknot unfolding pathway
title Molecular dynamics simulation of RNA pseudoknot unfolding pathway
title_full Molecular dynamics simulation of RNA pseudoknot unfolding pathway
title_fullStr Molecular dynamics simulation of RNA pseudoknot unfolding pathway
title_full_unstemmed Molecular dynamics simulation of RNA pseudoknot unfolding pathway
title_short Molecular dynamics simulation of RNA pseudoknot unfolding pathway
title_sort molecular dynamics simulation of rna pseudoknot unfolding pathway
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149040/
http://dx.doi.org/10.1007/s11859-013-0905-0
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