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Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes
[Image: see text] RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA mole...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10091408/ https://www.ncbi.nlm.nih.gov/pubmed/36989143 http://dx.doi.org/10.1021/acs.jcim.2c01438 |
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author | Kührová, Petra Mlýnský, Vojtěch Otyepka, Michal Šponer, Jiří Banáš, Pavel |
author_facet | Kührová, Petra Mlýnský, Vojtěch Otyepka, Michal Šponer, Jiří Banáš, Pavel |
author_sort | Kührová, Petra |
collection | PubMed |
description | [Image: see text] RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single-stranded, canonical (Watson–Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA. |
format | Online Article Text |
id | pubmed-10091408 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-100914082023-04-13 Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes Kührová, Petra Mlýnský, Vojtěch Otyepka, Michal Šponer, Jiří Banáš, Pavel J Chem Inf Model [Image: see text] RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single-stranded, canonical (Watson–Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA. American Chemical Society 2023-03-29 /pmc/articles/PMC10091408/ /pubmed/36989143 http://dx.doi.org/10.1021/acs.jcim.2c01438 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Kührová, Petra Mlýnský, Vojtěch Otyepka, Michal Šponer, Jiří Banáš, Pavel Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes |
title | Sensitivity of
the RNA Structure to Ion Conditions
as Probed by Molecular Dynamics Simulations of Common Canonical RNA
Duplexes |
title_full | Sensitivity of
the RNA Structure to Ion Conditions
as Probed by Molecular Dynamics Simulations of Common Canonical RNA
Duplexes |
title_fullStr | Sensitivity of
the RNA Structure to Ion Conditions
as Probed by Molecular Dynamics Simulations of Common Canonical RNA
Duplexes |
title_full_unstemmed | Sensitivity of
the RNA Structure to Ion Conditions
as Probed by Molecular Dynamics Simulations of Common Canonical RNA
Duplexes |
title_short | Sensitivity of
the RNA Structure to Ion Conditions
as Probed by Molecular Dynamics Simulations of Common Canonical RNA
Duplexes |
title_sort | sensitivity of
the rna structure to ion conditions
as probed by molecular dynamics simulations of common canonical rna
duplexes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10091408/ https://www.ncbi.nlm.nih.gov/pubmed/36989143 http://dx.doi.org/10.1021/acs.jcim.2c01438 |
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