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RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

[Image: see text] With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD),...

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Autores principales: Šponer, Jiří, Bussi, Giovanni, Krepl, Miroslav, Banáš, Pavel, Bottaro, Sandro, Cunha, Richard A., Gil-Ley, Alejandro, Pinamonti, Giovanni, Poblete, Simón, Jurečka, Petr, Walter, Nils G., Otyepka, Michal
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2018
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920944/
https://www.ncbi.nlm.nih.gov/pubmed/29297679
http://dx.doi.org/10.1021/acs.chemrev.7b00427
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author Šponer, Jiří
Bussi, Giovanni
Krepl, Miroslav
Banáš, Pavel
Bottaro, Sandro
Cunha, Richard A.
Gil-Ley, Alejandro
Pinamonti, Giovanni
Poblete, Simón
Jurečka, Petr
Walter, Nils G.
Otyepka, Michal
author_facet Šponer, Jiří
Bussi, Giovanni
Krepl, Miroslav
Banáš, Pavel
Bottaro, Sandro
Cunha, Richard A.
Gil-Ley, Alejandro
Pinamonti, Giovanni
Poblete, Simón
Jurečka, Petr
Walter, Nils G.
Otyepka, Michal
author_sort Šponer, Jiří
collection PubMed
description [Image: see text] With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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spelling pubmed-59209442018-04-30 RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview Šponer, Jiří Bussi, Giovanni Krepl, Miroslav Banáš, Pavel Bottaro, Sandro Cunha, Richard A. Gil-Ley, Alejandro Pinamonti, Giovanni Poblete, Simón Jurečka, Petr Walter, Nils G. Otyepka, Michal Chem Rev [Image: see text] With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. American Chemical Society 2018-01-03 2018-04-25 /pmc/articles/PMC5920944/ /pubmed/29297679 http://dx.doi.org/10.1021/acs.chemrev.7b00427 Text en Copyright © 2018 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Šponer, Jiří
Bussi, Giovanni
Krepl, Miroslav
Banáš, Pavel
Bottaro, Sandro
Cunha, Richard A.
Gil-Ley, Alejandro
Pinamonti, Giovanni
Poblete, Simón
Jurečka, Petr
Walter, Nils G.
Otyepka, Michal
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
title RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
title_full RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
title_fullStr RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
title_full_unstemmed RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
title_short RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
title_sort rna structural dynamics as captured by molecular simulations: a comprehensive overview
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920944/
https://www.ncbi.nlm.nih.gov/pubmed/29297679
http://dx.doi.org/10.1021/acs.chemrev.7b00427
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