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

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...

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Published in	Chemical reviews Vol. 118; no. 8; pp. 4177 - 4338
Main Authors	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
Format	Journal Article
Language	English
Published	United States American Chemical Society 25.04.2018
Subjects	Catalysis Chemical speciation Computer Simulation Decoding DNA - chemistry Dynamic structural analysis Molecular biology Molecular chemistry Molecular dynamics Molecular Dynamics Simulation Molecules Nucleic Acid Conformation Oligonucleotides Organic chemistry Proteins Review Ribonucleic acid RNA RNA - chemistry Sampling methods Simulation Spatial resolution
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Abstract	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.
AbstractList	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. 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.
Author	Bussi, Giovanni Jurečka, Petr Banáš, Pavel Cunha, Richard A Krepl, Miroslav Pinamonti, Giovanni Walter, Nils G Šponer, Jiří Gil-Ley, Alejandro Poblete, Simón Otyepka, Michal Bottaro, Sandro
AuthorAffiliation	University of Michigan Institute of Biophysics of the Czech Academy of Sciences Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science Structural Biology and NMR Laboratory, Department of Biology Palacky University Olomouc University of Copenhagen Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry
AuthorAffiliation_xml	– name: Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science – name: University of Michigan – name: Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry – name: Palacky University Olomouc – name: University of Copenhagen – name: Institute of Biophysics of the Czech Academy of Sciences – name: Structural Biology and NMR Laboratory, Department of Biology
Author_xml	– sequence: 1 givenname: Jiří orcidid: 0000-0001-6558-6186 surname: Šponer fullname: Šponer, Jiří email: sponer@ncbr.muni.cz organization: Institute of Biophysics of the Czech Academy of Sciences – sequence: 2 givenname: Giovanni orcidid: 0000-0001-9216-5782 surname: Bussi fullname: Bussi, Giovanni email: bussi@sissa.it – sequence: 3 givenname: Miroslav surname: Krepl fullname: Krepl, Miroslav organization: Palacky University Olomouc – sequence: 4 givenname: Pavel orcidid: 0000-0002-7137-8225 surname: Banáš fullname: Banáš, Pavel organization: Palacky University Olomouc – sequence: 5 givenname: Sandro surname: Bottaro fullname: Bottaro, Sandro organization: University of Copenhagen – sequence: 6 givenname: Richard A surname: Cunha fullname: Cunha, Richard A – sequence: 7 givenname: Alejandro surname: Gil-Ley fullname: Gil-Ley, Alejandro – sequence: 8 givenname: Giovanni surname: Pinamonti fullname: Pinamonti, Giovanni – sequence: 9 givenname: Simón surname: Poblete fullname: Poblete, Simón – sequence: 10 givenname: Petr orcidid: 0000-0002-3741-3672 surname: Jurečka fullname: Jurečka, Petr organization: Palacky University Olomouc – sequence: 11 givenname: Nils G surname: Walter fullname: Walter, Nils G organization: University of Michigan – sequence: 12 givenname: Michal orcidid: 0000-0002-1066-5677 surname: Otyepka fullname: Otyepka, Michal organization: Palacky University Olomouc
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/29297679$$D View this record in MEDLINE/PubMed
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Snippet	With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are... With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are...
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StartPage	4177
SubjectTerms	Catalysis Chemical speciation Computer Simulation Decoding DNA - chemistry Dynamic structural analysis Molecular biology Molecular chemistry Molecular dynamics Molecular Dynamics Simulation Molecules Nucleic Acid Conformation Oligonucleotides Organic chemistry Proteins Review Ribonucleic acid RNA RNA - chemistry Sampling methods Simulation Spatial resolution
Title	RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
URI	http://dx.doi.org/10.1021/acs.chemrev.7b00427 https://www.ncbi.nlm.nih.gov/pubmed/29297679 https://www.proquest.com/docview/2099978447 https://search.proquest.com/docview/1984243994 https://pubmed.ncbi.nlm.nih.gov/PMC5920944
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