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

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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.

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          Most cited references 1,211

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            We introduce a novel and powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of a coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates.A characteristic feature of this dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the free energy surface, allowing the efficient exploration and accurate determination of the free energy surface as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.
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                Author and article information

                Journal
                Chem Rev
                Chem. Rev
                cr
                chreay
                Chemical Reviews
                American Chemical Society
                0009-2665
                1520-6890
                03 January 2018
                25 April 2018
                : 118
                : 8 , RNA: From Single Molecules to Medicine
                : 4177-4338
                Affiliations
                []Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135, Brno 612 65, Czech Republic
                []Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265, Trieste 34136, Italy
                [§ ]Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , 17. listopadu 12, Olomouc 771 46, Czech Republic
                []Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen , Copenhagen 2200, Denmark
                []Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
                Author notes
                Article
                10.1021/acs.chemrev.7b00427
                5920944
                29297679
                Copyright © 2018 American Chemical Society

                This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

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                Custom metadata
                cr7b00427
                cr-2017-00427t

                Chemistry

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