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RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
- Source :
- Chemical Reviews
- Publication Year :
- 2018
- Publisher :
- American Chemical Society (ACS), 2018.
-
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.
- Subjects :
- 0301 basic medicine
Chemistry
RNA
DNA
Review
General Chemistry
Computational biology
Molecular Dynamics Simulation
Catalysis
Field (geography)
Settore FIS/03 - Fisica della Materia
03 medical and health sciences
Broad spectrum
Chemical species
Physical limitations
Molecular dynamics
030104 developmental biology
Nucleic Acid Conformation
Computer Simulation
Subjects
Details
- ISSN :
- 15206890 and 00092665
- Volume :
- 118
- Database :
- OpenAIRE
- Journal :
- Chemical Reviews
- Accession number :
- edsair.doi.dedup.....9adffdd69a58334607e18fa0b71c4bda