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

Chemical Reviews
Jiří ŠponerMichal Otyepka

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 RN...Continue Reading

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Methods Mentioned

BETA
X-ray
nuclear magnetic resonance
NMR
isothermal titration calorimetry
protein folding
electron microscopy
GTPase
dissection
RNA folding
surface plasmon resonance

Software Mentioned

SimRNA
naRES
MC
TRAM
CHARMM27
iFold
ENM
WHAM
SPQR
ff14SB

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