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.

• MeSH
• DNA chemistry   MeSH
• Catalysis MeSH
• Nucleic Acid Conformation * MeSH
• Computer Simulation MeSH
• RNA chemistry   MeSH
• Molecular Dynamics Simulation * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Research Support, N.I.H., Extramural MeSH
• Names of Substances
• DNA MeSH
• RNA MeSH

The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.

• MeSH
• Crystallography, X-Ray MeSH
• Humans MeSH
• RNA Recognition Motif genetics   MeSH
• Mutagenesis, Site-Directed MeSH
• Nuclear Magnetic Resonance, Biomolecular MeSH
• Recombinant Proteins chemistry   genetics   metabolism   MeSH
• RNA metabolism   MeSH
• RNA Splicing Factors chemistry   genetics   metabolism   MeSH
• Molecular Dynamics Simulation MeSH
• Amino Acid Substitution MeSH
• Binding Sites MeSH
• Water chemistry   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• RBFOX1 protein, human MeSH Browser
• Recombinant Proteins MeSH
• RNA MeSH
• RNA Splicing Factors MeSH
• Water MeSH

Helix 38 (H38) of the large ribosomal subunit, with a length of 110 A, reaches the small subunit through intersubunit bridge B1a. Previous cryo-EM studies revealed that the tip of H38 moves by more than 10 A from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible H38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. We investigate a region including the elbow-shaped kink-turn (Kt-38) in the Haloarcula marismortui archaeal ribosome, and equivalently positioned elbows in three eubacterial species, located at the H38 base. We performed explicit solvent molecular dynamics simulations on the H38 elbows in all four species. They are formed by at first sight unrelated sequences resulting in diverse base interactions but built with the same overall topology, as shown by X-ray crystallography. The elbows display similar fluctuations and intrinsic flexibilities in simulations indicating that the eubacterial H38 elbows are structural and dynamical analogs of archaeal Kt-38. We suggest that this structural element plays a pivotal role in the large motions of H38 and may act as fulcrum for the abovementioned tip motion. The directional flexibility inferred from simulations correlates well with the cryo-EM results.

• MeSH
• Potassium Chloride chemistry   MeSH
• Deinococcus genetics   MeSH
• Cryoelectron Microscopy MeSH
• Escherichia coli genetics   MeSH
• Haloarcula marismortui genetics   MeSH
• Nucleic Acid Conformation MeSH
• RNA, Ribosomal, 23S chemistry   MeSH
• Molecular Dynamics Simulation MeSH
• Sodium chemistry   MeSH
• Thermus thermophilus genetics   MeSH
• Ribosome Subunits, Large, Archaeal chemistry   MeSH
• Ribosome Subunits, Large, Bacterial chemistry   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Names of Substances
• Potassium Chloride MeSH
• RNA, Ribosomal, 23S MeSH
• Sodium MeSH

Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segment (Hinge1) is the highly anharmonic kink of Kt-42. The second one (Hinge2) is localized at the junction between helix 42 and helices 43/44. The rigid segments are the two arms of helix 42 flanking the kink. The whole molecule ends up with compact helices 43/44 (Head) which appear to be modestly compressed towards the subunit in the Haloarcula marismortui X-ray structure. Overall, the helix 42-44 rRNA is constructed as a sophisticated intrinsically flexible anisotropic molecular limb. The leading flexibility modes include bending at the hinges and twisting. The Head shows visible internal conformational plasticity, stemming from an intricate set of base pairing patterns including dynamical triads and tetrads. In summary, we demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries.

• MeSH
• RNA, Archaeal chemistry   MeSH
• Haloarcula marismortui genetics   MeSH
• Ions chemistry   MeSH
• Nucleic Acid Conformation MeSH
• Conserved Sequence MeSH
• Models, Molecular * MeSH
• Molecular Sequence Data MeSH
• Base Pairing MeSH
• Computer Simulation MeSH
• Motion MeSH
• RNA, Ribosomal, 23S chemistry   MeSH
• Base Sequence MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• RNA, Archaeal MeSH
• Ions MeSH
• RNA, Ribosomal, 23S MeSH

The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.

• MeSH
• Magnesium chemistry   MeSH
• Cations, Divalent chemistry   MeSH
• Cations, Monovalent chemistry   MeSH
• Nucleic Acid Conformation MeSH
• Models, Molecular MeSH
• Molecular Sequence Data MeSH
• RNA, Catalytic chemistry   MeSH
• Base Sequence MeSH
• Sodium chemistry   MeSH
• Binding Sites MeSH
• Hepatitis Delta Virus enzymology   MeSH
• Water chemistry   MeSH
• Hydrogen Bonding MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Names of Substances
• Magnesium MeSH
• Cations, Divalent MeSH
• Cations, Monovalent MeSH
• RNA, Catalytic MeSH
• Sodium MeSH
• Water MeSH

Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other SRD features is presented. The SRD is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean square deviation (r.m.s.d.) values between averaged MD and high-resolution X-ray structures of 1-1.4 A. Modest dynamics is observed in the tetraloop, namely, rotation of adenine in its apex and subtle reversible shift of the tetraloop with respect to the adjacent base pair. The deformed flexible region in low-resolution rat X-ray structure is repaired by simulations. The simulations reveal few backbone flips, which do not affect positions of bases and do not indicate a force field imbalance. Non-Watson-Crick base pairs are rigid and mediated by long-residency water molecules while there are several modest cation-binding sites around SRD. In summary, SRD is an unusually stiff rRNA building block. Its intrinsic structural and dynamical signatures seen in simulations are strikingly distinct from other rRNA motifs such as Loop E and Kink-turns.

• MeSH
• Endoribonucleases metabolism   MeSH
• Escherichia coli genetics   MeSH
• Fungal Proteins metabolism   MeSH
• Cations chemistry   MeSH
• Nucleic Acid Conformation MeSH
• Rats MeSH
• Crystallography, X-Ray MeSH
• Models, Molecular * MeSH
• Base Pairing MeSH
• Computer Simulation MeSH
• Ricin metabolism   MeSH
• RNA, Ribosomal, 23S chemistry   metabolism   MeSH
• RNA, Ribosomal, 28S chemistry   metabolism   MeSH
• Carbohydrates chemistry   MeSH
• Binding Sites MeSH
• Water chemistry   MeSH
• Hydrogen Bonding MeSH
• Animals MeSH
• Check Tag
• Rats MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Names of Substances
• alpha-sarcin MeSH Browser
• Endoribonucleases MeSH
• Fungal Proteins MeSH
• Cations MeSH
• Ricin MeSH
• RNA, Ribosomal, 23S MeSH
• RNA, Ribosomal, 28S MeSH
• Carbohydrates MeSH
• Water MeSH

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent molecular dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in domain III, and for the K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. We suggest that some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle.

• MeSH
• Adenine chemistry   MeSH
• Amino Acid Motifs MeSH
• Biophysics methods   MeSH
• Time Factors MeSH
• Cytosine chemistry   MeSH
• Peptide Elongation Factor G chemistry   MeSH
• Catalysis MeSH
• Nucleic Acid Conformation MeSH
• Protein Conformation MeSH
• Crystallography, X-Ray MeSH
• Macromolecular Substances MeSH
• Molecular Conformation MeSH
• Models, Molecular MeSH
• Molecular Sequence Data MeSH
• Oscillometry MeSH
• Base Pairing * MeSH
• Computer Simulation MeSH
• X-Rays MeSH
• Ribosomes chemistry   MeSH
• RNA, Small Nuclear chemistry   MeSH
• RNA, Ribosomal, 23S chemistry   MeSH
• RNA, Transfer chemistry   MeSH
• RNA chemistry   MeSH
• Protein Structure, Secondary MeSH
• Base Sequence MeSH
• Software MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH
• Names of Substances
• Adenine MeSH
• Cytosine MeSH
• Peptide Elongation Factor G MeSH
• Macromolecular Substances MeSH
• RNA, Small Nuclear MeSH
• RNA, Ribosomal, 23S MeSH
• RNA, Transfer MeSH
• RNA MeSH
• U4 small nuclear RNA MeSH Browser