Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

Bergonzo, Christina; Henriksen, Niel M.; Roe, Daniel R.; Cheatham, Thomas E.

doi:10.1261/rna.051102.115

Cited by 132 publications

(359 citation statements)

References 55 publications

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“…A recent study (44) of the efficacy of different AMBER (assisted model building with energy refinement) force fields in stabilizing folded RNA configurations at microsecond timescales reveals that the force field used in our study most effectively stabilizes the native loop configuration of a UNCG tetraloop. However, the results also indicate near-equal populations of native and suboptimal loops being adopted over the course of simulation.…”

Section: Discussionmentioning

confidence: 94%

Free-energy landscape of a hyperstable RNA tetraloop

Miner

Chen

Garcı́a

2016

Proc. Natl. Acad. Sci. U.S.A.

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We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the freeenergy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the lefthanded Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.RNA | free-energy landscape | molecular dynamics | tetraloop | pressure T he stability of a folded RNA molecule depends on a complex set of interactions between the RNA with itself and the surrounding environment. Secondary RNA structures fold by a combination of complimentary base pairing, nucleotide stacking, and screening of the anionic phosphate backbone (1), but these interactions depend heavily on the local solution environment, and the RNA configuration can be either stabilized or destabilized by a number of extrinsic factors, including temperature (2), pressure (3), denaturants, and salt concentration (4). Even in simple RNA duplexes, changes in pressure and ion concentrations have been shown to drive the formation of alternative configurations (5, 6) and change the RNA folded ensemble. Characterizing the effects that these different factors have on the folded free-energy landscape of RNA is crucial for determining the thermodynamic stability of different RNA motifs and the probability of transitions between configurations.Small RNA hairpins have been used as a model system for characterizing RNA folding and stability for decades because of their small size, their ubiquitous presence in many natural systems, and the complexity of their internal interactions (7-11). Hairpins result when a single oligonucleotide strand bends 180°t o form an antiparallel duplex through complementary base pairing. The bent, single-stranded loop region is capable of forming complex hydrogen bond networks (12) or long-range interactions with other RNAs (13). Some of the most thermodynamically stable RNA hairpins form loop regions of 4 nt, called tetraloops (14), which are highly compact, structurally conserved, and typically stabilized by the formation of a network of hydrogen bonds (15) that decrease the loop conformational entropy.These tetraloop structures have been explored through multiple experimental (16-23) and computational...

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Section: Discussionmentioning

confidence: 94%

Free-energy landscape of a hyperstable RNA tetraloop

Miner

Chen

Garcı́a

2016

Proc. Natl. Acad. Sci. U.S.A.

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“…2 While simulations initialized in the vicinity of the native state are stable on short time-scales under a variety of simulation conditions, [3][4][5][6][7][8] more recent works strongly suggest that these systems are not correctly modeled by the current Amber force field. [9][10][11][12][13][14] Although different improvements have been proposed, 15 there is growing evidence that none of the available corrections are able to capture the crucial non-canonical interactions present in these tetraloops. 12,13 Despite their small size, an ergodic sampling of these systems requires substantial computational resources, in the order of hundreds of µs using massively parallel simulations.…”

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confidence: 99%

“…[9][10][11][12][13][14] Although different improvements have been proposed, 15 there is growing evidence that none of the available corrections are able to capture the crucial non-canonical interactions present in these tetraloops. 12,13 Despite their small size, an ergodic sampling of these systems requires substantial computational resources, in the order of hundreds of µs using massively parallel simulations. 5,10,12 For this reason, full convergence of MD simulations on RNA has been so far achieved for simple systems such as tetranucleotides.…”

mentioning

confidence: 99%

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Bottaro

Banáš

Šponer

et al. 2016

J. Phys. Chem. Lett.

179

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We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered metadynamics. A key ingredient is the use of a recently developed metric distance, eRMSD, as a biased collective variable. We find that the native fold of both tetraloops is not the global free energy minimum using the Amber\c{hi}OL3 force field. The estimated folding free energies are 30.2kJ/mol for UUCG and 7.5 kJ/mol for GAGA, in striking disagreement with experimental data. We evaluate the viability of all possible one-dimensional backbone force field corrections. We find that disfavoring the gauche+ region of {\alpha} and {\zeta} angles consistently improves the existing force field. The level of accuracy achieved with these corrections, however, cannot be considered sufficient by judging on the basis of available thermodynamic data and solution experiments.Comment: Journal of Physical Chemistry Letters (2016

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“…We use the Visual Molecular Dynamics (VMD) (89) package to analyze the structural and energetic properties, such as the base pairing and base stacking interactions for each cluster. We implement two different nucleic acid force fields (90, 91) (AMBER ff99 and CHARMM27) with the same simulation protocol to examine the force field dependence of the predicted kinetics, and find the same general conclusions (92)(93)(94). From the kinetic connectivity between the conformations, we build a network of conformational clusters.…”

Section: Methodsmentioning

confidence: 99%

Understanding the kinetic mechanism of RNA single base pair formation

Chen

2015

Proc. Natl. Acad. Sci. U.S.A.

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RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/ dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. RNAs perform critical cellular functions at the level of gene expression and regulation (1-4). RNA functions are determined not only by RNA structure or structure motifs [e.g., tetraloop hairpins (5, 6)] but also by conformational distributions and dynamics and kinetics of conformational changes. For example, riboswitches can adopt different conformations in response to specific conditions of the cellular environment (7,8). Understanding the kinetics, such as the rate and pathways for the conformational changes, is critical for deciphering the mechanism of RNA function (9-19). Extensive experimental and theoretical studies on RNA folding kinetics have provided significant insights into the kinetic mechanism of RNA functions (19-36). However, due to the complexity of the RNA folding energy landscape (37-46) and the limitations of experimental tools (47-55), many fundamental problems, including single base flipping and base pair formation and fraying, remain unresolved. These unsolved fundamental problems have hampered our ability to resolve other important issues, such as RNA hairpin and larger structure folding kinetics. Several key questions remain unanswered, such as whether the hairpin folding is rate-limited by the conformational search of the native base pairs, whose formation leads to fast downhill folding of the whole structure, or by the breaking of misfolded base pairs before refolding to the native structure (18,19,(54)(55)(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72)(73).Motivated by the need to understand the basic steps of nucleic acids folding, Hagan et al. (74) performed forty-three 200-ps unfolding trajectories at 400 K and identified both on-and offpathway intermediates and two dominant unfolding pathways for a terminal C-G base pair in a DNA duplex. In one of the pathways, bas...

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Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

Cited by 132 publications

References 55 publications

Free-energy landscape of a hyperstable RNA tetraloop

Free-energy landscape of a hyperstable RNA tetraloop

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Understanding the kinetic mechanism of RNA single base pair formation

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