Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

Abstract

The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. 5′-UNCG-3′ and 5′-GNRA-3′ RNA tetraloops are the most important classes of RNA hairpin loops. Both tetraloops are highly structured with characteristic signature three-dimensional features and are recurrently seen in functional RNAs and ribonucleoprotein particles. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, the outcome of simulations is often compromised by imperfections in the parametrization of simplified pairwise additive empirical potentials referred to also as force fields. We have pointed out in several recent studies that a force field description of single-stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields. First, we utilized the three widely used variants of Cornell et al. (AMBER) force fields known as ff94, ff99, and ff99bsc0. Some simulations were also carried out with CHARMM27. The simulations reveal several problems which show that these force fields are not able to retain all characteristic structural features (structural signature) of the studied tetraloops. Then we tested four recent reparameterizations of glycosidic torsion of the Cornell et al. force field (two of them being currently parametrized in our laboratories). We show that at least some of the new versions show an improved description of the tetraloops, mainly in the syn glycosidic torsion region of the UNCG tetraloop. The best performance is achieved in combination with the bsc0 parametrization of the α/γ angles. Another critically important region to properly describe RNA molecules is the anti/high-anti region of the glycosidic torsion, where there are significant differences among the tested force fields. The tetraloop simulations are complemented by simulations of short A-RNA stems, which are especially sensitive to an appropriate description of the anti/high-anti region. While excessive accessibility of the high-anti region converts the A-RNA into a senseless “ladder-like” geometry, excessive penalization of the high-anti region shifts the simulated structures away from typical A-RNA geometry to structures with a visibly underestimated inclination of base pairs with respect to the helical axis.

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

“…It has been observed that penalizing high-anti conformers can also lead to a flattening of the A-helix geometry. 9 The results shown in Fig. 3 suggest that small adjustments to α and ζ angles can improve the agreement with experiments of the Amberχ OL3 force field.…”

“…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.…”

“…23 RNA was modeled using the Amber99 force field 24 with parmbsc0 25 and χ OL3 corrections. 9 We will refer to this combination of force field corrections as Amberχ OL3 in the remainder of this paper. Parameters are available at http://github.com/srnas/ff.…”

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

“…Conventional MD simulations were performed using a well-established protocol used for several other endonucleases (31), using the Amber ff12SB force field, which includes the ff99bsc0 corrections for DNA (32) and the ff99bsc0+χOL3 corrections for RNA (33,34). The Åqvist (35) force field has been used for Mg ions.…”

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

“…To test this notion and provide a window into the rapid (sub-microsecond), small-scale dynamics of the ribozyme, not easily accessible by experimental techniques (Ditzler et al 2010), we performed MD simulations on the crystallized trans-acting precursor using our established protocols (Krasovska et al 2005(Krasovska et al , 2006Rhodes et al 2006;McDowell et al 2007McDowell et al , 2010Sefcikova et al 2007a,b;Ditzler et al 2010). We used the latest parmbsc0χ OL3 (Perez et al 2007;Zgarbova et al 2011) variant of the Cornell et al AMBER force field (Cornell et al 1995), which is essential for stable RNA simulations (Banas et al 2010). We analyzed 49 simulations with an aggregate 1.8 µsec of simulation time (Table 2).…”