The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation
ABSTRACT The ability of the Amber ff99 force field to predict relative free energies of RNA helix formation was investigated. The test systems were three hexaloop RNA hairpins with identical loops and varying stems. The potential of mean force of stretching the hairpins from the native state to an extended conformation was calculated with umbrella sampling. Because the hairpins have identical loop sequence, the differences in free energy changes are only from the stem composition. The Amber ff99 force field was able to correctly predict the order of stabilities of the hairpins, although the magnitude of the free energy change is larger than that determined by optical melting experiments. The two measurements cannot be compared directly because the unfolded state in the optical melting experiments is a random coil, while the end state in the umbrella sampling simulations was an elongated chain. The calculations can be compared to reference data by using a thermodynamic cycle. By applying the thermodynamic cycle to the transitions between the hairpins using simulations and nearest neighbor data, agreement was found to be within the sampling error of simulations, thus demonstrating that ff99 force field is able to accurately predict relative free energies of RNA helix formation.
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ABSTRACT: We report the results of a series of 1 μs-long explicit-solvent molecular dynamics (MD) simulations performed to compare the free energies of stacking (ΔGstack) of all possible combinations of DNA and RNA nucleoside (NS) pairs and dinucleoside-monophosphates (DNMPs). For both NS-pairs and DNMPs we show that the computed stacking free energies are in reasonable qualitative agreement with experimental measurements, and appear to provide the closest correspondence with experiment yet found among computational studies; in all cases, however, the computed stacking free energies are too favorable relative to experiment. Comparisons of NS-pair systems indicate that stacking interactions are very similar in RNA and DNA systems except when a thymine or uracil base is involved: the presence of a thymine base favors stacking by ~0.3 kcal/mol relative to a uracil base. One exception is found in the self-stacking of cytidines, which are found to be significantly more favorable for the DNA form; an analysis of the rotational orientations sampled during stacking events suggests that this is likely to be due to more favorable sugar-sugar interactions in stacked complexes of deoxycytidines. Comparisons of the DNMP systems indicate that stacking interactions are more favorable in RNA than in DNA except, again, when thymine or uracil bases are involved. Finally, additional simulations performed using a previous generation of the Amber force field - in which the description of glycosidic bond rotations was less than optimal - produce computed stacking free energies that are in poorer agreement with experimental data. Overall, the simulations provide a comprehensive view of stacking thermodynamics in nucleoside pairs and in DNMPs as predicted by a state-of-the-art MD force field.Journal of Chemical Theory and Computation 04/2015; 11(5):150407163841004. DOI:10.1021/ct501170h · 5.31 Impact Factor
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ABSTRACT: Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and, in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNA structural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. These results nevertheless suggest that the sequence dependence of the A-RNA structure, usually attributed to base stacking, might be driven by the structural dynamics of specific hydration. Here, we present a systematic MD study that aimed to (i) clarify the atomistic mechanism of the water model sensitivity and (ii) discover whether and to what extent specific hydration modulates the A-RNA structural variability. We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2′-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Minor groove hydration is also responsible for the sequence dependence of these helical parameters. Our simulations suggest that TIP5P is not optimal for RNA simulations.Journal of Chemical Theory and Computation 01/2014; 10(1):401-411. DOI:10.1021/ct400663s · 5.31 Impact Factor
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ABSTRACT: RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5′-UNCG-3′ and 5′-GNRA-3′ families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 Å of the native structure, in contrast to results with earlier force fields. Although we find that the REMD simulation runs of a total of 19 μs (starting from both folded and unfolded state) in duration for each TL are still far from obtaining a representative equilibrium distribution at each temperature, we are nonetheless able to map the stable species on the folding energy landscape. The qualitative picture we obtain is consistent with experimental studies of RNA folding in that there are a number of stable on- and off-pathway intermediates en route to the native state. In particular, we have identified a misfolded-bulged state of GNRA TL, which shares many structural features with the X-ray structure of GNRA TL in the complex with restrictocin, namely the bulged out AL4 base. Since this is the same conformation observed in the complex of the TL with restrictocin, we argue that GNRA TL is able to bind restrictocin via a “conformational selection” mechanism, with the RL3 and AL4 bases being exposed to the solvent prior to binding. In addition we have identified a misfolded-anti state of UUCG TL, which is structurally close to the native state except that the GL4 nucleotide is in an anti-conformation instead of the native syn. Our data suggest that the UUCG misfolded-anti state may be a kinetic trap for the UUCG folding.Journal of Chemical Theory and Computation 04/2013; 9(4):2115–2125. DOI:10.1021/ct301086z · 5.31 Impact Factor