Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions

Abstract

Accurately modeling unpaired regions of RNA is important for predicting structure, dynamics, and thermodynamics of folded RNA. Comparisons between NMR data and molecular dynamics simulations provide a test of force fields used for modeling. Here, NMR spectroscopy, including NOESY, 1H–31P HETCOR, DQF-COSY, and TOCSY, was used to determine conformational preferences for single-stranded GACC RNA. The spectra are consistent with a conformational ensemble containing major and minor A-form-like structures. In a series of 50 ns molecular dynamics (MD) simulations with the AMBER99 force field in explicit solvent, initial A-form-like structures rapidly evolve to disordered conformations. A set of 50 ns simulations with revised χ torsions (AMBER99χ force field) gives two primary conformations, consistent with the NMR spectra. A single 1.9 μs MD simulation with the AMBER99χ force field showed that the major and minor conformations are retained for almost 68% of the time in the first 700 ns, with multiple transformations from A-form to non-A-form conformations. For the rest of the simulation, random-coil structures and a stable non-A-form conformation inconsistent with NMR spectra were seen. Evidently, the AMBER99χ force field improves structural predictions for single-stranded GACC RNA compared to the AMBER99 force field, but further force field improvements are needed.

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

“…These simulations show the UUCG loop conformation and dynamics on longer timescales and not only help to assess and validate the force field performance, but show that results obtained with the CPU and GPU versions of the PMEMD code behave similarly and also that similar results are seen with the specialized Anton supercomputer (Shaw Steinbrecher et al (2012). e Yildirim et al (2011). f Chen and García (2013).…”

“…However, Yildirim and colleagues also reported that they observed another non-Aform structure with significant population in their longer MD simulation. The results from our independent M-REMD simulations using these parameters (192 replicas, ∼1 µsec per replica) do in fact show that intercalated structures that are inconsistent with the NMR data are the main representatives of the ensemble, accounting for ∼40% of structures (including a conformation consistent with the non-A-form one reported by Yildirim et al 2011). While the overall populations of NMR major and NMR minor from the ff99 + χ Yil simulations do not reproduce the experimentally determined populations, the ratio of NMR major to NMR minor is roughly 2.5:1, which is consistent with the relative populations of these two structures from the experimental ensemble; we note that no other force field tested was able to do this.…”

“…Tetranucleotide ensembles provide interesting insight into force field deficiencies, initially described in Yildirim et al (2011) and Henriksen et al (2013). These ensembles can be very conformationally diverse, and initial results using modified χ parameters (ff99 + χ Yil ) shifted the populations of the RNA to sample mostly NMR major and minor conformations on the 100-nsec timescale (Yildirim et al 2011).…”

“…These ensembles can be very conformationally diverse, and initial results using modified χ parameters (ff99 + χ Yil ) shifted the populations of the RNA to sample mostly NMR major and minor conformations on the 100-nsec timescale (Yildirim et al 2011). Later, enhanced sampling identified four main structures in AMBER ff12, though convergence in T-REMD simulations remained elusive (Henriksen et al 2013).…”

Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement

“…Additionally, for a similar tetranucleotide (GACC) it was shown that intercalated structures would lead to peaks that would be easy to detect because they would appear in unique and uncrowded regions of the spectra. 57 Comparison of MD with NMR for the tetranucleotides is reported in figure 4. As it can be seen, the MaxEnt corrections improve the agreement with experimental scalar couplings for AAAA and CCCC with respect to both Amber and Amber αζ force fields.…”