Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

Abstract

The backbone dihedral parameters of the Amber RNA force field were improved by fitting using multiple linear regression to potential energies determined by quantum chemistry calculations. Five backbone and four glycosidic dihedral parameters were fit simultaneously to reproduce the potential energies determined by a high-level density functional theory calculation (B97D3 functional with the AUG-CC-PVTZ basis set). Umbrella sampling was used to determine conformational free energies along the dihedral angles, and these better agree with the population of conformations observed in the protein data bank for the new parameters than for the conventional parameters. Molecular dynamics simulations performed on a set of hairpin loops, duplexes and tetramers with the new parameter set show improved modeling for the structures of tetramers CCCC, CAAU, and GACC, and an RNA internal loop of noncanonical pairs, as compared to the conventional parameters. For the tetramers, the new parameters largely avoid the incorrect intercalated structures that dominate the conformational samples from the conventional parameters. For the internal loop, the major conformation solved by NMR is stable with the new parameters, but not with the conventional parameters. The new force field performs similarly to the conventional parameters for the UUCG and GCAA hairpin loops and the [U(UA)₆A]₂ duplex.

Figure 1

Procedure for fitting force field parameters. A diverse database of conformations was generated from X-ray structures and from dihedral scanning. For X-ray structures, bonds and angles were fixed to an A-form reference value using sander from the Amber software package. The dihedral scan structures were generated by energy minimization with restraints on selected torsions. Additional restraints were applied on bond and angles to set them to the A-form reference value. The database was then reduced in size by considering sequence identity and dihedrals to remove redundancies. Structures generated by scanning and taken from the PDB were both used for the linear least-square fit.

Figure 2

Dihedral term potential energy (kcal/mol) as a function of dihedral angle for Amber99 (red), Amber ff10 (Zgarbova et al. and α/γ bsc0; green),^, χ, and this work (blue). For comparison, the average energy of each curve was set to zero.

Figure 3

Dihedral potentials of mean force (PMF) for nine torsions. Shown are the new dihedrals from this work (blue), Amber ff10^, with χ and α/γ bsc0 correction (green), and a statistical potential derived from a set of crystal structures in the PDB (red). For bins of statistical data where there were no representatives in the pdb, the points are not plotted. The PMF is an average of 16 RNA dinucleotide molecules in explicit solvent (TIP3P) water model.

Figure 4

Histogram of mass-weighted RMSD to A-form-like reference. Histograms are provided for AAAA (panel A), CAAU (panel B), CCCC (panel C), GACC (panel D), and UUUU (panel E). Each histogram was generated by merging the conformations for four independent simulations. The bin widths are 0.01 Å. For major peaks in the histogram, corresponding centroid structures from clustering (Table 5) are labeled.

Figure 5

Comparison of Amber ff10 (right panels, green) to the dihedral parameters fit in this work (left panels, blue) for dynamics of the Watson–Crick duplex, 5′ U(UA)₆A 3′. Mass-weighted atomic RMSD to the solution structure is shown as a function of time for four independent simulations. The higher RMSD for ff10 of simulation 3 is an unfolding of four nucleotides of the 5′ terminal pairs. For comparison, these RMSDs as a function of time when excluding terminal base pairs are provided in Figure S5. The same trends are seen in both plots.

Figure 6

Comparison of Amber ff10 (right panel, green) and the dihedral parameters fit in this work (left panels, blue) for dynamics of 5′GGUGAAGGC3′/3′CCGAAGCCG5′ (major conformation). Mass-weighted atomic RMSD to the solution structure is shown as a function of time for four independent simulations. The higher RMSD for ff10 is a result of of stem nucleotides U3 and C17 frequently moving from their base pairing partner and flipping out into solution.

Figure 7

Comparison of Amber ff10 (right panel; green) and the dihedral parameters fit in this work (left panel; blue) for dynamics of the UUCG tetraloop, 2KOC. Mass-weighted atomic RMSD to the solution structure is shown as a function of time for four independent simulations. The higher RMSD for simulations with parameters derived in this work is a reflection of C8 (the loop C) leaves the conformation of the solution structure and becomes either exposed to solvent or extends into the helix major groove.

Figure 8

Comparison of Amber ff10 (right panel; green) and the dihedral parameters fit in this work (left panel; blue) for dynamics of the GCAA tetraloop, 1ZIH. Mass-weighted atomic RMSD to the solution structure is shown as a function of time for four independent simulations. The higher RMSD for both ff10 and this work is due to unfolding of the loop region away from the solution structure.