Volume 105, Issue 5, Pages (September 2013)

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Volume 105, Issue 5, Pages 1248-1257 (September 2013) A Novel Implicit Solvent Model for Simulating the Molecular Dynamics of RNA Yufeng Liu, Esmael Haddadian, Tobin R. Sosnick, Karl F. Freed, Haipeng Gong Biophysical Journal Volume 105, Issue 5, Pages 1248-1257 (September 2013) DOI: 10.1016/j.bpj.2013.07.033 Copyright © 2013 Biophysical Society Terms and Conditions

Figure 1 RMSD (left column) and RMSF (right column) time series for the explicit (black) and implicit (red) solvent simulations of the A-form RNA duplex (A), SRL rRNA (B), and tRNA (C). Only the productive trajectories are displayed here after excluding all preequilibration frames. Frames from the first 20 ns of the productive simulations are excluded from RMSF calculation. Biophysical Journal 2013 105, 1248-1257DOI: (10.1016/j.bpj.2013.07.033) Copyright © 2013 Biophysical Society Terms and Conditions

Figure 2 Time series of hydrogen bonds (left column) and electrostatic potentials (right column) for the explicit (black) and implicit (red) solvent simulations of the A-form RNA duplex (A), SRL rRNA (B), and tRNA (C). Only the productive trajectories are displayed here after excluding all preequilibration frames. Biophysical Journal 2013 105, 1248-1257DOI: (10.1016/j.bpj.2013.07.033) Copyright © 2013 Biophysical Society Terms and Conditions

Figure 3 The last frames in 10-ns simulations of tRNA using our model as well as from the GBHCT, GBOBC1, and GBOBC2 models, with (+Mg) or without Mg2+ (−Mg) ions included. Consistent with Table S2, the simulations using our model exhibit the tertiary structure of tRNA as intact when Mg2+ ions are present, but as partially distorted when Mg2+ ions are absent. In contrast, the tertiary topology is nearly completely disrupted in all other implicit solvent models tested, independent of whether or not Mg2+ ions are included in the simulation system. Biophysical Journal 2013 105, 1248-1257DOI: (10.1016/j.bpj.2013.07.033) Copyright © 2013 Biophysical Society Terms and Conditions