Last modified on 24 August 2012.

Literature Reference:

Xia Z., Gardner D.P., Gutell R.R., and Ren P. (2010).
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures.
Journal of Physical Chemistry B, 114:13497-13506.

Manuscript Figures and Tables:

Figure 1.
  1. Schematic representation of the CG model for RNA. Phosphate and sugar are represented as one CG particle. The bases A, G, C, and U are represented as three CG particles for each.
  2. The components of each CG base. The base is divided by the red dashed line.
  3. Schematic representation of all-atom RNA backbone.
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Figure 2. Superposition of the final snapshot from 10 ns CG simulations (colored green) and native structure (colored blue). The backbones are represented as thick sticks, and the bases are shown as lines.
  1. Superposition of RNA with 12 canonical Watson-Crick base pairs (PDB ID: 1QCU).
  2. Superposition of the frameshifting RNA pesudoknot from beet western yellow virus (PDB ID: 1L2X), a single chain with coaxial helices connected by two loops.
  3. Superposition of 24-nt dsRNA with a 5?5 nt internal loop (PDB ID: 1LNT).
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Figure 3.
  1. Comparison of all-atom rmsd's for the structures 1ZIH, 353D, and 1DQF during the 100 ns simulated annealing simulations. The simulation temperature was increased to 1000 K within the beginning 2000 steps and then cooled down to room temperature, 298 K. The rmsd's were calculated using all of the CG atoms. The figures show how the RNA molecules fold toward their native structures.
  2. Snapshots taken from simulated annealing of 1ZIH.
  3. The superposition of the final conformation (colored green) and native structure (colored blue) of the GCCA tetraloop after 20 ns full-atom MD refinement. The backbone is represented as a ribbon, and the base-stacking unit in a tetraloop is shown as sticks.
  4. Snapshots taken from simulated annealing simulation of 353D.
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Table 1. Properties of Nine CG Particles HTML
Table 2. Bond Stretching Interaction Parameters for the CG Model of RNA Fitted by the Gaussian Function and Obtained from Statistical Structures HTML
Table 3. Bond Angle Interaction Parametiers for the CG Model of RNA Fitted by the Gaussian Function and obtained from Statistical Structures HTML
Table 4. Optimized CG Parameters for Nonbonded Interaction Described by Equation 9, Including Similar and Unlike Pairs of CG Atoms HTML
Table 5. Optimized CG Parameters for the Dihedral Interaction Term Described by Equation 8 HTML
Table 6. Comparison of All-Atom Average rmsd's from the Native Crystal Structures for Both the CG Model and the Full-Atom Models HTML
Table 7. Comparison of All-Atom RMSDs between the Final Structures of 100 ns Simulated-Annealing Simulations to Their Native Structures HTML