The results of this study have been published in D., Zhang, R. Konecny, N.A. Baker, J.A. McCammon, Biopolymers, 75(4), 325-337 (2004).

Cowpea chlorotic mottle virus (CCMV) is used as a model system to investigate the organization of the RNA genome inside the virus capsid. A coarse grain model, in which each nucleic acid is treated as a sphere with negative charge, is necessary to simulate a system of the size of 34,200 amino acid residues and about 3,000 RNA nucleic acids. The electrostatic potential of the capsid is calculated using the Adaptive Poisson-Boltzmann Solver (APBS) over a grid of 2.5 Anstrom, and the potential grid is used to evaluate the electrostatic interaction energy of the RNA spheres inside the capsid.

In the crystal structure, there are some short strands of RNAs present. These RNAs are kept intact in the simulation. In another words, they are included in the electrostatic potential grid, and they do not move in the Monte Carlo simulation. The following conditions are used in the simulation:

• RNA sphere size 7.5 A, charge -0.25e, dielectric constant 4.0
• Electrostatic potential grid size 2.5 A
• Total energy of the system is the electrostatic interations between the RNAs and their electrostic energy within the potential grid of the capsid

• Energy plot of 10,000,000 steps of MC simulation
  The energy reaches equilibration after about 2,000,000 steps.
  
• Comparison of conformations of RNA spheres during different stages of simulation
  
  • Blue spheres are the initial conformation used at the start of the simulation
  • Gray spheres are the conformation with the lowest energy during the first 1 million steps of MC perturbation
  • Red spheres are the conformation with the lowest energy during 10 million steps of MC simulation
  A movie

  Inside stereo view

  Outside stereo view

• The conformation with the lowest energy showed together with the capsid and pre-existing RNAs
  • The red spheres are the conformation with the lowest energy during 10 million steps of MC simulation.
  • The orange spheres are those RNAs appearing in the crystal structure.
  A movie

  Inside stereo view

  Outside stereo view

• The difference of turning on/off the electrostatic field of the capsid
  • Blue -- The electrostatic field of the capsid is off
  • Red -- The electrostatic field of the capsid is on
  • Orange -- RNAs pre-existing in the crystal structure
    A movie

    Inside stereo view

    Outside stereo view

    Energy plot of 4 million steps of MC simulation when the electrostatic field of the capsid is turned off

    

    Please note that the energy scale is the same as in figure 1. This tells us that the huge energy (161000 kcal/mol) is the result of the repulsion of the negative charges carried by the phosphate groups of the RNA. However, the reorganization of the RNA spheres is determined by the electrostatic field of the capsid, as the energy changes very little when the field is turned off.