Table 1.
Corrections to equilibrium constants, on-rates, and off-rates for all possible combinations of four RNA effects.
Fig 1.
Contour plots of maximum assembly size and assembly time over the space of rate parameters.
(A) Contour plot of the average maximum assembly size for 54 rate parameter grid points and 16 RNA effect combinations (red dots). The colorbar shows average maximum assembly size. A completed CCMV capsid consists of 90 subunits. (B) Contour plot of the average time to reach a maximum assembly size for a simulation over the same grid points and effect combinations. The colorbar shows time in seconds. The four-digit binary codes for simulations are as explained in Table 1, with a zero in each bit corresponding to absence of a given RNA effect and a one in that bit to presence of the corresponding effect. The first digit represents RNA-RNA, the second Compression, the third RNA-protein, and the fourth Concentration.
Fig 2.
Comparing maximum assembly size and assembly time.
Log-scale scatter plot of maximum assembly size versus the time to reach that assembly size averaged over 100 simulation runs for each RNA effect combination. Boxes surround clusters of RNA effect combinations that have similar relationships between maximum assembly size and assembly time. The four-digit binary codes for simulations are as explained in Table 1, with a zero in each bit corresponding to absence of a given RNA effect and a one in that bit to presence of the corresponding effect. The first digit represents RNA-RNA, the second Compression, the third RNA-protein, and the fourth Concentration.
Fig 3.
Simulated light scattering curves for CCMV capsid assembly under different representative combinations of RNA effects.
Plot comparing simulated light scattering curves for CCMV capsid assembly averaged over 200 individual simulation trajectories for four representative combinations of RNA effects: hollow capsid (no effects considered), the two negative RNA effects (Compression + RNA-RNA), the two positive RNA effects (RNA-Protein + Concentration) and the combination of all four RNA effects. Time on the x axis is shown on a log scale.
Fig 4.
Mass fraction plots for representative combinations of RNA effects.
Mass fraction plots for (A) hollow CCMV capsid assembly, (B) CCMV capsid assembly with all combined RNA effects, (C) CCMV capsid assembly under both negative effects (1100), and (D) CCMV capsid assembly under both positive effects (0011). Each plot measures the mass fraction of each potential assembly size from individual monomers to completed capsids at each time point in a single simulation run. Approximate locations of putative nucleation events are labeled in each plot. Note that the time axis is on a different scale for each plot due to the very different timescales of the assembly reaction under the different effects models.
Fig 5.
Frequency matrix plots for representative combinations of RNA effects.
Frequency matrix plots for (a) hollow CCMV capsid assembly, (b) CCMV capsid assembly with all combined RNA effects, (c) CCMV capsid assembly under both negative RNA effects (1100), and (d) CCMV capsid assembly under both positive RNA effects. In each plot, each row corresponds to a product size and each column to reactant sizes that produce that product. Pixel color in each position corresponds to the frequency with which the given reactant size is used to produce the given product size. Insets within each plot expand the upper-left corner of the main plot, corresponding to products of size 20 or smaller, to better visualize pathways involved in production of small oligomers.
Fig 6.
Comparing Influence of Individual RNA Effects on Averaged Assembly Rate.
Simulated light scattering curves for CCMV capsid assembly under each individual RNA effect as well as the hollow capsid and combined RNA effects case. Fig 6A shows the entire simulation time course while Fig 6B shows the first second. Time on the x axis is shown on a log scale.
Fig 7.
Comparing Influence of Two RNA Effects on Averaged Assembly Rate.
Simulated light scattering curves for CCMV capsid assembly under all combinations of two RNA effects as well as the hollow capsid and combined RNA effects case. Fig 7A shows the entire simulation time course while Fig 7B shows the first five seconds. Time on the x axis is shown on a log scale.
Fig 8.
Comparing Influence of Three RNA Effects on Averaged Assembly Rate.
Simulated light scattering curves for CCMV capsid assembly under all combinations of three RNA effects as well as the hollow capsid and combined RNA effects case. Fig 8A shows the entire simulation time course while Fig 8B shows the first second. Time on the x axis is shown on a log scale.
Fig 9.
Mass fraction plots for CCMV capsid assembly with individual RNA effects.
Mass fraction plots for single trajectories of CCMV capsid assembly upon applying each effect: (A) RNA-RNA, (B) Compression, (C) RNA-protein, (D) Concentration. The negative RNA-RNA effect prevents any large intermediates from being formed, while the other three still allow for capsids to be completed.
Fig 10.
Mass fraction plots for CCMV capsid assembly with combinations of two RNA effects.
Combinations are described by a four digit binary code as explained in Table 1, where a 1 means an effect has been turned on and a 0 means an effect has been turned off. The first digit represents RNA-RNA, the second Compression, the third RNA-protein, and the fourth Concentration. (A) is 1010, (B) is 1001, (C) is 0110, (D) is 0101.
Fig 11.
Mass fraction plots for CCMV capsid assembly with combinations of three RNA effects.
Combinations are described by a four digit binary code as explained in Table 1 where a 1 means an effect has been turned on and a 0 means an effect has been turned off. The first digit represents RNA-RNA, the second Compression, the third RNA-protein, and the fourth Concentration. (A) is 1110, (B) is 1101, (C) is 1011, (D) is 0111.
Fig 12.
Frequency matrix plots for CCMV capsid assembly with individual RNA effects.
Frequency matrix plots averaged over 200 simulation runs for CCMV capsid assembly upon applying: (A) RNA- RNA, (B) Compression, (C) RNA-protein, (D) Concentration. In each plot, each row corresponds to a product size and each column to reactant sizes that produce that product. Pixel color in each position corresponds to the frequency with which the given reactant size is used to produce the given product size. Insets within each plot expand the upper-left corner of the main plot, corresponding to products of size 20 or smaller, to better visualize pathways involved in production of small oligomers.
Fig 13.
Frequency matrix plots for CCMV capsid assembly with combinations of two RNA effects.
Combinations are described by a four digit binary code as in Table 1 where a 1 means an effect has been turned on and a 0 means an effect has been turned off. The first digit represents RNA-RNA, the second Compression, the third RNA-protein, and the fourth Concentration.: (A) is 1010, (B) is 1001, (C) is 0110, (D) is 0101. In each plot, each row corresponds to a product size and each column to reactant sizes that produce that product. Pixel color in each position corresponds to the frequency with which the given reactant size is used to produce the given product size. Insets within each plot expand the upper-left corner of the main plot, corresponding to products of size 20 or smaller, to better visualize pathways involved in production of small oligomers.
Fig 14.
Frequency matrix plots for CCMV capsid assembly with combinations of three RNA effects.
Combinations are described by a four digit binary code as in Table 1 where a 1 means an effect has been turned on and a 0 means an effect has been turned off. The first digit represents RNA-RNA, the second Compression, the third RNA-protein, and the fourth Concentration. (A) is 1110, (B) is 1101, (C) is 1011, (D) is 0111. In each plot, each row corresponds to a product size and each column to reactant sizes that produce that product. Pixel color in each position corresponds to the frequency with which the given reactant size is used to produce the given product size. Insets within each plot expand the upper-left corner of the main plot, corresponding to products of size 20 or smaller, to better visualize pathways involved in production of small oligomers.