Figure 3.

The cooperative effects of PS distributions can only be observed in the presence of the protein ramp. (a) Differences in the PS affinity distributions for different RNAs, that is, different bead configurations in the mathematical model, result in differences in particle yield. The spectrum of different particle yields over 30 000 random RNAs is shown, with the best (RNA1) and worst (RNA2) performing RNA shown to the right. Cellular RNAs are modelled by strings of low affinity PSs (red beads). (b) In a viral infection, protein is synthesized while capsid assembly already takes place, a phenomenon known as the protein ramp. It is modelled via gradual addition of CP according to the graph shown. (c) The assembly of virus and malformed particles in the absence (left) and presence (right) of the protein ramp reveals the importance of the protein ramp for virion yield. In particular, in the presence of the protein ramp, assembly of RNAs (shown here for RNA1) is more efficient than in its absence, where malformed species deplete the protein resource. (d) Nucleation behaviour depends on the protein ramp: it is dispersed across the genome (indicated by hooks together with an indication of the percentage of sequences nucleating at any given pair of PSs) in the absence, and localized at the 5′ end in the presence of the protein ramp.