A coarse-grained model of the expansion of the human rhinovirus 2 capsid reveals insights in genome release

Figures

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  Figure 1.. The capsid. (a) Sketch of the arrangement of the coat proteins VP1–VP3 in the native virion. Small-case Latin letters label coat proteins in the same protomer: 5 protomers are highlighted, labelled by (a, b, c, g, m). (b) The HRV2 native particle (PDB ID 1fpn). VP1s are displayed in blue, VP2s in green and VP3s in red. The black circle at the centre of the figure highlights a twofold position where pores are going to open as a consequence of protein displacement. (c) The expanded particle (PDB ID 3tn9—same colour coding as in (b) applies). (d) Details of the hinge movement within the protomer due to the relative rotation of the subunits of VP1 (adapted from [10]): VP1, VP2 and VP3 are coloured in blue, green and red, respectively. (Online version in colour.)

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  Figure 2.. (a) Schlegel diagram of the capsid architecture, showing the numbering scheme used to identify individual protomers in the viral capsid. (b) Intra-pentamer interactions around the particle fivefold axes (adjacency matrix Aij) are shown as pentagons (red in the online version). (c) Inter-pentamer interactions across the particle twofold axes (adjacency matrix Bij) are shown as lines (green in the online version). (d) Inter-pentamer interactions around the particle threefold axes (adjacency matrix Cij) are shown as triangles (blue in the online version). (Online version in colour.)

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  Figure 3.. The individual energy terms for intra-protomer, intra-pentamer, inter-pentamer interactions and the terms for the mechanical and steric interactions. (a) Bistable intra-protomer energy f(θ); (b) plot of the function g(θi, θj) in the intra-pentamer and inter-pentamer interaction energies; (c) plot of the function r(θi, θj) accounting for the steric and mechanical interactions around a threefold axis; (d) plot of the function s(θi, θj) accounting for the steric and mechanical interactions around a fivefold axis. (Online version in colour.)

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  Figure 4.. Classes of transition pathways. Different transition pathways are classified according to the positions of the second and the third protomer undergoing an opening event.

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  Figure 5.. A typical energy cascade for the opening of the first 6 protomers in mode 2−. The energy is plotted along a path in R60 that is the union of the first 6 MEPs, and s is the arc parameter along the path.