Polymer Packaging and Ejection in Viral Capsids: Shape Matters

We use a mesoscale simulation approach to explore the impact of different capsid geometries on the packaging and ejection dynamics of polymers of different flexibility. We find that both packing and ejection times are faster for flexible polymers. For such polymers a sphere packs more quickly and ejects more slowly than an ellipsoid. For semiflexible polymers, however, the case relevant to DNA, a sphere both packs and ejects more easily. We interpret our results by considering both the thermodynamics and the relaxational dynamics of the polymers. The predictions could be tested with biomimetic experiments with synthetic polymers inside artificial vesicles. Our results suggest that phages may have evolved to be roughly spherical in shape to optimize the speed of genome ejection, which is the first stage in infection.

Figure 1

Schematic representation of the simulation. A semiflexible polymer is first packed into and then ejected from a rigid capsid. The first row (A) shows the capsid and the dangling tail of the polymer close to the end of a packing run. The second row (B) shows the configuration of the polymer chain inside the capsid. Column (I) refers to a spherical capsid, and column (II) to an ellipsoidal one.

Figure 2

Number of packed beads vs time during (a) packaging and (b) ejection for flexible and semiflexible polymers comparing a spherical and an ellipsoidal capsid.

Figure 3

Force opposing the motor (in units of $k_{B}T/\sigma$) during packaging and ejection for a semiflexible polymer in (top) a spherical and (bottom) an ellipsoidal capsid.

Figure 4

(a) Ejection rate as a function of the number of packed beads for flexible and semiflexible polymers comparing a spherical and an ellipsoidal capsid. (b) Data from one individual simulation of the ejection of a semiflexible polymer from a sphere. Arrows indicate pauses (corresponding to rearrangements of the polymer inside the capsid).