English abstract
We use simulation techniques to study the effect of temperature and viral capsid tail on the packing and ejection of semiflexible polymers into and out of spherical bacteriophage capsid. We also simulate the Hershey-Chase experiment to investigate viral polymer ejection in vivo. The polymers are coarse-grained into 100 beads using molecular dynamics simulations and the solvent particles are modeled using Stochastic Rotation Dynamics. We find that for tailless capsids at higher temperatures, the packing time slightly decreases for neutral polymers but packing becomes harder for charged polymers. On the other hand, ejection is slower at lower temperatures for both neutral and charged polymers. If the capsid has a tail, whether the polymer is charged or not, packing becomes much easier at any fixed temperature, whereas ejection is much slower. The dynamics for charged polymers is rather significant: the packing becomes much easier with tail at higher temperatures, whereas during ejection the last remaining beads are trapped inside the tail for some time before full ejection is complete. In regards to simulating the Hershey-Chase experiment, we model the bacterial cell as a box to which a capsid is attached via its tail. An additional coarse-grained polymer of 100 beads is added to our simulations to represent the bacterial genome 'and is confined within a certain region inside the bacterial box. The density of bacterial polymer has been varied to study its effect on the ejection. We also consider ejection of shorter (80 beads) viral polymers and different flexibilities of both viral and bacterial polymers Irrespective of flexibilities of both polymers, we find pauses during ejection. In some densities the pauses are very long and in others they are few in numbers. This has been interpreted by considering the behavior of viral polymer while ejecting from the capsid into the bacterial cell. The mean ejection time in all cases of flexibilities for both lengths (100 and 80 beads) are comparable. However, in some cases of flexibilities the shorter viral polymer ejects faster than the longer one, which is consistent with recent experimental data.
