الملخص الإنجليزي
We use coarse grained Langevin dynamics simulations to study packing and
ejection of semi-flexible polymers into and out of a spherical capsid inside a
crowded cell. The aim is to find the effect of crowding environment on the polymer
packing and ejection as a function of crowding particles type and interaction
(repulsive versus attractive) with the polymer. We also find in this environment
the effect of the capsid tail on the packing process. Such packing and ejection
conditions are relevant, for example, to λ DNA packing inside E.coli bacterial
cells, where the environment is crowded due to the presence of proteins, bacterial
DNA and salts. We use neutral and charged, but highly screened, polymers, and
compare packing and ejection rates of the two. For a neutral polymer packing
into a capsid with a tail, attractive interactions with the crowd particles make
packing slightly harder at higher crowd densities, but repulsive interactions make
it easier. Our results indicate that packing into a tailless capsid is less efficient at
low crowd densities than into one with a long tail. However, this trend is reversed
at higher densities. In addition, packing into a capsid with a long tail shows a
highly variable waiting time before packing initiates, a feature absent for a tailless
capsid. Electrostatic interactions at physiological conditions do not have much
effect. Some bacterial cells, such as Pseudomonas chlororaphis, form a nucleuslike structure encapsulating the phage 201φ2-1 DNA. We also study the packing
dynamics with the nucleus present. We find packing is faster compared to the case
of no-nucleus packing. We also observe knot formations but these knots untangle
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quickly while the polymer translocates. This knot formation is independent of
polymer charge and presence of crowd particles. For ejection process, our data
reveal that as the density of the crowded environment increases, the ejection time
increases due to entropy loss and the increasing of bead repulsion. However, if
these crowded environment attracts the polymer to the cell the ejection process
becomes faster because in this environment beads pull the polymer a way from
the capsid towards the cell, helping the ejection process. To compare our result
with the in vivo experiment in 2012, we plot the velocity of the ejection versus
the DNA remaining in the capsid and versus the DNA ejected for the ejection of
two polymers differing in length by 27% as done by the experiment. We find that
the velocity of the ejection of the longer polymer is faster, which agree with the
experimental data. But we did not find any overlap between the two curves.
