The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape

Abstract

The packaging of double-stranded DNA into bacteriophages leads to the arrangement of the genetic material into highly-packed and ordered structures. Although modern experimental techniques reveal the most probable location of DNA inside viral capsids, the individual conformations of DNA are yet to be determined. In the current study we present the results of molecular dynamics simulations of the DNA packaging into several bacteriophages performed within the framework of a coarse-grained model. The final DNA conformations depend on the size and shape of the capsid, as well as the size of the protein portal, if any. In particular, isometric capsids with small or absent portals tend to form concentric spools, whereas the presence of a large portal favors coaxial spooling; slightly and highly elongated capsids result in folded and twisted toroidal conformations, respectively. The results of the simulations also suggest that the predominant factor in defining the global DNA arrangement inside bacteriophages is the minimization of the bending stress upon packaging.

Figure 1

Models for polyhedral capsids used in the present study. (A) ε15, (B) ϕ29, (C) and (D) highly elongated icosahedrons. Each triangular face of the polyhedra was filled with pseudoatoms of radius 8 Å. Protein portals and short DNA fragments are also shown.

Figure 2

DNA conformations at 20%, 50%,70% and 100% of packed genomes inside the capsids used in the present study. (A) Concentric spooling, (B) Coaxial spooling, (C) Folded totoid, (D) and (E) twisted toroids.