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The Structure and Function of Highly Bent Toroidal DNA in Bacteriophage φ29

Authors :
Noel C. Perkins
Maryna Taranova
Troy A. Lionberger
Andrew D. Hirsh
Ioan Andricioaei
Todd D. Lillian
Source :
Biophysical Journal. 102(3):421a-422a
Publication Year :
2012
Publisher :
Elsevier BV, 2012.

Abstract

Tailed bacteriophages are highly efficient machines for infecting a host cell. A single virion must attach to the host surface, penetrate the cell wall, then release its double-stranded DNA genome. In these remarkable DNA delivery machines, controlling how and when the genome is released is a task of paramount importance. Recently, a three-dimensional cryo-electron microscopy (cryo-EM) reconstruction of mature bacteriophage φ29 revealed an intriguing toroidal DNA structure contained in a small cavity below the viral capsid. This highly bent toroidal DNA supercoil is thought to be 30-40 basepairs of dsDNA and its function remains unknown.In this study, we employ an elastic rod model to simulate highly strained DNA as it is compressed within the protein cavity. The model provides estimates of force and energy required to form the toroid as well as its equilibrium conformation. Results reveal that a toroid can indeed form under the biologically relevant forces for the viral packing motor (up to 100 pN). To understand the effects of the highly stressed toroid on DNA structure, we then employ molecular dynamics (MD) simulations starting with the rod model-computed equilibrium as the initial condition. Following equilibration in MD, we construct an approximate density map using the final predicted toroid to compare with the recently published cryo-EM data. The computed density map correctly predicts the major dimensions of the toroid as well as regions of high and low density. Finally, we simulate the start of the ejection process by integrating the rod model forward in time upon sudden removal of the protein “tail knob.” The resulting fast dynamic collapse of the toroid suggests that its function could be to prime the ejection of the remaining viral genome.

Details

ISSN :
00063495
Volume :
102
Issue :
3
Database :
OpenAIRE
Journal :
Biophysical Journal
Accession number :
edsair.doi.dedup.....d4c937c057cb6340437e56f2d2b1f91b
Full Text :
https://doi.org/10.1016/j.bpj.2011.11.2305