title: Structural ensemble and dynamics of toroidal-like DNA shapes in bacteriophage ϕ29 exit cavity.
abstract: In the bacteriophage ϕ29, DNA is packed into a preassembled capsid from which it ejects under high pressure. A recent cryo-EM reconstruction of ϕ29 revealed a compact toroidal DNA structure (30-40 basepairs) lodged within the exit cavity formed by the connector-lower collar protein complex. Using multiscale models, we compute a detailed structural ensemble of intriguing DNA toroids of various lengths, all highly compatible with experimental observations. In particular, coarse-grained (elastic rod) and atomistic (molecular dynamics) models predict the formation of DNA toroids under significant compression, a largely unexplored state of DNA. Model predictions confirm that a biologically attainable compressive force of 25 pN sustains the toroid and yields DNA electron density maps highly consistent with the experimental reconstruction. The subsequent simulation of dynamic toroid ejection reveals large reactions on the connector that may signal genome release.
authors.affiliation: Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA. adhirsh@umich.edu
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Hirsh
authors.forename: Maryna
authors.initials: M
authors.lastname: Taranova
authors.forename: Troy A
authors.initials: TA
authors.lastname: Lionberger
authors.forename: Todd D
authors.initials: TD
authors.lastname: Lillian
authors.forename: Ioan
authors.initials: I
authors.lastname: Andricioaei
authors.forename: N C
authors.initials: NC
authors.lastname: Perkins
mesh_terms: D017103:Bacillus Phages / Q000737:chemistry*; D001483:Base Sequence; D004279:DNA, Viral / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation
chemical_list: D004279:DNA, Viral