title: Energy landscape for DNA rotation and sliding through a phage portal.
abstract: Molecular motors involved in the packaging of DNA in tailed viruses are among the strongest known. The mechanism by which the motors operate has long been speculated to involve a coupling between rotation of the portal pore (the gate through which DNA passes upon its packaging or ejection), and translation of DNA. Recent experimental evidence rules out portal rotation with a substantial degree of certainty. We have created an atomistic model for the interaction between DNA and the portal of the bacteriophage SPP1, on the basis of cryo-electron microscopy images and of a recently solved crystal structure. A free energy surface describing the interaction is calculated using molecular dynamics simulations, and found to be inconsistent with a mechanism in which portal rotation drives DNA import. The low-energy pathways on the surface are used to advance a hypothesis on DNA import compatible with all available experiments. Additionally, temperature-dependent kinetic data are used to validate computed barriers to DNA ejection.
authors.forename: Jeremiah
authors.initials: J
authors.lastname: Nummela
authors.forename: Ioan
authors.initials: I
authors.lastname: Andricioaei
mesh_terms: D017103:Bacillus Phages / Q000737:chemistry / Q000502:physiology*; D001412:Bacillus subtilis; D003198:Computer Simulation; D004279:DNA, Viral / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D012399:Rotation; D014771:Virion / Q000737:chemistry / Q000378:metabolism*
chemical_list: D004279:DNA, Viral