Paper Citing NAMD - Abstract
Hirsh, Andrew D.; Taranova, Maryna; Lionberger, Troy A.; Lillian, Todd D.; Andricioaei, Ioan; Perkins, N. C.
Structural Ensemble and Dynamics of Toroidal-like DNA Shapes in Bacteriophage phi 29 Exit Cavity
BIOPHYSICAL JOURNAL, 104:2058-2067, MAY 7 2013
In the bacteriophage phi 29, DNA is packed into a preassembled capsid from which it ejects under high pressure. A recent cryo-EM reconstruction of phi 29 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.
