Journal
BIOPHYSICAL JOURNAL
Volume 96, Issue 4, Pages L29-L31Publisher
CELL PRESS
DOI: 10.1016/j.bpj.2008.12.3761
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Funding
- National Science Foundation Career Award [CHE-0548047]
- Direct For Mathematical & Physical Scien [0918817] Funding Source: National Science Foundation
- Division Of Chemistry [0918817] Funding Source: National Science Foundation
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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.
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