ArticleBiophysical journal2013
Structural ensemble and dynamics of toroidal-like DNA shapes in bacteriophage ϕ29 exit cavity.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Two-phase dynamics of DNA supercoiling based on DNA polymer physics.Biophysical journal · 2022Article
- Phage-like packing structures with mean field sequence dependence.Journal of computational chemistry · 2017Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
- Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density.The journal of physical chemistry. B · 2015Article
- Free-energy landscape and characteristic forces for the initiation of DNA unzipping.Biophysical journal · 2015Article
- Role of microscopic flexibility in tightly curved DNA.The journal of physical chemistry. B · 2014Article
- Sophisticated modeling uncovers atomic DNA structure in bacteriophage φ29 cavity.Biophysical journal · 2013Article
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6 authors.
Funding
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.
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