Journal
BIOPHYSICAL CHEMISTRY
Volume 101, Issue -, Pages 475-484Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/S0301-4622(02)00197-7
Keywords
viral packaging; computer simulation; molecular mechanics; nucleic acid structure; DNA condensation; bacteriophage P4
Funding
- NCRR NIH HHS [P41 RR12255] Funding Source: Medline
Ask authors/readers for more resources
A simple molecular mechanics model has been used to investigate optimal spool-like packing conformations of double-stranded DNA molecules in viral capsids with icosahedral symmetry. The model represents an elastic segmented chain by using one pseudoatom for each ten basepairs (roughly one turn of the DNA double helix). Force constants for the various terms in the energy function were chosen to approximate known physical properties, and a radial restraint was used to confine the DNA into a sphere with a volume corresponding to that of a typical bacteriophage capsid. When the DNA fills 90% of the spherical volume, optimal packaging is obtained for coaxially spooled models, but this result does not hold when the void volume is larger. When only 60% of the spherical volume is filled with DNA, the lowest energy structure has two layers, with a coiled core packed at an angle to an outer coaxially spooled shell. This relieves bending strain associated with tight curvature near the poles in a model with 100% coaxial spooling. Interestingly, the supercoiling density of these models is very similar to typical values observed in plasmids in bacterial cells. Potential applications of the methodology are also discussed. (C) 2002 Elsevier Science B.V. All rights reserved.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available