The role of DNA twist in the packaging of viral genomes

Biophysical Journal
Geoffrey C RollinsStephen C Harvey

Abstract

We performed molecular dynamics simulations of the genome packaging of bacteriophage P4 using two coarse-grained models of DNA. The first model, 1DNA6 (one pseudo-atom per six DNA basepairs), represents DNA as a string of beads, for which DNA torsions are undefined. The second model, 3DNA6 (three pseudo-atoms per six DNA basepairs), represents DNA as a series of base planes with torsions defined by the angles between successive planes. Bacteriophage P4 was packaged with 1DNA6, 3DNA6 in a torsionally relaxed state, and 3DNA6 in a torsionally strained state. We observed good agreement between the packed conformation of 1DNA6 and the packed conformations of 3DNA6. The free energies of packaging were in agreement, as well. Our results suggest that DNA torsions can be omitted from coarse-grained bacteriophage packaging simulations without significantly altering the DNA conformations or free energies of packaging that the simulations predict.

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Citations

Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Davide MarenduzzoCristian Micheletti
Mar 3, 2010·Annual Review of Biophysics·Dario MeluzziGaurav Arya
Dec 3, 2008·Annual Review of Physical Chemistry·Charles M Knobler, William M Gelbart
Jan 16, 2013·PloS One·Afaf Al LawatiMuataz Al Barwani
Aug 2, 2013·The Journal of Chemical Physics·A FathizadehM R Ejtehadi
Apr 10, 2014·The Journal of Chemical Physics·C A BrackleyD Marenduzzo
Nov 26, 2013·Proceedings of the National Academy of Sciences of the United States of America·Davide MarenduzzoDe Witt Sumners
May 11, 2010·Journal of Molecular Biology·Jin YuGeorge Oster
Jul 16, 2008·Biophysical Journal·C MichelettiD W Sumners
May 20, 2008·Biophysical Journal·Anton S Petrov, Stephen C Harvey
Nov 16, 2010·Journal of Structural Biology·Anton S Petrov, Stephen C Harvey
Feb 11, 2010·Physical Chemistry Chemical Physics : PCCP·Stephen C HarveyMustafa Burak Boz
Mar 15, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·D MarenduzzoE Orlandini
Sep 23, 2014·Journal of Physics. Condensed Matter : an Institute of Physics Journal·C MaffeoA Aksimentiev
Mar 21, 2015·The Journal of Physical Chemistry. B·Qian WangB Montgomery Pettitt

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