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.
References
Aug 25, 1981·Nucleic Acids Research·L F LiuR Calendar
Nov 5, 1997·Cell·M E CerritelliA C Steven
Oct 19, 2001·Nature·D E SmithC Bustamante
Nov 15, 2001·Proceedings of the National Academy of Sciences of the United States of America·J KindtW M Gelbart
Dec 19, 2002·Biophysical Chemistry·Javier ArsuagaStephen C Harvey
Mar 1, 2003·Biophysical Journal·Shelly TzlilAvinoam Ben-Shaul
Feb 3, 2004·Biopolymers·Jaclyn C LaMarqueStephen C Harvey
Nov 24, 2004·Biophysical Journal·Prashant K PurohitRob Phillips
Apr 5, 2005·Biophysical Journal·Andrew James Spakowitz, Zhen-Gang Wang
Feb 3, 2006·Nature·Wen JiangWah Chiu
Apr 18, 2006·Biophysical Journal·Christopher Forrey, M Muthukumar
May 20, 2006·Science·Gabriel C LanderJohn E Johnson
Jan 16, 2007·Structure·Anton S Petrov, Stephen C Harvey
Jun 19, 2007·Biophysical Journal·C Rebecca LockerStephen C Harvey
Jul 20, 2007·Structure·Anton S PetrovStephen C Harvey
Oct 9, 2007·Journal of Structural Biology·Anton S PetrovStephen C Harvey
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
Mar 13, 2014·The Journal of Chemical Physics·Kehong Zhang, Kaifu Luo
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
Oct 7, 2008·FEBS Letters·Guilherme Menegon GieselHugo Verli
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
Oct 16, 2016·Physical Review. E·D C Rapaport
May 1, 2020·Biophysical Journal·Brian CruzMariel Vazquez
Mar 21, 2015·The Journal of Physical Chemistry. B·Qian WangB Montgomery Pettitt