Monte Carlo simulations of polyelectrolytes inside viral capsids.
Structural features of polyelectrolytes as single-stranded RNA or double-stranded DNA confined inside viral capsids and the thermodynamics of the encapsidation of the polyelectrolyte into the viral capsid have been examined for various polyelectrolyte lengths by using a coarse-grained model solved by Monte Carlo simulations. The capsid was modeled as a spherical shell with embedded charges and the genome as a linear jointed chain of oppositely charged beads, and their sizes corresponded to those of a scaled-down T=3 virus. Counterions were explicitly included, but no salt was added. The encapisdated chain was found to be predominantly located at the inner capsid surface, in a disordered manner for flexible chains and in a spool-like structure for stiff chains. The distribution of the small ions was strongly dependent on the polyelectrolyte-capsid charge ratio. The encapsidation enthalpy was negative and its magnitude decreased with increasing polyelectrolyte length, whereas the encapsidation entropy displayed a maximum when the capsid and polyelectrolyte had equal absolute charge. The encapsidation process remained thermodynamically favorable for genome charges ca. 3.5 times the capsid charge. The chain stiffness had only a relatively weak effect on the thermodynamics of the encapsidation.
Angelescu
Daniel George
DG
Physical Chemistry 1, Lund University, Box 124, SE-221 00 Lund, Sweden.
Bruinsma
Robijn
R
Linse
Per
P
D002213:Capsid / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism; D004548:Elasticity; D004573:Electrolytes / Q000737:chemistry / Q000378:metabolism; D008954:Models, Biological; D008956:Models, Chemical; D015233:Models, Statistical; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D013314:Stress, Mechanical
D004279:DNA, Viral; D004573:Electrolytes; D012367:RNA, Viral