Ejection Dynamics of Polymeric Chains from Viral Capsids: Effect of Solvent Quality

We present simulations investigating the effects of solvent quality on the dynamics of flexible (RNA-like) and semiflexible (DNA-like) polymers ejecting from spherical viral capsids. We find that the mean ejection time increases and the ejection time distributions are broadened as the solvent qualit...

Full description

Saved in:
Bibliographic Details
Published in:Biophysical journal 2008-06, Vol.94 (11), p.4159-4164
Main Authors: Ali, I., Marenduzzo, D., Yeomans, J.M.
Format: Article
Language:English
Subjects:
Bacteria
Biophysical Theory and Modeling
Capsid - chemistry
Capsid - physiology
Computer Simulation
Deoxyribonucleic acid
DNA
DNA, Viral - chemistry
DNA, Viral - physiology
Fluid dynamics
Models, Biological
Models, Chemical
Molecular biology
Polymers
Polymers - chemistry
RNA, Viral - chemistry
RNA, Viral - physiology
Solvents
Solvents - chemistry
Virus Activation
Virus Integration - physiology
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We present simulations investigating the effects of solvent quality on the dynamics of flexible (RNA-like) and semiflexible (DNA-like) polymers ejecting from spherical viral capsids. We find that the mean ejection time increases and the ejection time distributions are broadened as the solvent quality decreases. Our results thus suggest that DNA ejection may be very efficiently controlled by tuning the salt concentration in the environment, in agreement with recent experimental findings. We also observe random pauses in the ejection. These become extremely long for semiflexible polymers at lower solvent quality, and we interpret this as a signature of a low driving force for ejection. We find that, for most polymers, ejection is an all-or-nothing process at the solvent conditions we investigated: polymers normally completely eject once the process is initiated.
ISSN:0006-3495
1542-0086
DOI:10.1529/biophysj.107.111963