Effect of temperature and capsid tail on the packing and ejection of viral DNA.
We use a simulation technique based on molecular dynamics and stochastic rotation model to present the effect of temperature and capsid tail on the packaging and ejection processes of semiflexible polymers. We consider two types of solvents, a good solvent, where the polymer is neutral and repulsion...
Main Authors: | , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2013-01-01
|
Series: | PLoS ONE |
Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23320080/pdf/?tool=EBI |
id |
doaj-c741725cb55d4116a371ff7479041803 |
---|---|
record_format |
Article |
spelling |
doaj-c741725cb55d4116a371ff74790418032021-03-03T20:25:31ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0181e5295810.1371/journal.pone.0052958Effect of temperature and capsid tail on the packing and ejection of viral DNA.Afaf Al LawatiIssam AliMuataz Al BarwaniWe use a simulation technique based on molecular dynamics and stochastic rotation model to present the effect of temperature and capsid tail on the packaging and ejection processes of semiflexible polymers. We consider two types of solvents, a good solvent, where the polymer is neutral and repulsion interactions among its various sections are favored, and one where the polymer is charged, giving rise to extra electrostatic reaction. For tailless capsids, we find that packing a neutral polymer is slightly slower at higher temperatures whereas its ejection is slightly slower at lower temperatures. We find the same trend for a charged polymer but the effect is noticeably larger. At a high enough temperature, we notice that packing a charged polymer can be stopped. On the other hand, at fixed temperature and regardless whether the polymer is charged, packing is much easier for a capsid with a tail whereas ejection is much slower. The effect of including the tail on the dynamics of a charged polymer, in particular, is rather significant: more packing fraction is facilitated at higher temperatures due to more ordered polymer configuration inside the capsid. In contrast, during ejection the tail traps the last remaining beads for quite some time before allowing full ejection. We interpret these results in terms of entropic and electrostatic forces.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23320080/pdf/?tool=EBI |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Afaf Al Lawati Issam Ali Muataz Al Barwani |
spellingShingle |
Afaf Al Lawati Issam Ali Muataz Al Barwani Effect of temperature and capsid tail on the packing and ejection of viral DNA. PLoS ONE |
author_facet |
Afaf Al Lawati Issam Ali Muataz Al Barwani |
author_sort |
Afaf Al Lawati |
title |
Effect of temperature and capsid tail on the packing and ejection of viral DNA. |
title_short |
Effect of temperature and capsid tail on the packing and ejection of viral DNA. |
title_full |
Effect of temperature and capsid tail on the packing and ejection of viral DNA. |
title_fullStr |
Effect of temperature and capsid tail on the packing and ejection of viral DNA. |
title_full_unstemmed |
Effect of temperature and capsid tail on the packing and ejection of viral DNA. |
title_sort |
effect of temperature and capsid tail on the packing and ejection of viral dna. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2013-01-01 |
description |
We use a simulation technique based on molecular dynamics and stochastic rotation model to present the effect of temperature and capsid tail on the packaging and ejection processes of semiflexible polymers. We consider two types of solvents, a good solvent, where the polymer is neutral and repulsion interactions among its various sections are favored, and one where the polymer is charged, giving rise to extra electrostatic reaction. For tailless capsids, we find that packing a neutral polymer is slightly slower at higher temperatures whereas its ejection is slightly slower at lower temperatures. We find the same trend for a charged polymer but the effect is noticeably larger. At a high enough temperature, we notice that packing a charged polymer can be stopped. On the other hand, at fixed temperature and regardless whether the polymer is charged, packing is much easier for a capsid with a tail whereas ejection is much slower. The effect of including the tail on the dynamics of a charged polymer, in particular, is rather significant: more packing fraction is facilitated at higher temperatures due to more ordered polymer configuration inside the capsid. In contrast, during ejection the tail traps the last remaining beads for quite some time before allowing full ejection. We interpret these results in terms of entropic and electrostatic forces. |
url |
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23320080/pdf/?tool=EBI |
work_keys_str_mv |
AT afafallawati effectoftemperatureandcapsidtailonthepackingandejectionofviraldna AT issamali effectoftemperatureandcapsidtailonthepackingandejectionofviraldna AT muatazalbarwani effectoftemperatureandcapsidtailonthepackingandejectionofviraldna |
_version_ |
1714822549319188480 |