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...

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Autores principales:	Afaf Al Lawati, Issam Ali, Muataz Al Barwani
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c741725cb55d4116a371ff7479041803
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spelling	oai:doaj.org-article:c741725cb55d4116a371ff74790418032021-11-18T08:02:19ZEffect of temperature and capsid tail on the packing and ejection of viral DNA.1932-620310.1371/journal.pone.0052958https://doaj.org/article/c741725cb55d4116a371ff74790418032013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23320080/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203We 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.Afaf Al LawatiIssam AliMuataz Al BarwaniPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e52958 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Afaf Al Lawati Issam Ali Muataz Al Barwani Effect of temperature and capsid tail on the packing and ejection of viral DNA.
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.
format	article
author	Afaf Al Lawati Issam Ali Muataz Al Barwani
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)
publishDate	2013
url	https://doaj.org/article/c741725cb55d4116a371ff7479041803
work_keys_str_mv	AT afafallawati effectoftemperatureandcapsidtailonthepackingandejectionofviraldna AT issamali effectoftemperatureandcapsidtailonthepackingandejectionofviraldna AT muatazalbarwani effectoftemperatureandcapsidtailonthepackingandejectionofviraldna
_version_	1718422632313913344

Effect of temperature and capsid tail on the packing and ejection of viral DNA.

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