Impact of the topology of viral RNAs on their encapsulation by virus coat proteins

Research output: Contribution to journalArticleAcademicpeer-review

18 Citations (Scopus)

Abstract

Single-stranded RNAs of simple viruses seem to be topologically more compact than other types of single-stranded RNA. It has been suggested that this has an evolutionary purpose: more compact structures are more easily encapsulated in the limited space that the cavity of the virus capsid offers. We employ a simple Flory theory to calculate the optimal amount of polymers confined in a viral shell. We find that the free energy gain or more specifically the efficiency of RNA encapsidation increases substantially with topological compactness. We also find that the optimal length of RNA encapsidated in a capsid increases with the degree of branching of the genome even though this effect is very weak. Further, we show that if the structure of the branching of the polymer is allowed to anneal, the optimal loading increases substantially.
Original languageEnglish
Pages (from-to)289-299
Number of pages11
JournalJournal of Biological Physics
Volume39
DOIs
Publication statusPublished - 2013

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Viral RNA
Capsid Proteins
viruses
topology
Capsid
RNA
Viruses
proteins
genome
Polymers
polymers
void ratio
RNA Viruses
free energy
cavities
Genome

Cite this

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title = "Impact of the topology of viral RNAs on their encapsulation by virus coat proteins",
abstract = "Single-stranded RNAs of simple viruses seem to be topologically more compact than other types of single-stranded RNA. It has been suggested that this has an evolutionary purpose: more compact structures are more easily encapsulated in the limited space that the cavity of the virus capsid offers. We employ a simple Flory theory to calculate the optimal amount of polymers confined in a viral shell. We find that the free energy gain or more specifically the efficiency of RNA encapsidation increases substantially with topological compactness. We also find that the optimal length of RNA encapsidated in a capsid increases with the degree of branching of the genome even though this effect is very weak. Further, we show that if the structure of the branching of the polymer is allowed to anneal, the optimal loading increases substantially.",
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Impact of the topology of viral RNAs on their encapsulation by virus coat proteins. / Schoot, van der, P.P.A.M.; Zandi, R.

In: Journal of Biological Physics, Vol. 39, 2013, p. 289-299.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Impact of the topology of viral RNAs on their encapsulation by virus coat proteins

AU - Schoot, van der, P.P.A.M.

AU - Zandi, R.

PY - 2013

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AB - Single-stranded RNAs of simple viruses seem to be topologically more compact than other types of single-stranded RNA. It has been suggested that this has an evolutionary purpose: more compact structures are more easily encapsulated in the limited space that the cavity of the virus capsid offers. We employ a simple Flory theory to calculate the optimal amount of polymers confined in a viral shell. We find that the free energy gain or more specifically the efficiency of RNA encapsidation increases substantially with topological compactness. We also find that the optimal length of RNA encapsidated in a capsid increases with the degree of branching of the genome even though this effect is very weak. Further, we show that if the structure of the branching of the polymer is allowed to anneal, the optimal loading increases substantially.

U2 - 10.1007/s10867-013-9307-y

DO - 10.1007/s10867-013-9307-y

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EP - 299

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JF - Journal of Biological Physics

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