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Building a viral capsid in the presence of genomic RNA

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Building a viral capsid in the presence of genomic RNA. / Dykeman, Eric C; Stockley, Peter G; Twarock, Reidun.

In: Physical Review E, Vol. 87, No. 2, 022717, 25.02.2013, p. 1-12.

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Harvard

Dykeman, EC, Stockley, PG & Twarock, R 2013, 'Building a viral capsid in the presence of genomic RNA', Physical Review E, vol. 87, no. 2, 022717, pp. 1-12. https://doi.org/10.1103/PhysRevE.87.022717

APA

Dykeman, E. C., Stockley, P. G., & Twarock, R. (2013). Building a viral capsid in the presence of genomic RNA. Physical Review E, 87(2), 1-12. [022717]. https://doi.org/10.1103/PhysRevE.87.022717

Vancouver

Dykeman EC, Stockley PG, Twarock R. Building a viral capsid in the presence of genomic RNA. Physical Review E. 2013 Feb 25;87(2):1-12. 022717. https://doi.org/10.1103/PhysRevE.87.022717

Author

Dykeman, Eric C ; Stockley, Peter G ; Twarock, Reidun. / Building a viral capsid in the presence of genomic RNA. In: Physical Review E. 2013 ; Vol. 87, No. 2. pp. 1-12.

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@article{c0f294e9f4524232a6b000bd53ff129e,
title = "Building a viral capsid in the presence of genomic RNA",
abstract = "Virus capsid assembly has traditionally been considered as a process that can be described primarily via self-assembly of the capsid proteins, neglecting interactions with other viral or cellular components. Our recent work on several ssRNA viruses, a major class of viral pathogens containing important human, animal, and plant viruses, has shown that this protein-centric view is too simplistic. Capsid assembly for these viruses relies strongly on a number of cooperative roles played by the genomic RNA. This realization requires a new theoretical framework for the modeling and prediction of the assembly behavior of these viruses. In a seminal paper Zlotnick [J. Mol. Biol. 241, 59 (1994)] laid the foundations for the modeling of capsid assembly as a protein-only self-assembly process, illustrating his approach using the example of a dodecahedral study system. We describe here a generalized framework for modeling assembly that incorporates the regulatory functions provided by cognate protein-nucleic-acid interactions between capsid proteins and segments of the genomic RNA, called packaging signals, into the model. Using the same dodecahedron system we demonstrate, using a Gillespie-type algorithm to deal with the enhanced complexity of the problem instead of a master equation approach, that assembly kinetics and yield strongly depend on the distribution and nature of the packaging signals, highlighting the importance of the crucial roles of the RNA in this process.",
keywords = "Capsid, Computer Simulation, Genome, Models, Biological, RNA, Viral, Virus Assembly",
author = "Dykeman, {Eric C} and Stockley, {Peter G} and Reidun Twarock",
note = "{\textcopyright}2013 American Physical Society",
year = "2013",
month = feb,
day = "25",
doi = "10.1103/PhysRevE.87.022717",
language = "English",
volume = "87",
pages = "1--12",
journal = "Physical Review E",
issn = "1539-3755",
publisher = "American Physical Society",
number = "2",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Building a viral capsid in the presence of genomic RNA

AU - Dykeman, Eric C

AU - Stockley, Peter G

AU - Twarock, Reidun

N1 - ©2013 American Physical Society

PY - 2013/2/25

Y1 - 2013/2/25

N2 - Virus capsid assembly has traditionally been considered as a process that can be described primarily via self-assembly of the capsid proteins, neglecting interactions with other viral or cellular components. Our recent work on several ssRNA viruses, a major class of viral pathogens containing important human, animal, and plant viruses, has shown that this protein-centric view is too simplistic. Capsid assembly for these viruses relies strongly on a number of cooperative roles played by the genomic RNA. This realization requires a new theoretical framework for the modeling and prediction of the assembly behavior of these viruses. In a seminal paper Zlotnick [J. Mol. Biol. 241, 59 (1994)] laid the foundations for the modeling of capsid assembly as a protein-only self-assembly process, illustrating his approach using the example of a dodecahedral study system. We describe here a generalized framework for modeling assembly that incorporates the regulatory functions provided by cognate protein-nucleic-acid interactions between capsid proteins and segments of the genomic RNA, called packaging signals, into the model. Using the same dodecahedron system we demonstrate, using a Gillespie-type algorithm to deal with the enhanced complexity of the problem instead of a master equation approach, that assembly kinetics and yield strongly depend on the distribution and nature of the packaging signals, highlighting the importance of the crucial roles of the RNA in this process.

AB - Virus capsid assembly has traditionally been considered as a process that can be described primarily via self-assembly of the capsid proteins, neglecting interactions with other viral or cellular components. Our recent work on several ssRNA viruses, a major class of viral pathogens containing important human, animal, and plant viruses, has shown that this protein-centric view is too simplistic. Capsid assembly for these viruses relies strongly on a number of cooperative roles played by the genomic RNA. This realization requires a new theoretical framework for the modeling and prediction of the assembly behavior of these viruses. In a seminal paper Zlotnick [J. Mol. Biol. 241, 59 (1994)] laid the foundations for the modeling of capsid assembly as a protein-only self-assembly process, illustrating his approach using the example of a dodecahedral study system. We describe here a generalized framework for modeling assembly that incorporates the regulatory functions provided by cognate protein-nucleic-acid interactions between capsid proteins and segments of the genomic RNA, called packaging signals, into the model. Using the same dodecahedron system we demonstrate, using a Gillespie-type algorithm to deal with the enhanced complexity of the problem instead of a master equation approach, that assembly kinetics and yield strongly depend on the distribution and nature of the packaging signals, highlighting the importance of the crucial roles of the RNA in this process.

KW - Capsid

KW - Computer Simulation

KW - Genome

KW - Models, Biological

KW - RNA, Viral

KW - Virus Assembly

U2 - 10.1103/PhysRevE.87.022717

DO - 10.1103/PhysRevE.87.022717

M3 - Article

C2 - 23496558

VL - 87

SP - 1

EP - 12

JO - Physical Review E

JF - Physical Review E

SN - 1539-3755

IS - 2

M1 - 022717

ER -