Role of genome topology in the stability of viral capsids
We explore how the stability of RNA viruses depends on genome topology and interactions between RNA and the capsid proteins. RNA is modeled as a branched polymer with 12 attractive sites (packaging signals) that can form bonds with 12 icosahedrally distributed capsid sites. The genome topology is en...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Physical Society
2023-03-01
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| Series: | Physical Review Research |
| Online Access: | http://doi.org/10.1103/PhysRevResearch.5.L012040 |
| _version_ | 1797210505509601280 |
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| author | James Daniel Farrell Jure Dobnikar Rudolf Podgornik |
| author_facet | James Daniel Farrell Jure Dobnikar Rudolf Podgornik |
| author_sort | James Daniel Farrell |
| collection | DOAJ |
| description | We explore how the stability of RNA viruses depends on genome topology and interactions between RNA and the capsid proteins. RNA is modeled as a branched polymer with 12 attractive sites (packaging signals) that can form bonds with 12 icosahedrally distributed capsid sites. The genome topology is encoded as a graph by mapping pairs of adjacent packaging signals to edges. We perform replica exchange molecular dynamics simulations and evaluate the osmotic pressure of all unique branched topologies of encapsulated RNA. We find that virion stability depends in a complex fashion on both genome topology and degree of confinement, and predict that MS2 bacteriophage should prefer a more linear genome topology. |
| first_indexed | 2024-04-24T10:11:40Z |
| format | Article |
| id | doaj.art-4ffd2e1e8a394e808a8be17d5f9fccbb |
| institution | Directory Open Access Journal |
| issn | 2643-1564 |
| language | English |
| last_indexed | 2024-04-24T10:11:40Z |
| publishDate | 2023-03-01 |
| publisher | American Physical Society |
| record_format | Article |
| series | Physical Review Research |
| spelling | doaj.art-4ffd2e1e8a394e808a8be17d5f9fccbb2024-04-12T17:29:27ZengAmerican Physical SocietyPhysical Review Research2643-15642023-03-0151L01204010.1103/PhysRevResearch.5.L012040Role of genome topology in the stability of viral capsidsJames Daniel FarrellJure DobnikarRudolf PodgornikWe explore how the stability of RNA viruses depends on genome topology and interactions between RNA and the capsid proteins. RNA is modeled as a branched polymer with 12 attractive sites (packaging signals) that can form bonds with 12 icosahedrally distributed capsid sites. The genome topology is encoded as a graph by mapping pairs of adjacent packaging signals to edges. We perform replica exchange molecular dynamics simulations and evaluate the osmotic pressure of all unique branched topologies of encapsulated RNA. We find that virion stability depends in a complex fashion on both genome topology and degree of confinement, and predict that MS2 bacteriophage should prefer a more linear genome topology.http://doi.org/10.1103/PhysRevResearch.5.L012040 |
| spellingShingle | James Daniel Farrell Jure Dobnikar Rudolf Podgornik Role of genome topology in the stability of viral capsids Physical Review Research |
| title | Role of genome topology in the stability of viral capsids |
| title_full | Role of genome topology in the stability of viral capsids |
| title_fullStr | Role of genome topology in the stability of viral capsids |
| title_full_unstemmed | Role of genome topology in the stability of viral capsids |
| title_short | Role of genome topology in the stability of viral capsids |
| title_sort | role of genome topology in the stability of viral capsids |
| url | http://doi.org/10.1103/PhysRevResearch.5.L012040 |
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