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  • Letter
  • Open Access

Role of genome topology in the stability of viral capsids

James Daniel Farrell1,2,*, Jure Dobnikar1,2,3,†, and Rudolf Podgornik2,4,1,5,‡

  • 1CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
  • 2School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
  • 3Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
  • 4Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
  • 5Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China

  • *farrelljd@iphy.ac.cn
  • †jd489@cam.ac.uk
  • ‡podgornikrudolf@ucas.ac.cn; Also at Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000 Ljubljana, Slovenia.
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Phys. Rev. Research 5, L012040 – Published 21 March, 2023

DOI: https://doi.org/10.1103/PhysRevResearch.5.L012040

Abstract

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.

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Phys. Rev. Research 5, L012040– Published 21 March, 2023
  • Received 1 August 2022
  • Accepted 2 February 2023
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Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

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