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Electrostatics of capsid-induced viral RNA organization

J. Chem. Phys. 131, 105101 (2009); doi:10.1063/1.3216550

Published 8 September 2009

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Christopher Forrey and M. Muthukumar
Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
We have addressed the role of electrostatics in the formation of genome structure in the Pariacoto virus, where substantial experimental data are available. We have used Langevin dynamics simulation of a coarse-grained model, based on the published crystal structure of the rigid portion of the Pariacoto capsid and including flexible N-terminal protein arms, attached to the rigid capsid at the appropriate locations. The inclusion of charged residues in our model was dictated solely by the location of charges inherent in the Pariacoto sequence itself. Although the viral genome and other exogenous RNA sequences used in experimental studies can assume secondary structures, we have intentionally used uniformly charged flexible polyelectrolyte lacking predetermined secondary structures as the substitute for the viral genome, in order to see whether the same final assembled genome structure emerges without invoking secondary RNA structures. The intent of our study was to investigate the internal environment presented by the capsid proteins of Pariacoto virus, specifically whether the topological features and electrostatic potential at the inner capsid surface can induce complexation of generic negatively charged polyelectrolyte into structures similar to those observed experimentally with packaged RNA. We find that the charge decoration on the interior of the capsid templates the assembly of the flexible polyelectrolyte, allowing hybridizationlike folding of similarly charged strands, and eventually organizing dodecahedral assembly of the polymer. Our results from a generic flexible polyelectrolyte for the assembled structure and bimodal monomer distribution are remarkably matched to that of the viral RNA found experimentally. Results of our work can be interpreted primarily as a consequence of electrostatics, as consideration of base-pairing has been omitted. We propose that our work supports the growing body of evidence that electrostatic interactions play a crucial role in RNA viral assembly and structure. ©2009 American Institute of Physics
History: Received 1 June 2009; accepted 12 August 2009; published 8 September 2009
Permalink: http://link.aip.org/link/?JCPSA6/131/105101/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.-v
    Biomolecules: structure and physical properties
  • 87.14.E-
    Proteins
  • 87.15.Pc
    Electronic and electrical properties of biomolecules
  • 36.20.-r
    Macromolecules and polymer molecules
  • YEAR: 2009

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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