All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

J Chem Phys. 2014 Oct 28;141(16):165101. doi: 10.1063/1.4897557.

Abstract

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10(6) all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200,000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Capsid / chemistry*
  • Capsid / metabolism
  • Capsid Proteins / chemistry
  • Capsid Proteins / metabolism
  • Molecular Dynamics Simulation*
  • Poliovirus*
  • Pressure
  • Protein Conformation
  • RNA, Viral / metabolism
  • Solutions
  • Water / chemistry

Substances

  • Capsid Proteins
  • RNA, Viral
  • Solutions
  • Water