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

Journal Article · Tue Oct 28 04:00:00 EDT 2014 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4897557· OSTI ID:22310772

Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Fujimoto, K. ^[1]; Nakagawa, A. ^[2]; Nomoto, A. ^[3]

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1. Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan)
2. Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan)
3. Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)

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{sup 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.

• OSTI ID: 22310772
• Journal Information: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 16 Vol. 141; ISSN JCPSA6; ISSN 0021-9606
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
ATOMS
DEACTIVATION
INTERACTIONS
ION EXCHANGE
MOLECULAR DYNAMICS METHOD
MOLECULES
POLIO VIRUS
RNA
SIMULATION
SOLUTIONS