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

Area of Science:

• Virology
• Biophysics
• Computational Biology

Background:

• Picornaviruses, like poliovirus, possess a capsid protecting a single-stranded RNA (ssRNA) genome.
• Viral capsids are generally stable in aqueous solutions.

Purpose of the Study:

• To investigate the molecular-level properties of poliovirus capsids.
• To understand the dynamics of water and ion exchange across the viral capsid.

Main Methods:

• All-atom molecular dynamics simulations.
• Long-time (6.5 × 10^6) and large-scale calculations.
• Simulations of the Mahoney strain of poliovirus.

Main Results:

• Rapid, equilibrium exchange of water molecules across the capsid was observed (25 μs).
• No ion exchange occurred within the simulation time (200 ns), indicating semipermeable properties.
• Negative pressure was detected inside the capsid without the genome, attributed to excess charges.

Conclusions:

• The capsid's water permeability explains its tolerance to pressure and susceptibility to dehydration.
• The capsid functions as a semipermeable membrane, regulating ion passage.
• Internal negative pressure may be balanced by osmotic pressure from the ssRNA genome and counterions.