Complete virus capsid at all-atom resolution: Simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

Abstract

Simulations of complete virus capsid at atomistic details have been performed using standard molecular dynamics as well as original hybrid molecular dynamics/hydrodynamics methodologies. The results show that the capsid is stable in water solution at room temperature and ions composition similar to physiological conditions. Detailed analysis of the flow of water molecules and ions through the capsid's wall is performed. It demonstrates that ions do not cross the capsid shell, while water exhibits substantial flows in both directions. This behaviour can be classified as a semipermeable membrane and may play a role in mechanical properties of the virus particle.