Structure and energetics guide dynamic behaviour in a T = 3 icosahedral virus capsid

Area of Science:

• Structural biology
• Virology
• Computational biophysics

Background:

• Virus capsids often appear structurally rigid in static images.
• Biochemical data suggests significant flexibility within viral particles.
• Understanding capsid dynamics is key to viral life cycle processes.

Purpose of the Study:

• To investigate the structural flexibility of the Flock House Virus (FHV) capsid using all-atom simulations.
• To analyze and compare the flexibility of different capsid subunits and RNA fragments.
• To explore the role of water molecule movement through the capsid in viral mechanisms.

Main Methods:

• All-atom molecular dynamics simulations of the icosahedral Flock House Virus capsid.
• Analysis of flexibility in beta and gamma subunits and RNA fragments.
• Investigation of water molecule permeability and distribution within the capsid shell.

Main Results:

• Simulations showed differential flexibility among quasi-equivalent capsid subunits, aligning with biological observations.
• The gammaA subunit and RNA fragment displayed greater flexibility than gammaB and gammaC subunits.
• The capsid shell is permeable to water, with higher water content along the I2 symmetry axis compared to I5 and I3 axes.

Conclusions:

• The observed flexibility differences are consistent with Flock House Virus's biological behavior.
• The enriched water environment along the I2 axis may be critical for RNA release.
• Physical characterization of virus capsids is essential for understanding viral infectivity and life cycle transitions.