DNA packaging in viral capsids with peptide arms

Area of Science:

• Biophysics
• Structural Biology
• Computational Biology

Background:

• Viral DNA packaging involves overcoming strong chain rigidity and electrostatic repulsion.
• Existing models often oversimplify or neglect long-range electrostatic interactions and capsid structure.
• Understanding these forces is crucial for viral assembly and genome packaging dynamics.

Purpose of the Study:

• To investigate the role of electrostatic interactions in viral DNA packaging dynamics.
• To explore how peptide arms (PAs), DNA, and counterions influence this process.
• To analyze the effect of PA layer structure on DNA conformation and packaging rate.

Main Methods:

• Utilized molecular dynamics simulations with a coarse-grained model.
• Explicitly included peptide arms (PAs) on the capsid inner surface and counterions.
• Investigated electrostatic interactions between PAs, DNA, and counterions.

Main Results:

• Electrostatic interactions between PAs, DNA, and counterions significantly impact DNA packaging dynamics.
• Packed DNA conformations are strongly influenced by the structure of the PA layer.
• The DNA packaging rate was found to be insensitive to the PA layer structure.

Conclusions:

• Electrostatic forces play a critical role in shaping DNA conformation during viral packaging.
• While DNA conformation is sensitive to capsid internal structure, packaging speed is not.
• This study provides a more detailed molecular-level understanding of viral genome packaging.