A Thermodynamic Model for Genome Packaging in Hepatitis B Virus

Area of Science:

• Virology
• Biophysics
• Computational Biology

Background:

• Viral genome packaging into capsids is essential for viral replication and infectivity.
• Understanding these processes informs antiviral development and gene therapy applications.
• Experimental methods like cryo-EM and X-ray diffraction reveal structure but not in vivo driving forces.

Purpose of the Study:

• To investigate the thermodynamic basis of pregenomic RNA packaging in Hepatitis B virus (HBV) in vivo.
• To elucidate the role of electrostatic interactions between RNA and capsid C-terminal domains (CTDs) in nucleocapsid formation.
• To model the in vivo assembly and stability of HBV nucleocapsids.

Main Methods:

• Development and application of a coarse-grained molecular model for HBV genome packaging.
• Inclusion of nonspecific intermolecular interactions, electrostatic forces, and excluded-volume effects.
• Comparison of theoretical predictions with experimental mutagenesis data.

Main Results:

• The model predicts optimal RNA content in HBV nucleocapsids, correlating with experimental findings.
• Electrostatic interactions and excluded-volume effects are confirmed as key drivers of genome packaging.
• Encapsidated RNA amount is not linearly correlated with CTD net charge.
• Approximately 10% of CTD residues remain unbound to RNA, forming partially exposed tails.
• Thermodynamic analysis accurately predicts the impact of CTD truncation on nucleocapsid stability.

Conclusions:

• Electrostatic interactions and excluded-volume effects are critical for HBV genome packaging.
• The HBV capsid's genome content is regulated by CTD charge and length.
• Partially exposed CTD tails suggest a regulatory role in capsid assembly and stability.
• The thermodynamic model provides a framework for understanding viral genome packaging and capsid formation.