A general method to quantify quasi-equivalence in icosahedral viruses

Area of Science:

• Structural biology
• Virology
• Biophysics

Background:

• Icosahedral virus capsids are complex protein shells with quasi-equivalent surface lattices.
• Comparing protein subunit interfaces is crucial for understanding capsid assembly and function.

Purpose of the Study:

• To develop and apply a quantitative, atom-based method for comparing protein subunit interfaces in icosahedral virus capsids.
• To classify capsid architectures based on structural and geometric features using a novel scoring system.

Main Methods:

• A quantitative, atom-based method was developed to compute an integrated, normalized value (Q-score) for subunit interactions.
• The Q-score is based on equivalent residue contacts and ranges from 0 to 1.
• The method was applied to quasi-equivalent capsid structures (T=3, 4, 7, 13) from the Protein Data Bank.

Main Results:

• Significantly positive Q-scores identify quasi-equivalent interfaces.
• Analysis classified T=3 structures into three groups resembling different polyhedra.
• High Q-scores reflected dimer preference in the T=4 Hepatitis B virus capsid.
• Differences between T=7 and polyoma-like capsids were identified.
• Modest distortion in T=13 Blue tongue virus core interfaces was highlighted.
• Quasi 2-fold symmetry in inner capsids of BTV and reovirus was identified.

Conclusions:

• The Q-score serves as a 'fingerprint' for virus capsid architecture.
• This method enables classification of virus particles based on structural and geometric features.
• The approach provides insights into the structural underpinnings of quasi-equivalence in viral capsids.