Molecular dynamics study of T = 3 capsid assembly

Area of Science:

• Computational biology
• Biophysics
• Structural biology

Background:

• Virus capsid self-assembly is a complex process crucial for viral replication.
• Understanding quasi-equivalence is key to modeling T=3 capsids.
• Previous models often lack atomistic detail or explicit solvent effects.

Purpose of the Study:

• To model the self-assembly of T=3 virus capsids using molecular dynamics.
• To investigate the role of particle shape and quasi-equivalence in shell formation.
• To reveal intermediate structures during the self-assembly pathway.

Main Methods:

• Utilized molecular dynamics simulations.
• Modeled self-assembly of 180 trapezoidal particles representing T=3 capsids.
• Incorporated three slightly different particle shapes to account for quasi-equivalence.
• Included reversible bond formation and explicit atomistic solvent.

Main Results:

• Achieved formation of complete polyhedral shells under suitable conditions.
• Observed majority of unused particles remaining as monomers.
• Reported no significant formation of incorrect clusters or misassembled structures.
• Identified and detailed intermediate structures along the assembly pathway.

Conclusions:

• Molecular dynamics simulations can accurately model virus capsid self-assembly.
• Quasi-equivalence plays a significant role in the formation of T=3 capsids.
• The simulation provides valuable insights into the kinetics and intermediates of capsid formation, relevant for experimental validation.