Minimum energy paths for conformational changes of viral capsids

Area of Science:

• Biophysics
• Statistical Mechanics
• Computational Biology

Background:

• Viral capsids are complex protein structures with remarkable mechanical stability.
• Understanding capsid destabilization is crucial for viral infection, maturation, and general complex system stability.
• Previous models often simplify the intricate interactions within viral capsids.

Purpose of the Study:

• To investigate the conformational changes and destabilization pathways of viral capsids.
• To apply large deviations theory to model the dynamics of a simplified dodecahedral viral capsid.
• To analyze the stability of intermediate states during capsid transitions.

Main Methods:

• Utilizing large deviations theory for stochastic differential equations.
• Modeling a dodecahedral viral capsid with rigid plaquette capsomers, each with one degree of freedom.
• Computing minimum energy paths to determine the most probable transition pathways.

Main Results:

• The study successfully computed the most probable transition path from a closed to an open capsid configuration.
• Analysis revealed insights into the mechanical resistance and destabilization dynamics of viral capsids.
• The stability of intermediate configurations during the transition process was discussed.

Conclusions:

• Large deviations theory provides a powerful framework for studying viral capsid conformational dynamics.
• The findings contribute to understanding the stability of complex systems built from weakly interacting units.
• This research offers a simplified yet insightful model for viral capsid behavior relevant to biological processes.