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Molecular Dynamics Simulations of Deformable Viral Capsomers
Lauren B Nilsson1, Fanbo Sun1, J C S Kadupitiya1
1Intelligent Systems Engineering, Indiana University, Bloomington, IN 47408, USA.
Viruses
|August 26, 2023
Summary
This study introduces a new coarse-grained model for viral capsomers, accounting for their flexibility. Simulations show that capsomer deformability influences viral capsid assembly, enabling transitions from malformed structures to proper icosahedral forms.
Area of Science:
- Computational biology
- Biophysics
- Structural biology
Background:
- Coarse-grained models often use rigid viral capsomers.
- Lack of shape adaptation in models limits understanding of viral assembly dynamics.
Purpose of the Study:
- To develop a deformable coarse-grained model for viral capsomers.
- To investigate the role of capsomer flexibility in viral capsid self-assembly.
Main Methods:
- Developed a coarse-grained model incorporating stretching and bending energies for capsomers.
- Utilized molecular dynamics simulations to study self-assembly of T=1 icosahedral virus systems.
- Analyzed assembly pathways under varying steric attraction and capsomer deformability.
Main Results:
- Simulations reproduced complex self-assembly behaviors, including transitions to icosahedral capsids and malformed structures.
- An assembly diagram revealed that higher capsomer deformability necessitates greater steric attraction for capsid formation.
- Increased deformability facilitated correction of malformed structures, but excessive softness led to fluid-like states.
Conclusions:
- Capsomer deformability is a critical factor in viral capsid self-assembly.
- The balance between steric attraction and deformability governs the fidelity of capsid formation.
- This model provides insights into the physical principles underlying viral structure formation.
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