Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses

Area of Science:

• Structural biology
• Computational virology
• Biophysics

Background:

• Icosahedral viruses possess complex structures requiring simplified models for analysis.
• Existing coarse-grained models may not fully capture the intricate details of viral architecture.

Purpose of the Study:

• To develop a novel coarse-grained modeling approach for icosahedral viruses.
• To represent viral structures using a digital modeling lattice based on atomic positions.
• To enable variable levels of detail in viral structural analysis.

Main Methods:

• Utilizing a six-dimensional icosahedral lattice to define a three-dimensional digital modeling lattice.
• Indexing backbone atomic positions (Cα and P atoms) to the nearest lattice points.
• Applying the digital modeling approach to Satellite tobacco mosaic virus, bacteriophage MS2, and Pariacoto virus using Protein Data Bank data.

Main Results:

• A fine-grained lattice point characterization of viral chains was achieved.
• Coarse-grained models were generated by selecting specific indexed backbone positions.
• The method was successfully applied to three distinct icosahedral viruses, with detailed positional data provided.

Conclusions:

• The digital modeling approach offers a versatile method for coarse-grained representation of icosahedral viruses.
• This technique allows for adjustable model coarseness, facilitating diverse analytical needs.
• The study provides a framework for further research in viral structural modeling and analysis.