Symmetry-adapted digital modeling I. Axial symmetric proteins

Area of Science:

• Structural biology
• Computational biology
• Biophysics

Background:

• Axial symmetric proteins exhibit diverse symmetries (e.g., tetragonal, trigonal, pentagonal).
• Existing coarse-grained models vary in their representation of protein structures.

Purpose of the Study:

• To develop a new coarse-grained modeling method for axial symmetric proteins.
• To establish a lattice-based indexing system for protein residues.

Main Methods:

• Utilizing a protein enclosing form and a digital modeling lattice (Λ) for residue indexing.
• Projecting atomic positions onto a plane and indexing Cα atoms to the nearest lattice point.
• Selecting residues based on their z-coordinate relative to lattice points to define coarse-grained beads.

Main Results:

• Developed a coarse-grained protein description based on lattice indexing.
• Demonstrated that Cα indexing is independent of the chosen model granularity (δ).
• The method allows for variable levels of detail in coarse-grained models.

Conclusions:

• The proposed lattice-based indexing offers a consistent approach to coarse-grained protein modeling.
• This method provides a flexible framework for representing protein structures at different resolutions.
• The indexing strategy is robust and independent of the specific granularity chosen for the model.