Dielectric Continuum Modeling for the De Novo Designed Calcium Channel Calc6_3: Structure Preparation, Mesh Generation, and Calcium Selectivity
Year: 2026
Type: preprint
Abstract: This paper presents an integrated software package for continuum dielectric studies of the de novo designed calcium channel CalC6_3. The package combines Python scripts for cleaning and repairing the original PDB structure (PDB ID: 9DZW) with PDB2PQR to generate a corresponding PQR file containing atomic coordinates, partial charges, and radii. It incorporates the Gaussian Ion Channel Molecular Surface Generation package to construct high-quality triangular molecular surface meshes that preserve the complex channel pore geometry while maintaining sufficiently smooth exterior molecular surfaces. These surface meshes are used to generate interface-fitted tetrahedral meshes of a simulation box consisting of protein, membrane, and solvent regions. The integrated software package further integrates the structure-preparation and mesh-generation procedures with the nonuniform size-modified Poisson–Boltzmann ion channel finite element solver to compute electrostatic potentials and ionic concentrations, streamlining the complete workflow from structure preparation to numerical solution. Numerical experiments for an ionic solution containing Ca 2+ , Na + , and Cl − ions show preferential Ca 2+ accumulation in the narrow selectivity filter formed by six Glu residues, supporting the experimentally observed calcium selectivity of CalC6_3. They also suggest that a smoother molecular surface mesh can improve the convergence and performance of the finite element solver. AMS subject classifications 92-08, 65N50, 65N30
Authors: Dexuan Xie, Robert S. Eisenberg
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7223472749