An Improved Method for Modeling Voltage-Gated Ion Channels at Atomic Accuracy Applied to Human Ca_v Channels

Area of Science:

• Structural biology
• Biophysics
• Human genetics

Background:

• Voltage-gated ion channels (VGICs) are crucial membrane proteins implicated in numerous human diseases.
• Despite their importance, high-resolution 3D structural models of human VGICs have been lacking.
• Existing structural data in the Protein Data Bank (PDB) required validation for accuracy.

Purpose of the Study:

• To develop a metric for evaluating the structural integrity of VGIC models.
• To build accurate, atomic-resolution 3D homology models of human calcium channel (Ca_v) α₁ subunits.
• To analyze the structural locations of disease-associated mutations in Ca_v channels.

Main Methods:

• Development of a novel 3D structural integrity metric.
• Application of the metric to VGIC structures in the PDB.
• Homology modeling utilizing validated structural data.
• Analysis of human Ca_v Mendelian mutation locations within the 3D models.

Main Results:

• The developed metric identified inaccuracies in existing VGIC structures, particularly those from cryo-electron microscopy.
• Highly accurate homology models of human Ca_v channel α₁ subunits were generated.
• Human Ca_v Mendelian mutations were found to cluster in voltage-sensing and gating segments.
• Equivalent structural locations were identified for mutations causing different clinical phenotypes.
• The ion selectivity filter architecture was found to be highly conserved across bacterial and human VGICs, and between sodium and calcium channels.

Conclusions:

• The structural integrity metric is essential for reliable VGIC structural modeling.
• Accurate 3D models provide insights into the structural basis of VGIC function and disease.
• Conserved structural features highlight fundamental mechanisms across diverse ion channels.