Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• Cation-aromatic interactions are crucial in protein structure and function.
• The Cation-Aromatic Database (CAD) previously cataloged these motifs.
• An updated repository is needed to reflect the growing PDB data.

Purpose of the Study:

• To update and expand the Cation-Aromatic Database (CAD) with recent protein structure data.
• To analyze the prevalence and characteristics of cation-aromatic motifs.
• To identify specific cation-aromatic interaction preferences in proteins.

Main Methods:

• Retrieval of protein structures from the Protein Data Bank (PDB) as of June 2023.
• Identification and classification of cation-aromatic motifs using distance parameters (r, d1, d2).
• Analysis of motif geometry (spherical vs. cylindrical) and specific residue pair interactions.

Main Results:

• The updated CAD V2.0 contains over 27.26 million cation-aromatic motifs from 193,936 protein structures.
• Spherical motifs (94.09%) are more common than cylindrical motifs (5.91%).
• Metal ion interactions are frequent, with 82.08% involving histidine; HIS-HIS and TYR-LYS are prevalent pairs.

Conclusions:

• The updated CAD provides a comprehensive resource for studying cation-aromatic interactions.
• Analysis reveals significant roles of histidine in metal ion binding and specific residue preferences.
• This data aids in understanding the biological functions of cation-aromatic interactions in biomolecules.