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Mining anion-aromatic interactions in the Protein Data Bank.

Emilia Kuzniak-Glanowska1, Michał Glanowski2, Rafał Kurczab3

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This study identifies and analyzes unique anion-aromatic motifs within the Protein Data Bank (PDB), revealing key interaction areas and their prevalence in biological structures like RNA and proteins.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Non-covalent interactions, particularly anion-aromatic motifs, are fundamental to biological system function.
  • Comprehensive analysis of the Protein Data Bank (PDB) is essential for understanding these interactions.
  • Previous analyses have not fully characterized the spatial distribution and types of anion-aromatic motifs.

Purpose of the Study:

  • To systematically screen the PDB for unique anion-aromatic motifs.
  • To identify and categorize distinct areas of anion-aromatic motif accumulation.
  • To analyze the prevalence and characteristics of these motifs in various biological residues.

Main Methods:

  • Analysis of anions within 5 Å spheres around aromatic rings in PDB structures.
  • Utilized a specialized (x, h) coordinate system for motif analysis.
  • Categorized motifs into three distinct spatial areas (A, B, C) relative to the aromatic ring.

Main Results:

  • Identified 555,259 unique anion-aromatic motifs from 171,588 PDB files.
  • Discovered three primary accumulation areas for motifs: A (over ring), B (over bonds), C (in-plane).
  • Nucleotides and ligands showed a strong tendency for anion-π contacts in area A, particularly in RNA tetraloops and protein helices.

Conclusions:

  • The (x, h) coordinate system provides a novel framework for describing anion-aromatic interactions.
  • The study offers a quantitative and qualitative understanding of anion-aromatic motif distribution in biological systems.
  • Developed and released open-source code for PDB supramolecular searches, facilitating future research.