Computational chemistry
Anion–π contacts are common in the PDB
Open access · cc by · source: Europe PMC
A PDB-wide search finds anion–π interactions in most protein structures, with Asp/Glu carboxylates packing on aromatics and frequent cation–π partners opposite.
How this study connects
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- Halogen bonds are not purely electrostatic — the orbital term does real work
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Anion–π contacts are common in the PDB
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Which residues supply most anions?
Due to their abundance, Asp and Glu are found in the vast majority of anion–π interactions
How do those carboxylates orient?
a preferred close-to-parallel orientation of their carboxylate with respect to the interacting aromatic system
Key findings
Thousands of anion–π contacts exist. 61.3% of 62 033 processed PDB structures contain them. Asp/Glu dominate with near-parallel carboxylates; His is the most common protein aromatic, but Tyr rises at interfaces. DNA vs RNA differ in Glu/Asp and base preferences. Opposite-face cation–π and stacking are common, implying cooperativity.
Methodology
Authors scanned the PDB for anion–π pairs among carboxylates, phosphates, and aromatic side chains/nucleobases, classified geometry, tested enrichment statistically, and looked for ternary anion–π–cation and anion–π–π contacts that could cooperate.
Limitations
This is a structural census, not a measured binding free energy for a designed host; predicted cooperativity is inferred from geometry, not from a new titration series.
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