Anion–π contacts are common in the PDB
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.
Source
A thorough anion-π interaction study in biomolecules: on the importance of cooperativity effects
What they did
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.
What they found
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.
The limits
What it doesn't show
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.
Key terms
- Anion–π interaction
- Contact between an anion (often carboxylate) and the face of an aromatic ring.
- Cooperativity
- A second interaction (cation–π or stacking) on the same ring that can strengthen a weak anion–π contact.
- Cation–π
- Attraction of a cation to an aromatic face, often opposite the anion here.
- PDB census
- Statistical search of deposited crystal/NMR structures for a contact type.
- Close-to-parallel carboxylate
- Preferred orientation of Asp/Glu relative to the aromatic plane.
Flashcards
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Quiz yourself
Fraction of processed PDB entries with anion–π contacts:
Common questions
How common are anion–π contacts in proteins?
In 61.3% of processed PDB structures.
Which anions dominate?
Asp and Glu carboxylates.
Which protein aromatic is most common?
His overall; Tyr at interfaces.
DNA vs RNA?
DNA shows no Glu/Asp selectivity; Glu is more present in RNA, with different base partners.
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