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pi-Stacking interactions. Alive and well in proteins

G B McGaughey¹, M Gagné, A K Rappé

¹Wyeth-Ayerst Research, Structural Biology, Princeton, New Jersey 08540, USA.

The Journal of Biological Chemistry

|June 23, 1998

Summary

Aromatic amino acids in proteins prefer a parallel-displaced pi-stacking orientation. This interaction is more stable than T-shaped arrangements, offering insights into protein structure and stability.

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Area of Science:

Structural biology
Biochemistry
Computational chemistry

Background:

Noncovalent interactions between aromatic amino acids are crucial for protein structure and function.
Previous studies on aromatic amino acid interactions in proteins have yielded varied results regarding preferred orientations.

Purpose of the Study:

To determine the preferred positions and orientations of noncovalent interactions between aromatic amino acid side chains (phenylalanine, tyrosine, histidine, tryptophan) in proteins.
To investigate the energetic stability of different aromatic amino acid dimer orientations.

Main Methods:

Analysis of high-resolution X-ray crystal structures of nonhomologous proteins.
Focus on isolated aromatic amino acid pairs (dimers) to avoid complexities of higher-order clusters.
Comparison of experimental findings with ab initio and molecular mechanics calculations.

Main Results:

Aromatic amino acid side chains preferentially align in an off-centered parallel orientation, termed parallel-displaced pi-stacking.
The parallel-displaced structure is energetically more favorable than T-shaped structures by 0.5-1.0 kcal/mol.
Findings align with benzene dimer calculations but contrast with some prior protein analyses.

Conclusions:

The parallel-displaced pi-stacking is the dominant interaction mode for aromatic amino acid dimers in proteins.
This preferred orientation contributes to protein stability and influences higher-order structural arrangements.
The study provides a refined understanding of aromatic interactions in biological macromolecules.

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