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C-H...pi-interactions in proteins.

M Brandl1, M S Weiss, A Jabs

  • 1Department of Structural Biology and Crystallography, Institute of Molecular Biology, Jena, Germany.

Journal of Molecular Biology
|March 13, 2001
PubMed
Summary

Researchers identified over 31,000 C-H…π interactions in protein structures, classifying them as weak hydrogen bonds. These interactions, particularly between C-H donors and pi-acceptors, are crucial for protein stability.

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Area of Science:

  • Structural biology
  • Biochemistry
  • Computational chemistry

Background:

  • Proteins are stabilized by various non-covalent interactions.
  • C-H…π interactions, a type of weak hydrogen bond, play a role in molecular recognition and stabilization.

Purpose of the Study:

  • To systematically investigate the occurrence and characteristics of C-H…π interactions in a comprehensive set of protein structures.
  • To classify and analyze these interactions based on donor and acceptor groups.

Main Methods:

  • Analysis of a non-redundant set of 1154 protein structures from the Protein Data Bank.
  • Identification and geometric analysis of over 31,000 C-H…π interactions.
  • Classification of interactions into 12 distinct classes based on donor and acceptor groups.

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Main Results:

  • C-H…π interactions were frequently observed, particularly between aliphatic C-H donors and aromatic pi-acceptors, and aromatic C-H donors and aromatic pi-acceptors.
  • Specific amino acid residues like Tryptophan, Phenylalanine, Tyrosine, and Histidine frequently participate as pi-acceptors.
  • Resolution dependence of interaction distances suggests limitations in current protein structure refinement force fields.
  • Interactions are predominantly located in the protein interior, with hydrophilic interactions closer to the surface.
  • Approximately 40% of interactions occur between residues separated by nine or fewer sequence positions.

Conclusions:

  • C-H…π interactions are a significant and prevalent feature in protein structures.
  • These interactions exhibit preferences for specific amino acid types, secondary structures, and residue proximity.
  • The findings suggest that C-H…π interactions contribute substantially to overall protein stability.
  • Further refinement of computational models may be necessary to accurately represent these interactions.