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An electrophile-nucleophile interaction in metalloprotein structures

P Chakrabarti1, D Pal

  • 1Division of Physical Chemistry, National Chemical Laboratory, Pune, India. pinak@ncl.ernet.in

Protein Science : a Publication of the Protein Society
|April 1, 1997
PubMed
Summary

Researchers discovered a novel interaction in metalloproteins where cysteine thiolates attack peptide carbonyls. This interaction, observed in 23 structures, involves specific distances and angles, suggesting a role in protein dynamics and reactions.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Chemistry

Background:

  • Metalloproteins are crucial biological molecules containing metal ions coordinated by amino acid residues.
  • Cysteine residues, particularly their thiolate anions, are common ligands for metal ions in metalloproteins.
  • Peptide bonds form the backbone of proteins, with carbonyl groups acting as potential electrophilic sites.

Purpose of the Study:

  • To identify and characterize a novel attractive interaction between cysteine thiolate anions and peptide carbonyl groups in metalloprotein structures.
  • To determine the geometric parameters and prevalence of this interaction across various metalloprotein families.
  • To explore the implications of this interaction for protein structure, dynamics, and potential reaction mechanisms.

Main Methods:

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  • Analysis of 82 metalloprotein structures from the Protein Data Bank (PDB).
  • Identification and geometric analysis of interactions between sulfur atoms of metal-bound cysteine and carbonyl carbons of peptide groups.
  • Comparison of torsion angles in interacting cysteine residues with those in non-interacting cysteines.

Main Results:

  • A new interaction was identified between the thiolate anion of metal-bound cysteine (nucleophile) and the carbonyl carbon of a peptide group (electrophile).
  • The interacting S and C atoms were found at a distance of 3.2 ± 2 Å, with an S...C-O angle of 109 ± 15 degrees.
  • This interaction typically occurs within the same cysteine residue, requiring deviations in side-chain and main-chain torsion angles compared to uncomplexed cysteines.

Conclusions:

  • The identified interaction represents a significant structural motif in metalloproteins, potentially influencing protein stability and function.
  • The geometric constraints suggest this interaction could be a 'snapshot' of an intra-residue nucleophilic attack by cysteine on a peptide bond.
  • Further investigation is warranted to elucidate the functional and mechanistic significance of this cysteine-carbonyl interaction in metalloprotein chemistry.