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Related Experiment Videos

Where metal ions bind in proteins.

M M Yamashita1, L Wesson, G Eisenman

  • 1Molecular Biology Institute, University of California, Los Angeles 90024.

Proceedings of the National Academy of Sciences of the United States of America
|August 1, 1990
PubMed
Summary
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Metal ions bind to proteins within a unique environment. A hydrophilic shell, surrounded by a hydrophobic shell, creates a high hydrophobicity contrast, aiding in identifying metal-binding sites.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Metal ions are crucial for protein function and structure.
  • Understanding metal-binding sites is key to protein engineering and drug design.
  • Previous studies have focused on specific metal-protein interactions, lacking a unifying principle.

Purpose of the Study:

  • To identify a common structural feature of metal-binding sites across various proteins and metal ions.
  • To develop an analytical method for characterizing these binding sites.
  • To assess the utility of this method for predicting and designing metal-binding sites.

Main Methods:

  • Analysis of the atomic environments of 11 different metal ions in 23 metal-host molecules.
  • Evaluation of the hydrophobicity contrast function (C) based on atomic solvation parameters (delta sigma).

Related Experiment Videos

  • Comparison of predicted binding site locations using the hydrophobicity contrast function with experimentally observed metal binding sites.

    • Main Results:

    • A consistent pattern was observed: metal ions are ligated by a hydrophilic shell embedded within a hydrophobic shell.
    • The hydrophobicity contrast function (C) quantifies this observation, showing large positive values at metal-binding centers.
    • Maximum values of the contrast function closely corresponded to known metal binding sites in the examined molecules.

    Conclusions:

    • Metal ions bind at sites characterized by high hydrophobicity contrast.
    • The hydrophobicity contrast function is a valuable tool for locating and characterizing metal-binding sites in proteins.
    • This function holds potential for the rational design of novel metal-binding sites.