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Strange bedfellows: interactions between acidic side-chains in proteins

M M Flocco1, S L Mowbray

  • 1Department of Molecular Biology, Uppsala University, Sweden.

Journal of Molecular Biology
|November 17, 1995
PubMed
Summary
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Protein acidic side-chains often form hydrogen bonds. This study reveals two common configurations: metal ligand interactions and shared protonation, impacting enzyme function.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Science

Background:

  • Acidic amino acid residues (aspartate and glutamate) are crucial in protein structure and function.
  • The oxygen atoms of these residues frequently interact via hydrogen bonds within protein interiors and at active sites.

Purpose of the Study:

  • To investigate the structural arrangements and hydrogen-bonding patterns of proximate acidic side-chain oxygen atoms in proteins.
  • To understand the implications of these interactions for protein function, particularly in metal binding and catalysis.

Main Methods:

  • Analysis of protein structures from databases.
  • Examination of distances and geometries between oxygen atoms of acidic residues.
  • Consideration of pH-dependent phenomena and pKa alterations.

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Main Results:

  • Two prevalent hydrogen-bonding configurations for acidic oxygen atoms were identified: metal coordination and shared protonation.
  • Metal-ligand interactions result in an average closest approach of 3.0 Å.
  • Shared protonation leads to shorter O-O distances (≤2.7 Å), indicative of strong hydrogen bonds, observed even at pH 8.0.

Conclusions:

  • The proximity and hydrogen-bonding of acidic residues are key structural motifs in proteins.
  • These interactions play significant roles in metal ion coordination and proton sharing mechanisms.
  • Understanding these patterns provides insights into enzyme mechanisms involving acidic residues in binding and catalysis.