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Domain swapping: entangling alliances between proteins

M J Bennett1, S Choe, D Eisenberg

  • 1Department of Chemistry and Biochemistry, University of California, Los Angeles 90024-1570.

Proceedings of the National Academy of Sciences of the United States of America
|April 12, 1994
PubMed
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Diphtheria toxin (DT) forms a unique dimer through domain swapping, where receptor-binding domains are exchanged between molecules. This protein association mechanism explains the dimer's stability and may be key to protein evolution.

Area of Science:

  • Structural biology
  • Biochemistry
  • Protein dynamics

Background:

  • Diphtheria toxin (DT) is a protein toxin.
  • Understanding protein association mechanisms is crucial for molecular biology.

Purpose of the Study:

  • To elucidate the structural basis of diphtheria toxin (DT) dimerization.
  • To define and identify the phenomenon of domain swapping in protein association.

Main Methods:

  • X-ray crystallography was used to determine the structures of monomeric and dimeric DT at high resolution (2.0-2.3 Å).
  • Comparative structural analysis of monomeric and dimeric forms to identify conformational changes.
  • Analysis of protein chain tracing to understand the molecular rearrangements during dimerization.

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Main Results:

  • The structure of dimeric DT was refined to 2.0 Å resolution, with a corrected loop compared to previous lower-resolution structures.
  • The monomeric DT structure was determined at 2.3 Å resolution, revealing a Y-shaped molecule with catalytic (C), transmembrane (T), and receptor-binding (R) domains.
  • Dimerization involves an unprecedented domain swapping mechanism where the R domain from each monomer is exchanged, involving significant atomic movement (up to 65 Å).
  • This domain swapping explains the long-lived, metastable nature of the DT dimer.

Conclusions:

  • Domain swapping is identified as a novel mode of protein association, exemplified by diphtheria toxin.
  • The identified domain swapping mechanism provides a molecular explanation for the stability of the DT dimer.
  • Domain swapping may represent a general molecular mechanism for the evolution of dimeric and oligomeric proteins.