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High-affinity single-domain binding proteins with a binary-code interface.

Akiko Koide1, Ryan N Gilbreth, Kaori Esaki

  • 1Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

Proceedings of the National Academy of Sciences of the United States of America
|April 11, 2007
PubMed
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Protein interfaces can be highly specific using only two amino acids, Tyr and Ser. This study shows engineered fibronectin type III domain monobodies achieve low-nanomolar binding affinity with binary-code interfaces.

Area of Science:

  • Protein engineering
  • Structural biology
  • Biochemistry

Background:

  • Natural protein interactions often rely on complex interfaces.
  • Previous work demonstrated binary-code interfaces (Tyr/Ser) in antibodies.
  • The scaffold's role in enhancing binary-code binding was unclear.

Purpose of the Study:

  • To test the generality of binary-code interfaces in a different scaffold.
  • To engineer specific binding proteins using a fibronectin type III domain scaffold.
  • To elucidate the binding mechanisms of binary-code interfaces.

Main Methods:

  • Engineering of fibronectin type III domain (FN3)-based monobodies.
  • Utilizing a Tyr/Ser binary-code interface within the FN3 scaffold.
  • X-ray crystallography to determine the structure of a monobody-target complex.

Related Experiment Videos

  • Mutation analysis to assess residue contributions to binding.

    • Main Results:

    • Engineered monobodies with Tyr/Ser binary-code interfaces achieved low-nanomolar dissociation constants (K(d)).
    • Structural analysis revealed dominant binding contributions from Tyr residues.
    • The binary interface exhibited molecular mimicry of a substrate (beta-cyclodextrin).

    Conclusions:

    • Low chemical diversity, high conformational diversity interfaces are sufficient for specific protein recognition.
    • Fibronectin type III domain scaffolds can support effective binary-code binding.
    • This provides fundamental insights into protein-protein interaction principles.