Abstract

Affibody molecules are engineered binding proteins, in which the three-helix bundle motif of the Z domain derived from protein A is used as a scaffold for sequence variation. We used phage display to select Affibody binders to staphylococcal protein A itself. The best binder, called ZpA963, binds with similar affinity and kinetics to the five homologous E, D, A, B and C domains of protein A, and to a five-domain protein A construct with an average dissociation constant, K-D, of 20 nM. The structure of ZpA963 in complex with the Z domain shows that it interacts with a surface on Z that is identical in the five protein A domains, which explains the multi-domain affinity. This property allows for high-affinity binding by dimeric Affibody molecules that simultaneously engage two protein A domains in a complex. We studied two ZpA963 dimers in which the subunits were linked by a C-terminal disulfide in a symmetric dimer or head-to-tail in a fusion protein, respectively. The dimers both bind protein A with high affinity, very slow off-rates and with saturation-dependent kinetics that can be understood in terms of dimer binding to multiple sites. The head-to-tail (ZpA963)(2)htt dimer binds with an off-rate of k(off) 5 10(6) s(1) and an estimated K-D 16 pM. The results illustrate how dimers of selected monomer binding proteins can provide an efficient route for engineering of high-affinity binders to targets that contain multiple homologous domains or repeated structural units.

Keywords

molecular recognition; phage display; protein engineering; proteinprotein interactions; protein structure

Published in

Protein Engineering, Design and Selection
2013, Volume: 26, number: 10, pages: 635-644
Publisher: OXFORD UNIV PRESS

SLU Authors

• Dubnovitsky, Anatoly

  • Department of Molecular Biology, Swedish University of Agricultural Sciences
    
  • Karolinska Institute

• Härd, Torleif

  • Department of Molecular Biology, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Biocatalysis and Enzyme Technology
Biochemistry and Molecular Biology
Physical Chemistry


Publication identifier

DOI: https://doi.org/10.1093/protein/gzt038

Permanent link to this page (URI)

https://res.slu.se/id/publ/53197