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Research article2013Peer reviewedOpen access

High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule

Lindborg, Malin; Dubnovitsky, Anatoly; Olesen, Kenneth; Björkman, Tomas; Lars, Abrahmsen; Feldwisch, Joachim; Härd, Torleif


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.


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

      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


      Permanent link to this page (URI)