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Licensed Unlicensed Requires Authentication Published by De Gruyter December 21, 2018

Peptide binding affinity redistributes preassembled repeat protein fragments

  • Erich Michel EMAIL logo , Andreas Plückthun and Oliver Zerbe EMAIL logo
From the journal Biological Chemistry


Designed armadillo repeat proteins (dArmRPs) are modular peptide binders composed of N- and C-terminal capping repeats Y and A and a variable number of internal modules M that each specifically recognize two amino acids of the target peptide. Complementary fragments of dArmRPs obtained by splitting the protein between helices H1 and H2 of an internal module show conditional and specific assembly only in the presence of a target peptide (Michel, E., Plückthun, A., and Zerbe, O. (2018). Peptide-guided assembly of repeat protein fragments. Angew. Chem. Int. Ed. 57, 4576–4579). Here, we investigate dArmRP fragments that already spontaneously assemble with high affinity, e.g. those obtained from splits between entire modules or between helices H2 and H3. We find that the interaction of the peptide with the assembled fragments induces distal conformational rearrangements that suggest an induced fit on a global protein level. A population analysis of an equimolar mixture of an N-terminal and three C-terminal fragments with various affinities for the target peptide revealed predominant assembly of the weakest peptide binder. However, adding a target peptide to this mixture altered the population of the protein complexes such that the combination with the highest affinity for the peptide increased and becomes predominant when adding excess of peptide, highlighting the feasibility of peptide-induced enrichment of best binders from inter-modular fragment mixtures.


We gratefully acknowledge financial support by a SINERGIA grant from the Swiss National Science Foundation to A.P and O.Z. (funder id: 10.13039/501100001711, grant no. 122686) and from the Research Council of the University of Zurich (grant no. K-73539-01-01) to E.M.


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Supplementary Material

The online version of this article offers supplementary material (

Received: 2018-08-24
Accepted: 2018-11-21
Published Online: 2018-12-21
Published in Print: 2019-02-25

©2019 Walter de Gruyter GmbH, Berlin/Boston

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