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Peptide binding affinity redistributes preassembled repeat protein fragments


Michel, Erich; Plückthun, Andreas; Zerbe, Oliver (2018). Peptide binding affinity redistributes preassembled repeat protein fragments. Biological Chemistry:Epub ahead of print.

Abstract

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 presence of a target peptide (Michel et al., 2018). 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 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 access of peptide, highlighting the feasibility of peptide-induced enrichment of best binders from inter-modular fragment mixtures.

Abstract

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 presence of a target peptide (Michel et al., 2018). 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 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 access of peptide, highlighting the feasibility of peptide-induced enrichment of best binders from inter-modular fragment mixtures.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry

07 Faculty of Science > Department of Chemistry
Dewey Decimal Classification:540 Chemistry
Uncontrolled Keywords:NMR spectroscopy; peptide binding; protein fragment complementation; protein design; repeat protein
Language:English
Date:20 December 2018
Deposited On:04 Jan 2019 10:48
Last Modified:08 Jan 2019 14:24
Publisher:De Gruyter
ISSN:1431-6730
OA Status:Closed
Publisher DOI:https://doi.org/10.1515/hsz-2018-0355
PubMed ID:30517075
Project Information:
  • : FunderSwiss National Science Foundation
  • : Grant ID
  • : Project Title
  • : FunderForschungskredit der Universität Zürich
  • : Grant ID
  • : Project Title

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Language: English
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Embargo till: 2019-12-01
Content: Published Version
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Embargo till: 2019-12-01