Peptides in headlock--a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy

Sci Rep. 2016 Jan 21:6:19211. doi: 10.1038/srep19211.


Nanobodies are highly valuable tools for numerous bioanalytical and biotechnical applications. Here, we report the characterization of a nanobody that binds a short peptide epitope with extraordinary affinity. Structural analysis reveals an unusual binding mode where the extended peptide becomes part of a β-sheet structure in the nanobody. This interaction relies on sequence-independent backbone interactions augmented by a small number of specificity-determining side chain contacts. Once bound, the peptide is fastened by two nanobody side chains that clamp it in a headlock fashion. Exploiting this unusual binding mode, we generated a novel nanobody-derived capture and detection system. Matrix-coupled nanobody enables the fast and efficient isolation of epitope-tagged proteins from prokaryotic and eukaryotic expression systems. Additionally, the fluorescently labeled nanobody visualizes subcellular structures in different cellular compartments. The high-affinity-binding and modifiable peptide tag of this system renders it a versatile and robust tool to combine biochemical analysis with microscopic studies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibody Affinity
  • Epitope Mapping
  • Epitopes / chemistry
  • Epitopes / metabolism
  • Microscopy*
  • Models, Molecular
  • Mutation
  • Peptide Library
  • Peptides / chemistry
  • Peptides / genetics
  • Peptides / metabolism*
  • Protein Binding
  • Protein Conformation
  • Proteomics / methods*
  • Single-Domain Antibodies / chemistry
  • Single-Domain Antibodies / metabolism*
  • Structure-Activity Relationship


  • Epitopes
  • Peptide Library
  • Peptides
  • Single-Domain Antibodies