Unfolding and Translocation of Proteins Through an Alpha-Hemolysin Nanopore by ClpXP

Methods Mol Biol. 2021;2186:145-155. doi: 10.1007/978-1-0716-0806-7_11.


Proteins present a significant challenge for nanopore-based sequence analysis. This is partly due to their stable tertiary structures that must be unfolded for linear translocation, and the absence of regular charge density. To address these challenges, here we describe how ClpXP, an ATP-dependent protein unfoldase, can be harnessed to unfold and processively translocate multi-domain protein substrates through an alpha-hemolysin nanopore sensor. This process results in ionic current patterns that are diagnostic of protein sequence and structure at the single-molecule level.

Keywords: ClpXP; Nanopore; Protein folding; Protein sequencing; Single-molecule; Unfoldase; α-Hemolysin.

MeSH terms

  • Endopeptidase Clp / metabolism*
  • Hemolysin Proteins / chemistry*
  • Hemolysin Proteins / metabolism*
  • Lipid Bilayers / metabolism*
  • Nanopores*
  • Protein Transport
  • Protein Unfolding*


  • Hemolysin Proteins
  • Lipid Bilayers
  • Endopeptidase Clp