Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Unfoldase-mediated protein translocation through an α-hemolysin nanopore


Using nanopores to sequence biopolymers was proposed more than a decade ago1. Recent advances in enzyme-based control of DNA translocation2 and in DNA nucleotide resolution using modified biological pores3 have satisfied two technical requirements of a functional nanopore DNA sequencing device. Nanopore sequencing of proteins was also envisioned1. Although proteins have been shown to move through nanopores4,5,6, a technique to unfold proteins for processive translocation has yet to be demonstrated. Here we describe controlled unfolding and translocation of proteins through the α-hemolysin (α-HL) pore using the AAA+ unfoldase ClpX. Sequence-dependent features of individual engineered proteins were detected during translocation. These results demonstrate that molecular motors can reproducibly drive proteins through a model nanopore—a feature required for protein sequence analysis using this single-molecule technology.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Experimental set-up.
Figure 2: Ionic current traces during ClpX-mediated protein translocation.
Figure 3: Ionic current state dwell times during translocation of model proteins through the nanopore.


  1. Church, G.M., Deamer, D.W., Branton, D., Baldarelli, R. & Kasianowicz, J. Characterization of individual polymer molecules based on monomer-interface inter- action. US patent 5,795,782 (1998).

  2. Cherf, G.M. et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat. Biotechnol. 30, 344–348 (2012).

    Article  CAS  Google Scholar 

  3. Manrao, E.A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349–353 (2012).

    Article  CAS  Google Scholar 

  4. Mohammad, M.M., Prakash, S., Matouschek, A. & Movileanu, L. Controlling a single protein in a nanopore through electrostatic traps. J. Am. Chem. Soc. 130, 4081–4088 (2008).

    Article  CAS  Google Scholar 

  5. Talaga, D.S. & Li, J. Single-molecule protein unfolding in solid state nanopores. J. Am. Chem. Soc. 131, 9287–9297 (2009).

    Article  CAS  Google Scholar 

  6. Merstorf, C. et al. Wild type, mutant protein unfolding and phase transition detected by single-nanopore recording. ACS Chem. Biol. 7, 652–658 (2012).

    Article  CAS  Google Scholar 

  7. Baker, T.A. & Sauer, R.T. ClpXP, an ATP-powered unfolding and protein-degradation machine. Biochim. Biophys. Acta 1823, 15–28 (2012).

    Article  CAS  Google Scholar 

  8. Aubin-Tam, M.E. et al. Single-molecule protein unfolding and translocation by an ATP-fueled proteolytic machine. Cell 145, 257–267 (2011).

    Article  CAS  Google Scholar 

  9. Maillard, R.A. et al. ClpX(P) generates mechanical force to unfold and translocate its protein substrates. Cell 145, 459–469 (2011).

    Article  CAS  Google Scholar 

  10. Simon, S.M. & Blobel, G. A protein-conducting channel in the endoplasmic reticulum. Cell 65, 371–380 (1991).

    Article  CAS  Google Scholar 

  11. Johnson, E.S., Schweinhorst, I., Dohmen, R.J. & Blobel, G. The ubiquitin-like protein Smt3p is activated for conjugation to other proteins by an Aos1p/Uba2p heterodimer. EMBO J. 16, 5509–5519 (1997).

    Article  CAS  Google Scholar 

  12. Sheng, W. & Liao, X. Solution structure of a yeast ubiquitin-like protein Smt3: the role of structurally less defined sequences in protein-protein recognitions. Protein Sci. 11, 1482–1491 (2002).

    Article  CAS  Google Scholar 

  13. Gottesman, S., Roche, E., Zhou, Y. & Sauer, R.T. The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12, 1338–1347 (1998).

    Article  CAS  Google Scholar 

  14. Kim, Y. et al. Dynamics of substrate denaturation and translocation by the ClpXP degradation machine. Mol. Cell 5, 639–648 (2000).

    Article  CAS  Google Scholar 

  15. Christensen, C. et al. Effect of charge, topology and orientation of the electric field on the interaction of peptides with the α-hemolysin pore. J. Pept. Sci. 17, 726–734 (2011).

    Article  CAS  Google Scholar 

  16. Movileanu, L. Interrogating single proteins through nanopores: challenges and opportunities. Trends Biotechnol. 27, 333–341 (2009).

    Article  CAS  Google Scholar 

  17. Oukhaled, G. et al. Unfolding of proteins and long transient conformations detected by single nanopore recording. Phys. Rev. Lett. 98, 158101 (2007).

    Article  CAS  Google Scholar 

  18. Olasagasti, F. et al. Replication of individual DNA molecules under electronic control using a protein nanopore. Nat. Nanotechnol. 5, 798–806 (2010).

    Article  CAS  Google Scholar 

  19. Martin, A., Baker, T.A. & Sauer, R.T. Rebuilt AAA+ motors reveal operating principles for ATP-fuelled machines. Nature 437, 1115–1120 (2005).

    Article  CAS  Google Scholar 

  20. Kenniston, J.A., Baker, T.A., Fernandez, J.M. & Sauer, R.T. Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell 114, 511–520 (2003).

    Article  CAS  Google Scholar 

Download references


The authors thank Oxford Nanopore Technologies (Oxford, UK) for supplying α-HL heptamers, and A. Martin (UC Berkeley) for supplying ClpX-related expression plasmids and for helpful discussions on their use. R. Abu-Shumays, D. Bernick, K. Lieberman and H. Olsen commented on drafts of the manuscript. This work was supported by a UC startup grant to M.A., and by equipment purchased previously using National Human Genome Research Institute grant R01HG006321. The ClpX-ΔN3 BLR expression strain was obtained from A. Martin (UC Berkeley), as was a his-tagged ClpP expression strain.

Author information

Authors and Affiliations



J.N. conceived and designed the project, performed the protein engineering and production, conceived and performed experiments and co-wrote the manuscript. D.B.M. performed and conceived experiments, analyzed data and co-wrote the manuscript. M.A. co-wrote the manuscript, designed the nanopore platform and directed the project.

Corresponding author

Correspondence to Mark Akeson.

Ethics declarations

Competing interests

M.A. is a consultant to Oxford Nanopore Technologies, Oxford, UK.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 (PDF 1211 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Nivala, J., Marks, D. & Akeson, M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat Biotechnol 31, 247–250 (2013).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research