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Controlling protein translocation through nanopores with bio-inspired fluid walls

Nature Nanotechnology volume 6, pages 253–260 (2011)Cite this article

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Abstract

Synthetic nanopores have been used to study individual biomolecules in high throughput, but their performance as sensors does not match that of biological ion channels. Challenges include control of nanopore diameters and surface chemistry, modification of the translocation times of single-molecule analytes through nanopores, and prevention of non-specific interactions with pore walls. Here, inspired by the olfactory sensilla of insect antennae, we show that coating nanopores with a fluid lipid bilayer tailors their surface chemistry and allows fine-tuning and dynamic variation of pore diameters in subnanometre increments. Incorporation of mobile ligands in the lipid bilayer conferred specificity and slowed the translocation of targeted proteins sufficiently to time-resolve translocation events of individual proteins. Lipid coatings also prevented pores from clogging, eliminated non-specific binding and enabled the translocation of amyloid-beta (Aβ) oligomers and fibrils. Through combined analysis of their translocation time, volume, charge, shape and ligand affinity, different proteins were identified.

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Figure 1: Bio-inspired synthetic nanopores with bilayer-coated fluid walls.
Figure 2: Capture, affinity-dependent pre-concentration and translocation of specific proteins after binding to ligands on mobile lipid anchors.
Figure 3: Controlling the translocation times, td, of single lipid-anchored proteins by the viscosity of the bilayer coating and distinguishing proteins by their most probable td values.
Figure 4: Distribution of ΔI values and corresponding molecular volumes and shape factors of individual proteins translocating through bilayer-coated nanopores with biotinylated lipids.
Figure 5: Comparison of experimental and theoretical values of charge-dependent translocation times of streptavidin.
Figure 6: Bilayer-coated nanopores resist clogging and enable monitoring of the aggregation of Aβ peptides.

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Acknowledgements

The authors thank D. Sept and D. Talaga for assistance in modelling distributions of translocation times and Y.N. Billeh for valuable discussions. The authors also thank D.J. Estes and J.D. Uram for their work on the LabView recording software. This work was supported by a National Science Foundation Career Award (M.M., grant no. 0449088), the National Institutes of Health (M.M., grant no. 1R01GM081705), the Alzheimer's Disease Research Center (J.Y., 3P50 AG005131), the Alzheimer's Association (J.Y., NIRG-08-91651), the National Human Genome Research Institute (J.L., grant nos HG003290 and HG004776) and a Graduate Assistance in Areas of National Need Fellowship (E.C.Y).

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Authors and Affiliations

  1. Department of Biomedical Engineering, University of Michigan, Ann Arbor, 48109, Michigan, USA

    Erik C. Yusko, Jay M. Johnson, Sheereen Majd, Panchika Prangkio & Michael Mayer

  2. Department of Physics, University of Arkansas, Fayetteville, 72701, Arkansas, USA

    Ryan C. Rollings & Jiali Li

  3. Department of Chemistry and Biochemistry, University of California, San Diego, 92093, California, USA

    Jerry Yang

  4. Department of Chemical Engineering, University of Michigan, Ann Arbor, 48109, Michigan, USA

    Michael Mayer

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Contributions

E.C.Y., J.Y., and M.M. conceived and designed the experiments. E.C.Y., J.M.J., S.M. and P.P. performed the experiments. R.C.R. and J.L. fabricated the nanopores. E.C.Y., J.L., J.Y. and M.M. co-wrote the manuscript and Supplementary Information.

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Correspondence to Jerry Yang or Michael Mayer.

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Yusko, E., Johnson, J., Majd, S. et al. Controlling protein translocation through nanopores with bio-inspired fluid walls. Nature Nanotech 6, 253–260 (2011). https://doi.org/10.1038/nnano.2011.12

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