journal article·2017-04Open access

Real-time shape approximation and fingerprinting of single proteins using a nanopore

Erik C. Yusko, Brandon R. Bruhn, Olivia M. Eggenberger, Jared Houghtaling, Ryan C. Rollings, Nathan C. Walsh, Santoshi Nandivada, Mariya Pindrus, Adam R. Hall, David Sept, Jiali Li, Devendra S. Kalonia, Michael Mayer

Nature Nanotechnology· Volume 12· Issue 4

Abstract

Established methods for characterizing proteins typically require physical or chemical modification steps or cannot be used to examine individual molecules in solution. Ionic current measurements through electrolyte-filled nanopores can characterize single native proteins in an aqueous environment, but currently offer only limited capabilities. Here we show that the zeptolitre sensing volume of bilayer-coated solid-state nanopores can be used to determine the approximate shape, volume, charge, rotational diffusion coefficient and dipole moment of individual proteins. To do this, we developed a theory for the quantitative understanding of modulations in ionic current that arise from the rotational dynamics of single proteins as they move through the electric field inside the nanopore. The approach allows us to measure the five parameters simultaneously, and we show that they can be used to identify, characterize and quantify proteins and protein complexes with potential implications for structural biology, proteomics, biomarker detection and routine protein analysis.
Source: europepmc · Quality: candidate unverified · Source record ↗

Research context

OpenAlex topics: Nanopore and Nanochannel Transport Studies · Electrostatics and Colloid Interactions · Ion-surface interactions and analysis

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (47)

Show source-provided references
1. Picotti, P. & Aebersold, R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 9, 555–566 (2012).10.1038/nmeth.2015 ↗
2. Herr, A. E. Disruptive by design: a perspective on engineering in analytical chemistry. Anal. Chem. 85, 7622–7628 (2013).10.1021/ac4010887 ↗
3. Rusk, N. Disruptive nanopores. Nat. Methods 10, 35–35 (2013).10.1038/nmeth.2292 ↗
4. Sali, A., Glaeser, R., Earnest, T. & Baumeister, W. From words to literature in structural proteomics. Nature 422, 216–225 (2003).10.1038/nature01513 ↗
5. Oncley, J. L. The investigation of proteins by dielectric measurements. Chem. Rev. 30, 433–450 (1942).10.1021/cr60097a008 ↗
6. Felder, C. E., Prilusky, J., Silman, I. & Sussman, J. L. A server and database for dipole moments of proteins. Nucl. Acids Res. 35, W512–W521 (2007).10.1093/nar/gkm307 ↗
7. Singh, S., Yadav, S., Shire, S. & Kalonia, D. Dipole-dipole interaction in antibody solutions: correlation with viscosity behavior at high concentration. Pharm. Res. 31, 2549–2558 (2014).10.1007/s11095-014-1352-0 ↗
8. Mehl, J. W., Oncley, J. L. & Simha, R. Viscosity and the shape of protein molecules. Science 92, 132–133 (1940).10.1126/science.92.2380.132 ↗
9. Bonincontro, A. & Risuleo, G. Dielectric spectroscopy as a probe for the investigation of conformational properties of proteins. Spectrochim. Acta Part A 59, 2677–2684 (2003).10.1016/S1386-1425(03)00085-4 ↗
10. Howorka, S. & Siwy, Z. Nanopore analytics: sensing of single molecules. Chem. Soc. Rev. 38, 2360–2384 (2009).10.1039/b813796j ↗
11. Wei, R., Gatterdam, V., Wieneke, R., Tampe, R. & Rant, U. Stochastic sensing of proteins with receptor-modified solid-state nanopores. Nat. Nanotech. 7, 257–263 (2012).10.1038/nnano.2012.24 ↗
12. Qin, Z. P., Zhe, J. A. & Wang, G. X . Effects of particle's off-axis position, shape, orientation and entry position on resistance changes of micro Coulter counting devices. Meas. Sci. Technol. 22, 045804 (2011).10.1088/0957-0233/22/4/045804 ↗
13. Golibersuch, D. C. Observation of aspherical particle rotation in Poiseuille flow via the resistance pulse technique. Part 1. Application to human erythrocytes. Biophys. J. 13, 265–280 (1973).10.1016/S0006-3495(73)85984-3 ↗
14. Fologea, D., Ledden, B., David, S. M. & Li, J. Electrical characterization of protein molecules by a solid-state nanopore. Appl. Phys. Lett. 91, 053901 (2007).10.1063/1.2767206 ↗
15. Sexton, L. T. et al. Resistive-pulse studies of proteins and protein/antibody complexes using a conical nanotube sensor. J. Am. Chem. Soc. 129, 13144–13152 (2007).10.1021/ja0739943 ↗
16. Yusko, E. C. et al. Controlling protein translocation through nanopores with bio-inspired fluid walls. Nat. Nanotech. 6, 253–260 (2011).10.1038/nnano.2011.12 ↗
17. Robertson, J. W. F. et al. Single-molecule mass spectrometry in solution using a solitary nanopore. Proc. Natl Acad. Sci. USA 104, 8207–8211 (2007).10.1073/pnas.0611085104 ↗
18. Raillon, C. et al. Nanopore detection of single molecule RNAP-DNA transcription complex. Nano Lett. 12, 1157–1164 (2012).10.1021/nl3002827 ↗
19. Soni, G. V. & Dekker, C . Detection of nucleosomal substructures using solid-state nanopores. Nano Lett. 12, 3180–3186 (2012).10.1021/nl301163m ↗
20. Di Fiori, N. et al. Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores. Nat. Nanotech. 8, 946–951 (2013).10.1038/nnano.2013.221 ↗
21. Yusko, E. C. et al. Single-particle characterization of Aβ oligomers in solution. ACS Nano 6, 5909–5919 (2012).10.1021/nn300542q ↗
22. German, S. R., Hurd, T. S., White, H. S. & Mega, T. L. Sizing individual Au nanoparticles in solution with sub-nanometer resolution. ACS Nano 9, 7186–7194 (2015).10.1021/acsnano.5b01963 ↗
23. Nir, I., Huttner, D. & Meller, A. Direct sensing and discrimination among ubiquitin and ubiquitin chains using solid-state nanopores. Biophys. J. 108, 2340–2349 (2015).10.1016/j.bpj.2015.03.025 ↗
24. Stefureac, R. I., Kachayev, A. & Lee, J. S. Modulation of the translocation of peptides through nanopores by the application of an AC electric field. Chem. Commun. 48, 1928–1930 (2012).10.1039/c2cc17015a ↗
25. Li, J. et al. Ion-beam sculpting at nanometre length scales. Nature 412, 166–169 (2001).10.1038/35084037 ↗
26. DeBlois, R. W., Uzgiris, E. E., Cluxton, D. H. & Mazzone, H. M. Comparative measurements of size and polydispersity of several insect viruses. Anal. Biochem. 90, 273–288 (1978).10.1016/0003-2697(78)90032-5 ↗
27. Smythe, W. R. Flow around a spheroid in a circular tube. Phys. Fluids 7, 633–638 (1964).10.1063/1.1711260 ↗
28. Fricke, H. The electric permittivity of a dilute suspension of membrane-covered ellipsoids. J. Appl. Phys. 24, 644–646 (1953).10.1063/1.1721343 ↗
29. Velick, S. & Gorin, M. The electrical conductance of suspensions of ellipsoids and its relation to the study of avian erythrocytes. J. Gen. Physiol. 23, 753–771 (1940).10.1085/jgp.23.6.753 ↗
30. Plesa, C. et al. Fast translocation of proteins through solid state nanopores. Nano Lett. 13, 658–663 (2013).10.1021/nl3042678 ↗
31. Hernandez-Ainsa, S . et al. Lipid-coated nanocapillaries for DNA sensing. Analyst 138, 104–106 (2013).10.1039/C2AN36397F ↗
32. Woodside, M. T. et al. Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science 314, 1001–1004 (2006).10.1126/science.1133601 ↗
33. Deen, W. M. Hindered transport of large molecules in liquid-filled pores. AIChE J. 33, 1409–1425 (1987).10.1002/aic.690330902 ↗
34. Happel, J. & Brenner, H. Low Reynolds Number Hydrodynamics: With Special Applications to Particulate Media 1st edn (Springer, 1983).10.1007/978-94-009-8352-6 ↗
35. Yuan, Y. & Axelrod, D. Subnanosecond polarized fluorescence photobleaching: rotational diffusion of acetylcholine receptors on developing muscle cells. Biophys. J. 69, 690–700 (1995).10.1016/S0006-3495(95)79944-1 ↗
36. Li, W. et al. Single protein molecule detection by glass nanopores. ACS Nano 7, 4129–4134 (2013).10.1021/nn4004567 ↗
37. Kasianowicz, J. J., Brandin, E., Branton, D. & Deamer, D. W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl Acad. Sci. USA 93, 13770–13773 (1996).10.1073/pnas.93.24.13770 ↗
38. 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).10.1038/nbt.2171 ↗
39. Nivala, J., Marks, D. B. & Akeson, M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat. Biotechnol. 31, 247–250 (2013).10.1038/nbt.2503 ↗
40. Jijin, Y. et al. Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection. Nanotechnology 22, 285310 (2011).10.1088/0957-4484/22/28/285310 ↗
41. Rosenstein, J. K., Wanunu, M., Merchant, C. A., Drndic, M. & Shepard, K. L. Integrated nanopore sensing platform with sub-microsecond temporal resolution. Nat. Methods 9, 487–492 (2012).10.1038/nmeth.1932 ↗
42. Lee, M.-H. et al. A low-noise solid-state nanopore platform based on a highly insulating substrate. Sci. Rep. 4, 7448 (2014).
43. Uram, J. D., Ke, K. & Mayer, M. Noise and bandwidth of current recordings from submicrometer pores and nanopores. ACS Nano 2, 857–872 (2008).10.1021/nn700322m ↗
44. Ortega, A., Amoros, D. & Garcia de la Torre, J. Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models. Biophys. J. 101, 892–898 (2011).10.1016/j.bpj.2011.06.046 ↗
45. De Pascalis, A. R. et al. Binding of ferredoxin to ferredoxin: NADP+ oxidoreductase: the role of carboxyl groups, electrostatic surface potential, and molecular dipole moment. Protein Sci. 2, 1126–1135 (1993).10.1002/pro.5560020707 ↗
46. Pedone, D., Firnkes, M. & Rant, U. Data analysis of translocation events in nanopore experiments. Anal. Chem. 81, 9689–9694 (2009).10.1021/ac901877z ↗
47. Talaga, D. S. & Li, J. L. Single-molecule protein unfolding in solid state nanopores. J. Am. Chem. Soc. 131, 9287–9297 (2009).10.1021/ja901088b ↗