Nanopores pp 203-225 | Cite as

Nanopore Recordings to Quantify Activity-Related Properties of Proteins

  • Erik C. Yusko
  • Yazan N. Billeh
  • Jerry Yang
  • Michael Mayer
Chapter
First Online:

Abstract

Electrical current recordings through electrolyte-filled nanopores (so called resistive pulse-sensing experiments) are attracting increasing attention for identifying and characterizing biomolecules. The majority of the work employing this method so far has focused on detection of oligonucleotides, polymers, and viruses. Most recently nanopores have been used to detect single proteins. This chapter reviews the very first attempts to use nanopores for characterizing properties of proteins that relate to their activity. The emphasis lies on those studies that provided quantitative information on activity-related properties of proteins, such as protein conformation, ligand binding, and enzyme activity. Nanopore-based studies have tremendous potential for investigating the function of proteins because the technique is capable of interrogating individual proteins at high-throughput without requiring labeling.

Keywords

Protein Virus Nucleotide Polymer Protein conformation Protein volume Protein charge Electrophoretic mobility Drift velocity Isoelectric point Ligand affinity Stoichiometry Association constant Dissociation constant Kinetics On-rate Off-rate Binding isotherm Drug-protein interaction Bovine serum albumin Ovalbumin Avidin Streptavidin Antibody Immunoglobulin G Immunoglobulin E Antibody fab fragments Staphylococcal enterotoxin B β-Lactoglobulin E. coli maltose binding protein Lectin Carbonic anhydrase II Sulfonamide RNA aptamer Fibrinogen Poly (ethylene glycol) Biotin Ricin Enzyme activity Protease Phospholipase Membrane-active enzyme Catalytic rate constant Forward rate constant Michaelis constant Phospholipase C Phospholipase D Anthrax lethal factor Trypsin Alkaline phosphatase Amyloid-β Phosphatidylcholine Phosphatidylinositol α-hemolysin Gramicidin Alamethicin Resistive pulse Current blockage Translocation time Sojourn time Biosensing BLM Planar lipid bilayer 
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Notes

Acknowledgments

The authors acknowledge the following funding sources: National Institutes of Health (M.M., grant no. 1RO1GM081705), NSF Career Award (M.M., grant no. 0449088), AISIN/IMRA America Inc., and Thermo Fisher – CCG Collaborative Pilot Project Initiative.

References

  1. 1.
    Ali M, Schiedt B, Healy K et al. (2008) Modifying the surface charge of single track-etched conical nanopores in polyimide. Nanotechnology, 19: 085713CrossRefGoogle Scholar
  2. 2.
    Ali M, Yameen B, Neumann R et al. (2008) Biosensing and supramolecular bioconjugation in single conical polymer nanochannels. Facile incorporation of biorecognition elements into nanoconfined geometries. J. Am. Chem. Soc., 130: 16351–16357CrossRefGoogle Scholar
  3. 3.
    Blake S, Capone R, Mayer M et al. (2008) Chemically reactive derivatives of gramicidin a for developing ion channel-based nanoprobes. Bioconjug. Chem., 19: 1614–1624CrossRefGoogle Scholar
  4. 4.
    Capone R, Blake S, Restrepo M R et al. (2007) Designing nanosensors based on charged derivatives of gramicidin a. J. Am. Chem. Soc., 129: 9737–9745CrossRefGoogle Scholar
  5. 5.
    Chang H, Venkatesan B M, Iqbal S M et al. (2006) DNA counterion current and saturation examined by a mems-based solid state nanopore sensor. Biomed. Microdevices, 8: 263–269CrossRefGoogle Scholar
  6. 6.
    Chun K Y and Stroeve P (2002) Protein transport in nanoporous membranes modified with self-assembled monolayers of functionalized thiols. Langmuir, 18: 4653–4658CrossRefGoogle Scholar
  7. 7.
    Chun K Y, Mafe S, Ramirez P et al. (2006) Protein transport through gold-coated, charged nanopores: effects of applied voltage. Chem. Phys. Lett., 418: 561–564CrossRefGoogle Scholar
  8. 8.
    Clarke J, Wu H C, Jayasinghe L et al. (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol., 4: 265–270CrossRefGoogle Scholar
  9. 9.
    Cockroft S L, Chu J, Amorin M et al. (2008) A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution. J. Am. Chem. Soc., 130: 818–820CrossRefGoogle Scholar
  10. 10.
    Copeland R A (2000) Enzymes. John Wiley & Sons, New YorkCrossRefGoogle Scholar
  11. 11.
    DeBlois R W and Bean C P (1970) Counting and sizing of submicron particles by the resistive pulse technique. Rev. Sci. Instrum., 41: 909–916CrossRefGoogle Scholar
  12. 12.
    Ding S, Gao C L and Gu L Q (2009) Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore. Anal. Chem., 81: 6649–6655CrossRefGoogle Scholar
  13. 13.
    Fologea D, Ledden B, David S M et al. (2007) Electrical characterization of protein molecules by a solid-state nanopore. Appl. Phys. Lett., 91: 053901CrossRefGoogle Scholar
  14. 14.
    Hammann C H, Hamnett A and Vielstich W (1998) Electrochemistry. Wiley-VCH, New YorkGoogle Scholar
  15. 15.
    Han A, Creus M, Schurmann G et al. (2008) Label-free detection of single protein molecules and protein-protein interactions using synthetic nanopores. Anal. Chem., 80: 4651–4658CrossRefGoogle Scholar
  16. 16.
    Han A P, Schurmann G, Mondin G et al. (2006) Sensing protein molecules using nanofabricated pores. Appl. Phys. Lett., 88: 093901CrossRefGoogle Scholar
  17. 17.
    Hille B (2001) Ion channels of excitable membranes. Sinauer Associates, Inc., SunderlandGoogle Scholar
  18. 18.
    Hladky S B and Haydon D A (1970) Discreteness of conductance change in bimolecular lipid membranes in presence of certain antibiotics. Nature, 225: 451–453CrossRefGoogle Scholar
  19. 19.
    Hou X, Guo W, Xia F et al. (2009) A biomimetic potassium responsive nanochannel: G-quadruplex DNA conformational switching in a synthetic nanopore. J. Am. Chem. Soc., 131: 7800–7805CrossRefGoogle Scholar
  20. 20.
    Howorka S and Siwy Z (2009) Nanopore analytics: sensing of single molecules. Chem. Soc. Rev., 38: 2360–2384CrossRefGoogle Scholar
  21. 21.
    Howorka S, Nam J, Bayley H et al. (2004) Stochastic detection of monovalent and bivalent protein-ligand interactions. Angew. Chem. Int. Ed., 43: 842–846CrossRefGoogle Scholar
  22. 22.
    Howorka S, Movileanu L, Lu X et al. (2000) A protein pore with a single polymer chain tethered within the lumen. J. Am. Chem. Soc., 122: 2411–2416CrossRefGoogle Scholar
  23. 23.
    Jovanovic-Talisman T, Tetenbaum-Novatt J, McKenney A S et al. (2009) Artificial nanopores that mimic the transport selectivity of the nuclear pore complex. Nature, 457: 1023–1027CrossRefGoogle Scholar
  24. 24.
    Kasianowicz J J, Henrickson S E, Weetall H H et al. (2001) Simultaneous multianalyte detection with a nanometer-scale pore. Anal. Chem., 73: 2268–2272CrossRefGoogle Scholar
  25. 25.
    Ku J-R and Stroeve P (2004) Protein diffusion in charged nanotubes: “On-off” Behavior of molecular transport. Langmuir, 20: 2030–2032CrossRefGoogle Scholar
  26. 26.
    Laitinen O H, Hytonen V P, Nordlund H R et al. (2006) Genetically engineered avidins and streptavidins. Cell. Mol. Life Sci., 63: 2992–3017CrossRefGoogle Scholar
  27. 27.
    Macrae M X, Blake S, Jiang X et al. (2009) A semi-synthetic ion channel platform for detection of phosphatase and protease activity. ACS Nano, 3: 3567–3580CrossRefGoogle Scholar
  28. 28.
    Majd S, Yusko E C, MacBriar A D et al. (2009) Gramicidin pores report the activity of membrane-active enzymes. J. Am. Chem. Soc., 131: 16119–16126CrossRefGoogle Scholar
  29. 29.
    Majd M, Yusko E C, Billeh Y N et al. (2010) Applications of biological pores in nanomedicine, sensing and nanoelectronics. Curr. Opin. in Biotechnol., 21: 439–476Google Scholar
  30. 30.
    Makarov D E (2009) Computer simulations and theory of protein translocation. Acc. Chem. Res., 42: 281–289CrossRefGoogle Scholar
  31. 31.
    Maxwell J C (1904) Treatise on Electricity and Magnetism. 3 ed. Clarendon: Oxford. Vol 1Google Scholar
  32. 32.
    Mayer M, Semetey V, Gitlin I et al. (2008) Using ion channel-forming peptides to quantify protein-ligand interactions. J. Am. Chem. Soc., 130: 1453–1465CrossRefGoogle Scholar
  33. 33.
    Movileanu L, Howorka S, Braha O et al. (2000) Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore. Nat. Biotechnol., 18: 1091–1095CrossRefGoogle Scholar
  34. 34.
    Neher E and Sakmann B (1976) Single-channel currents recorded from membrane of denervated frog muscle-fibers. Nature, 260: 799–802CrossRefGoogle Scholar
  35. 35.
    Nelson D L and Cox M M (2008) Lehninger principles of biochemistry. W. H. Freeman and Company, New YorkGoogle Scholar
  36. 36.
    Oukhaled G, Mathe J, Biance A L et al. (2007) Unfolding of proteins and long transient conformations detected by single nanopore recording. Phys. Rev. Lett., 98: 158101CrossRefGoogle Scholar
  37. 37.
    Rokitskaya T I, Antonenko Y N and Kotova E A (1996) Photodynamic inactivation of gramicidin channels: a flash-photolysis study. Biochim. Biophys. Acta Bioenerg., 1275: 221–226CrossRefGoogle Scholar
  38. 38.
    Saleh O A and Sohn L L (2003) Direct detection of antibody-antigen binding using an on-chip artificial pore. Proc. Natl. Acad. Sci. U.S.A., 100: 820–824CrossRefGoogle Scholar
  39. 39.
    Schneider S W, Larmer J, Henderson R M et al. (1998) Molecular weights of individual proteins correlate with molecular volumes measured by atomic force microscopy. Pflugers Arch., 435: 362–367CrossRefGoogle Scholar
  40. 40.
    Sexton L T, Horne L P, Sherrill S A et al. (2007) Resistive-pulse studies of proteins and protein/antibody complexes using a conical nanotube sensor. J. Am. Chem. Soc., 129: 13144–13152CrossRefGoogle Scholar
  41. 41.
    Siwy Z, Heins E, Harrell C C et al. (2004) Conical-nanotube ion-current rectifiers: the role of surface charge. J. Am. Chem. Soc., 126: 10850–10851CrossRefGoogle Scholar
  42. 42.
    Siwy Z, Gu Y, Spohr H A et al. (2002) Rectification and voltage gating of ion currents in a nanofabricated pore. Europhys. Lett., 60: 349–355CrossRefGoogle Scholar
  43. 43.
    Siwy Z S (2006) Ion-current rectification in nanopores and nanotubes with broken symmetry. Adv. Funct. Mater., 16: 735–746CrossRefGoogle Scholar
  44. 44.
    Smeets R M M, Keyser U F, Krapf D et al. (2006) Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett., 6: 89–95CrossRefGoogle Scholar
  45. 45.
    Storm A J, Storm C, Chen J H et al. (2005) Fast DNA translocation through a solid-state nanopore. Nano Lett., 5: 1193–1197CrossRefGoogle Scholar
  46. 46.
    Talaga D S and Li J L (2009) Single-molecule protein unfolding in solid state nanopores. J. Am. Chem. Soc., 131: 9287–9297CrossRefGoogle Scholar
  47. 47.
    Uram J D and Mayer M (2007) Estimation of solid phase affinity constants using resistive-pulses from functionalized nanoparticles. Biosens. Bioelectron., 22: 1556–1560CrossRefGoogle Scholar
  48. 48.
    Uram J D, Ke K and Mayer M (2008) Noise and bandwidth of current recordings from submicrometer pores and nanopores. ACS Nano., 2: 857–872CrossRefGoogle Scholar
  49. 49.
    Uram J D, Ke K, Hunt A J et al. (2006) Label-free affinity assays by rapid detection of immune complexes in submicrometer pores. Angew. Chem. Int. Ed., 45: 2281–2285CrossRefGoogle Scholar
  50. 50.
    Uram J D, Ke K, Hunt A J et al. (2006) Submicrometer pore-based characterization and quantification of antibody-virus interactions. Small, 2: 967–972CrossRefGoogle Scholar
  51. 51.
    Vlassiouk I, Kozel T R and Siwy Z S (2009) Biosensing with nanofluidic diodes. J. Am. Chem. Soc., 131: 8211–8220CrossRefGoogle Scholar
  52. 52.
    Yameen B, Ali M, Neumann R et al. (2009) Synthetic proton-gated ion channels via single solid-state nanochannels modified with responsive polymer brushes. Nano Lett., 9: 2788–2793CrossRefGoogle Scholar
  53. 53.
    Yusko E C, An R and Mayer M (2010) Electroosmotic flow can generate ion current rectification in nano- and micropores. ACS Nano., 4: 477–487Google Scholar
  54. 54.
    Yusko E C, Johnson J M, Majd S et al. (2011) Controlling protein translocation through nanopores with bio-inspired fluid walls. Nature Nanotech., 6: 254–260Google Scholar
  55. 55.
    Zhao Q T, de Zoysa R S S, Wang D Q et al. (2009) Real-time monitoring of peptide cleavage using a nanopore probe. J. Am. Chem. Soc., 131: 6324–6325CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Erik C. Yusko
  • Yazan N. Billeh
  • Jerry Yang
  • Michael Mayer
    • 1
  1. 1.Department of Biomedical EngineeringUniversity of MichiganAnn ArborUSA

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