Skip to main content
Disciplines
Automotive Business IT + Informatics Construction + Real Estate Electrical Engineering + Electronics Energy + Sustainability Insurance + Risk Finance + Banking Management + Leadership Marketing + Sales Mechanical Engineering + Materials
Events
DE
EN
Books
Journals
Topic Page
Marketing
Start single access now
Access for companies
EXTENDED SEARCH
Log in
Top
Published in:
Solid-State Nanopore Sensors for Nucleic Acid Analysis Read chapter Read first chapter

2011 | OriginalPaper | Chapter

6. Sensing Single Protein Molecules with Solid-State Nanopores

Authors : Bradley Ledden, Daniel Fologea, David S. Talaga, Jiali Li

Published in: Nanopores

Publisher: Springer US

Log in

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

This chapter is focused on the development of experiments and theory of using solid-state nanopores for sensing single protein molecules in their native and unfolded states. Proteins serve diverse roles such as transport carriers, catalysts, molecular motors, cellular structural support, and others that make life possible. Because of these widely differing roles, proteins have an enormously diverse set of shapes, sizes, and charge structures as compared to polynucleic acids. Solid-state nanopores are particularly suitable for characterizing single protein molecules because they can be fabricated with adjustable dimensions and are stable under conditions that denature proteins. This chapter describes the nanopore experimental setup, signal recording, data analysis, and basic principles related to the experiments and the theory connecting the electrical signal with the properties of proteins. Examples of experimental results illustrate the ability of solid-state nanopores to differentiate proteins in their folded and unfolded states. Native-state protein nanopore translocation follows biased one-dimensional diffusion of charged particles that is sensitive to size and electrical charge. Due to the heterogeneous charge sequence of polypeptides, unfolded proteins obey a coupled electrophoretic and thermally activated process that is sequence specific. The chapter concludes with a discussion of future directions and open challenges for single protein characterization using solid-state nanopores.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

inform now
previous chapter Solid State Nanopores for Selective Sensing of DNA
next chapter Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane
Literature
1.
Rapoport, T.A., Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature, 2007. 450(29): p. 663–669.CrossRef
2.
Wickner, W. and R. Schekman, Protein Translocation Across Biological Membranes. Science, 2005. 310(5753): p. 1452–1456.CrossRef
3.
Simon, S.M. and G. Blobel, A protein-conducting channel in the endoplasmic reticulum. 1991. 65(3): p. 371–380.
4.
Sutherland, T.C., Y.-T. Long, R.-l. Stefureac, I. Bediako-Amoa, H.-B. Kraatz and J.S. Lee, Structure of Peptides Investigated by Nanopore Analysis. Nano Lett, 2004. 4(7): p. 1273–1277.CrossRef
5.
Stefureac, R., L. Waldner, P. Howard and J.S. Lee, Nanopore Analysis of a Small 86-Residue Protein. Small, 2008. 4(1): p. 59–63CrossRef
6.
Oukhaled, G., J. Mathe, A.L. Biance, L. Bacri, J.M. Betton, D. Lairez, J. Pelta and L. Auvray, Unfolding of Proteins and Long Transient Conformations Detected by Single Nanopore Recording. Physical Review Letters, 2007. 98(15): p. 158101–4CrossRef
7.
Pastoriza-Gallego, G.G. M., B. Thiebot, J.-M. Betton and J. Pelta, Polyelectrolyte and unfolded protein pore entrance depends on the pore geometry. Biochimica et Biophysica Acta - Biomembranes 2009. 1788: p. 1377–1386.CrossRef
8.
Mohammad, S. Prakash, A. Matouschek and L. Movileanu, Controlling a Single Protein in a Nanopore through Electrostatic Traps. Journal of the American Chemical Society, 2008. 130(12): p. 4081–4088.CrossRef
9.
Movileanu, L., S. Howorka, O. Braha and H. Bayley, Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore. Nat Biotech, 2000. 18(10): p. 1091–1095.CrossRef
10.
Han, A., G. Schurman, G. Mondin, R.A. Bitterli, N.G. Hegelbach, N.F. de Rooij and U. Staufer, Sensing protein molecules using nanofabricated pores. APPLIED PHYSICS LETTER, 2006. 88: p. 093901–3.CrossRef
11.
Han, A., M. Creus, G. Schurmann, V. Linder, T.R. Ward, N.F. de Rooij and U. Staufer, Label-Free Detection of Single Protein Molecules and Protein−Protein Interactions Using Synthetic Nanopores. Analytical Chemistry, 2008. 80(12): p. 4651–4658%U http://​dx.​doi.​org/​10.​1021/​ac7025207.
12.
Fologea, D., B. Ledden, D.S. McNabb and J. Li, Electrical Characterization of Protein Molecules by a Solid-State Nanopore. APPLIED PHYSICS LETTERS, 2007. 91.
13.
Talaga, D.S. and J. Li, Single-Molecule Protein Unfolding in Solid State Nanopores. Journal of American Chemical Society, 2009. 131(26): p. 9287–9297.CrossRef
14.
Firnkes, M., D. Pedone, J. Knezevic, M. Döblinger and U. Rant, Electrically Facilitated Translocations of Proteins through Silicon Nitride Nanopores: Conjoint and Competitive Action of Diffusion, Electrophoresis, and Electroosmosis. Nano Letters, 2010. 10(6): p. 2162–2167.
15.
Niedzwiecki, D.J., J. Grazul and L. Movileanu, Single-Molecule Observation of Protein Adsorption onto an Inorganic Surface. Journal of the American Chemical Society, 2010. 132(31): p. 10816–10822.CrossRef
16.
Li, J., M. Gershow, D. Stein, E. Brandin and J.A. Golovchenko, DNA Molecules and Configurations in a Solid-state Nanopore Microscope. Nat. Mater., 2003. 2: p. 611–615.CrossRef
17.
Bezrukov, S.M., Ion Channels as Molecular Coulter Counters to Probe Metabolite Transport. Journal of Membrane Biology, 2000. 174(1): p. 1–13.CrossRefMathSciNet
18.
DeBlois, R.W. and C.P. Bean, Counting and Sizing of Submicron Particles by the Resistive Pulse Technique. Review of Scientific Instruments, 1970. 41(7): p. 909.CrossRef
19.
Gregg, E.C. and k.D. Steidley, Electrical Counting and Sizing of Mammalian Cells in Suspension. Biophysical Journal, 1965. 5(4): p. 393–405.
20.
Henriquez, R.R., T. Ito, L. Sun and R.M. Crooks, The resurgence of Coulter counting for analyzing nanoscale objects. The Analyst, 2004. 2004(129): p. 478–482.CrossRef
21.
Smeets, R.M., U.F. Keyser, D. Krapf, M.-Y. Wu, D. Nynke H and C. Dekker, Salt Dependence of Ion Transport and DNA Translocation through Solid-state nanopores. Nano Lett., 2006. 6(1): p. 89–95.CrossRef
22.
King, G.M. and J.A. Golovchenko, Probing Nanotube-Nanopore Interactions. Physical Review Letters, 2005. 95(21): p. 216103.CrossRef
23.
Levadny, V., V.M. Aguilella and M. Belaya, Access resistance of a single conducting membrane channel. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1998. 1368(2): p. 338–342.
24.
Vodyanoy, I. and S.M. Bezrukov, Sizing of an ion pore by access resistance measurements. Biophysical Journal, 1992. 62(1): p. 10–11.CrossRef
25.
Dekker, C., Solid-state nanopores. Nature Nanotechnology, 2007. 2: p. 209–215.
26.
Healy, K., B. Schiedt and A.P. Morrison, Solid-state nanopore technologies for nanopore-based DNA analysis. Nanomedicine, 2007. 2(6): p. 875–897.CrossRef
27.
Li, J., D. Stein, C. McMullan, D. Branton, M.J. Aziz and J.A. Golovchenko, Ion-beam sculpting at nanometre length scales. Nature, 2001. 412(12 July): p. 166–169.
28.
Gierhart, B.C., D.G. Howitt, S.J. Chen, Z. Zhu, D.E. Kotecki, R.L. Smith and S.D. Collins, Nanopore with Transverse Nanoelectrodes for Electrical Characterization and Sequencing of DNA, in The 14th International Conference on Solid-State Sensors, Actuators and Microsystems. 2007, Transducers & Eurosensors: Lyon, France.
29.
Stein, D., J. Li and J.A. Golovchenko, Ion-Beam Sculpting Time Scales. Physical Review Letters, 2002. 89(27).
30.
Storm, A.J., J.H. Chen, X.S. Ling, H.W. Zandbergen and C. Dekker, Fabrication of solid-state nanopores with single-nanometre precision. Nature Materials, 2003. 2: p. 537–540.CrossRef
31.
Venkatesan, B.M., B. Dorvel, S. Yemenicioglu, N. Watkins, I. Petrov and R. Bashir, Highly Sensitive, Mechanically Stable Nanopore Sensors for DNA Analysis. Adv. Mater., 2009. 21: p. 1–6.
32.
Venkatesan, B.M., A.B. Shah, J.-M. Zuo and R. Bashir, DNA Sensing Using Nanocrystalline Surface-Enhanced Al2O3 Nanopore Sensors. Adv. Funct. Mater., 2010. 20: p. 1266–1275.CrossRef
33.
Stein, D.M., C.J. McMullan, J. Li and J.A. Golovchenko, Feedback-controlled ion beam sculpting apparatus. Review of Scientific Instruments, 2004. 75(4): p. 900–905.CrossRef
34.
Cai, Ledden, Krueger, Golovchenko and Li, Nanopore sculpting with noble gas ions. Journal of Applied Physics, 2006. 100.
35.
Talaga, D. and J. Li, Single-molecule protein unfolding in solid state nanopores. J. Am. Chem. Soc., 2009. 131: p. 9287–9297.CrossRef
36.
Fologea, D., B. Ledden, D.S. McNabb and J. Li, Electrical Characterization of Protein Molecules in a Solid-State Nanopore. Appl. Phys. Lett., 2007. 91.
37.
Peters, T., Jr., Serum Albumin. Adv. Protein Chem., 1985. 37: p. 161–245.
38.
Collins, B.E., K.-P.S. Dancil, G. Abbi and M.J. Sailor, Determining Protein Size Using an Electrochemically Machined Pore Gradient in Silicon. Advanced Functional Material, 2002. 12 (3): p. 187–191.CrossRef
39.
Bloomfield, V., The Structure of Bovine Serum Albumin at Low pH. Biochemistry, 1966. 5(2): p. 684–689.CrossRef
40.
Kramers, H.A., Brownian motion in a field of force and the diffusion model of chemical reactions. Physica (Utrecht), 1940. 7: p. 284–304.
41.
Cotton, F.A., J. Edward E. Hazen and M.J. Legg, Staphylococcal nuclease: Proposed mechanism of action based on structure of enzyme—thymidine 3′,5′-bisphosphate—calcium ion complex at 1.5-Å resolution Proc. Nati. Acad. Sci. USA, 1979. 76(6): p. 2551–2555.
42.
Tucker, P.W., E.E. Hazen and F.A. Cotton, Staphylococcal nuclease reviewed: A prototypic study in contemporary enzymology Molecular and Cellular Biochemistry, 1979. 23(3).
Metadata
Title
Sensing Single Protein Molecules with Solid-State Nanopores
Authors
Bradley Ledden
Daniel Fologea
David S. Talaga
Jiali Li
Copyright Year
2011
Publisher
Springer US
Book
Nanopores

Print ISBN: 978-1-4419-8251-3

Electronic ISBN: 978-1-4419-8252-0

Copyright Year: 2011

DOI
https://doi.org/10.1007/978-1-4419-8252-0_6