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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Rapoport, T.A., Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature, 2007. 450(29): p. 663–669.
Wickner, W. and R. Schekman, Protein Translocation Across Biological Membranes. Science, 2005. 310(5753): p. 1452–1456.
Simon, S.M. and G. Blobel, A protein-conducting channel in the endoplasmic reticulum. 1991. 65(3): p. 371–380.
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.
Stefureac, R., L. Waldner, P. Howard and J.S. Lee, Nanopore Analysis of a Small 86-Residue Protein. Small, 2008. 4(1): p. 59–63
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. 158101–4
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Bezrukov, S.M., Ion Channels as Molecular Coulter Counters to Probe Metabolite Transport. Journal of Membrane Biology, 2000. 174(1): p. 1–13.
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.
Gregg, E.C. and k.D. Steidley, Electrical Counting and Sizing of Mammalian Cells in Suspension. Biophysical Journal, 1965. 5(4): p. 393–405.
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.
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.
King, G.M. and J.A. Golovchenko, Probing Nanotube-Nanopore Interactions. Physical Review Letters, 2005. 95(21): p. 216103.
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.
Vodyanoy, I. and S.M. Bezrukov, Sizing of an ion pore by access resistance measurements. Biophysical Journal, 1992. 62(1): p. 10–11.
Dekker, C., Solid-state nanopores. Nature Nanotechnology, 2007. 2: p. 209–215.
Healy, K., B. Schiedt and A.P. Morrison, Solid-state nanopore technologies for nanopore-based DNA analysis. Nanomedicine, 2007. 2(6): p. 875–897.
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.
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.
Stein, D., J. Li and J.A. Golovchenko, Ion-Beam Sculpting Time Scales. Physical Review Letters, 2002. 89(27).
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.
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.
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.
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.
Cai, Ledden, Krueger, Golovchenko and Li, Nanopore sculpting with noble gas ions. Journal of Applied Physics, 2006. 100.
Talaga, D. and J. Li, Single-molecule protein unfolding in solid state nanopores. J. Am. Chem. Soc., 2009. 131: p. 9287–9297.
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.
Peters, T., Jr., Serum Albumin. Adv. Protein Chem., 1985. 37: p. 161–245.
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.
Bloomfield, V., The Structure of Bovine Serum Albumin at Low pH. Biochemistry, 1966. 5(2): p. 684–689.
Kramers, H.A., Brownian motion in a field of force and the diffusion model of chemical reactions. Physica (Utrecht), 1940. 7: p. 284–304.
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.
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).
Acknowledgments
We thank Professor J. Golovchenko and Harvard nanopore group for nanopore fabrication, Ryan Rollings, Edward W. Graef Jr., Denis F. Tita, and Errol Porter for nanopore fabrication and characterization. We acknowledge the funding support provided by NHGRI/NIH R21HG003290, NHGRI/NIH R21HG00477, NSF/MRSEC 080054, ABI-111/710, and NIH R01GM071684 to DST.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Ledden, B., Fologea, D., Talaga, D.S., Li, J. (2011). Sensing Single Protein Molecules with Solid-State Nanopores. In: Iqbal, S., Bashir, R. (eds) Nanopores. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-8252-0_6
Download citation
DOI: https://doi.org/10.1007/978-1-4419-8252-0_6
Published:
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4419-8251-3
Online ISBN: 978-1-4419-8252-0
eBook Packages: EngineeringEngineering (R0)