Skip to main content

Part of the book series: Integrated Analytical Systems ((ANASYS))

  • 974 Accesses

Abstract

Various combinatorial libraries were screened for short peptides of 4–10 mer, which were used as sensor molecules for capturing target chemicals or biomolecules. Immuno-antibodies can be synthesized in the living bodies of higher animals even for low-molecular-weight nonnatural chemical compounds, such as dioxins or PCBs. Recently, some peptide ligands that can even bind to inorganic crystals have been reported. This indicates that the 20 natural amino acids have the potential to recognize almost all types of molecules and substances. The question arises whether one should design a “rational” mini library of peptides consisting of a limited number of amino acids according to the motifs in epitopes or paratopes or the binding pocket sequences in receptors, or a completely “random” combinatorial library containing all sequences. If one wants to obtain a peptide binder to target a small chemical compound, the answer is a “random” library, since the molecular interaction between the target compound and an amino acid cannot be precisely predicted beforehand. In this section, we discuss the possibility of using short combinatorial peptides as binders for biosensors to detect chemical compounds.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Morita, Y.; Ohsugi, T.; Iwasa, Y.; Tamiya, E., A screening of phage displayed peptides for the recognition of fullerene (c60). J. Mol. Catal. B: Enzym. 2004, 28, 185–190

    Article  CAS  Google Scholar 

  2. Sano, K.; Shiba, K., A hexapeptide motif that electrostatically binds to the surface of titanium. J. Am. Chem. Soc. 2003, 125, 14234–14235

    Article  CAS  Google Scholar 

  3. Su, Z.; Leung, T.; Honek, J. F., Conformational selectivity of peptides for single-walled carbon nanotubes. J. Phys. Chem. B Condens. Matter. Mater. Surf. Interfaces Biophys. 2006, 110, 23623–23627

    CAS  Google Scholar 

  4. Wang, G.; De, J.; Schoeniger, J.; Roe, D.; Carbonell, R., A hexamer peptide ligand that binds selectively to staphylococcal enterotoxin b: Isolation from a solid phase combinatorial library. J. Pept. Res. 2004, 64, 51–64.

    Article  CAS  Google Scholar 

  5. Mascini, M.; Macagnano, A.; Monti, D.; Del Carlo, M.; Paolesse, R.; Chen, B.; Warner, P.; D’Amico, A.; Di Natale, C.; Compagnone, D., Piezoelectric sensors for dioxins: A biomimetic approach. Biosens. Bioelectron. 2004, 20, 1203–1210

    Article  CAS  Google Scholar 

  6. Boon, C. L.; Frost, D.; Chakrabartty, A., Identification of stable helical bundles from a combinatorial library of amphipathic peptides. Biopolymers 2004, 76, 244–257

    Article  CAS  Google Scholar 

  7. Obataya, I.; Kotaki, T.; Sakamoto, S.; Ueno, A.; Mihara, H., Design, synthesis and peroxidase-like activity of 3alpha-helix proteins covalently bound to heme. Bioorg. Med. Chem. Lett. 2000, 10, 2719–2722

    Article  CAS  Google Scholar 

  8. Obataya, I.; Sakamoto, S.; Ueno, A.; Mihara, H., Design and synthesis of 3alpha-helix peptides forming a cavity for a fluorescent ligand. Biopolymers 2001, 59, 65–71

    Article  CAS  Google Scholar 

  9. Fukumori, T.; Morita, Y.; Tamiya, E.; Yokoyama, K., Design of peptide that recognizes double-stranded DNA. Anal. Sci. 2003, 19, 181–183

    Article  CAS  Google Scholar 

  10. Meyer, S. C.; Gaj, T.; Ghosh, I., Highly selective cyclic peptide ligands for neutravidin and avidin identified by phage display. Chem. Biol. Drug. Des. 2006, 68, 3–10

    Article  CAS  Google Scholar 

  11. Qin, C.; Bu, X.; Zhong, X.; Ng, N. L.; Guo, Z., Optimization of antibacterial cyclic decapeptides. J. Comb. Chem. 2004, 6, 398–406

    Article  CAS  Google Scholar 

  12. Fink, A. L., Natively unfolded proteins. Curr. Opin. Struct. Biol. 2005, 15, 35–41

    Article  CAS  Google Scholar 

  13. Kawakami, J.; Kitano, T.; Sugimoto, N., A selection of short peptides that interact with a porphyrin as a small target by immobilized phage display. Chem. Commun. 1999, 1765–1766

    Google Scholar 

  14. Karlsson, R.; Stahlberg, R., Surface plasmon resonance detection and multispot sensing for direct monitoring of interactions involving low-molecular-weight analytes and for determination of low affinities. Anal. Biochem. 1995, 228, 274–280

    Article  CAS  Google Scholar 

  15. Nakamura, C.; Inuyama, Y.; Shirai, K.; Nakano, S.; Sugimoto, N.; Miyake, J., Analysis for peptide binding to porphyrin using surface plasmon resonance. Synthetic Met. 2001, 117, 127–129

    Article  CAS  Google Scholar 

  16. Nakamura, C.; Inuyama, Y.; Shirai, K.; Sugimoto, N.; Miyake, J., Detection of porphyrin using a short peptide immobilized on a surface plasmon resonance sensor chip. Biosens. Bioelectron 2001, 16, 1095–1100

    Article  CAS  Google Scholar 

  17. Kanazawa, K.; Gordon, J. G., The oscillation frequency of a quartz resonator in contact with liquid. Anal. Chem. Acta 1985, 175, 99–105

    Article  CAS  Google Scholar 

  18. Nakamura, C.; Song, S.-H.; Chang, S.-M.; Sugimoto, N.; Miyake, J., Quartz crystal microbalance sensor targeting low molecular weight compounds using oligopeptide binder and peptide-immobilized latex beads. J. Anal. Chim. Acta. 2002, 469, 183–188

    Article  CAS  Google Scholar 

  19. Sugimoto, N.; Nakano, S., Sandwiching interaction of peptides with a porphyrin. Chem. Lett. 1997, 939–940

    Google Scholar 

  20. Grandbois, M.; Beyer, M.; Rief, M.; Clausen-Schaumann, H.; Gaub, H. E., How strong is a covalent bond? Science 1999, 283, 1727

    Article  CAS  Google Scholar 

  21. Florin, E. L.; Moy, V. T.; Gaub, H. E., Adhesion forces between individual ligand-recepter pairs. Science 1994, 264, 415–417

    Article  CAS  Google Scholar 

  22. Yuan, C.; Chen, A.; Kolb, P.; Moy, V., Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy. Biochemistry 2000, 39, 10219–10223

    Article  CAS  Google Scholar 

  23. Nakamura, C.; Takeda, S.; Kageshima, M.; Ito, M.; Sugimoto, N.; Sekizawa, K.; Miyake, J., Mechanical force analysis of peptide interactions using atomic force microscopy. Biopolymers. 2004, 76, 48–54

    Article  CAS  Google Scholar 

  24. Solomon, K.; Bake, D. B.; Richards, R. P.; Dixon, K. R.; Klaine, S. J.; Point, T. W. L.; Kendall, R. J.; Weisskopf, C. P.; Giddings, J. M., About atrazine. Environ. Toxicol. Chem. 1997, 15, 31–76

    Article  Google Scholar 

  25. Wauchope, R. D.; Buttler, T. M.; Hornsby, A. G.; Augustijn-Beckers, P. M. W.; Burt, J. P., Scs/ ars/ces pesticide properties database for environmental decision making. Rev. Environ. Contam. Toxicol. 1992, 123, 1–157

    CAS  Google Scholar 

  26. Taets, C.; Aref, S.; Rayburn, A. L., The clastogenic potential of triazine herbicide combinations found in potable water supplies. Environ. Health Perspect 1998, 106, 197–201

    CAS  Google Scholar 

  27. Sathiakumar, N.; Delzell, E., A review of epidemic studies of triazine herbicides and cancer. Crit. Rev. Toxicol. 1997, 27, 599–612

    Article  CAS  Google Scholar 

  28. Van Leeuwen, J. A.; Waltner-Toews, D.; Abernathy, T.; Smit, B.; Shoukri, M., Associations between stomach cancer incidence and drinking water contamination with atrazine and nitrate in ontario (canada) agroecosystems, 1987–1991. Int. J. Epidemiol. 1999, 28, 836–840

    Article  Google Scholar 

  29. Chan, W. C.; White, P. D.; Chan, W. C. White, P. D. ed.; Oxford University Press: New York, NY, 2000, pp 41–7630.

    Google Scholar 

  30. Eisenberg, D.; Schwarz, E.; Komarony, M.; Wall, R., Amino acid scale: Normalized consensus hydrophobicity scale. J. Mol. Biol. 1984, 179, 125–142.

    Article  CAS  Google Scholar 

  31. Obataya, I.; Nakamura, C.; Enomoto, H.; Hoshino, T.; Nakamura, N.; Miyake, J., Development of a herbicide biosensor using a peptide receptor screened from a combinatorial library. J. Mol. Catal. B: Enzym 2004, 28, 265–271

    Article  CAS  Google Scholar 

  32. Shan, G.; Leeman, W. R.; Gee, S. J.; Sanborn, J. R.; Jones, A. D.; Chang, D. P. Y.; Hammock, B. D., Highly sensitive dioxin immunoassay and its application to soil and biota samples. Anal. Chim. Acta. 2001, 444, 169–178

    Article  CAS  Google Scholar 

  33. Morita, Y.; Murakami, Y.; Yokoyama, K.; Tamiya, E., Synthesis and analysis of peptide ligand for biosensor application using combinatorial chemistry. Biol. Sys. Eng. 2002, (ACS Symposium Series 830), 210–219

    Google Scholar 

  34. Nakamura, C.; Inuyama, Y.; Goto, H.; Obataya, I.; Kaneko, N.; Nakamura, N.; Santo, N.; Miyake, J., Dioxin-binding pentapeptide for use in a high-sensitivity on-bead detection assay. Anal. Chem. 2005, 77, 7750–7757

    Article  CAS  Google Scholar 

  35. Inuyama, Y.; Nakamura, C.; Oka, T.; Yoneda, Y.; Obataya, I.; Santo, N.; Miyake, J., Simple and high-sensitivity detection of dioxin using dioxin-binding pentapeptide., Biosens. Bioelectron. 2007, 22, 2093–2099

    Article  CAS  Google Scholar 

  36. O’Shannessy, D. J.; Brigham-Burke, M.; K., S. K.; Hensley, P.; Brooks, I., Determination of rate and equilibrium binding constants for macromolecular interactions using surface plasmon resonance: Use of nonlinear least squares analysis methods. Anal. Biochem. 1993, 212, 457–468

    Article  Google Scholar 

  37. Roy, S.; Mysior, P.; Brzezinski, R., Comparison of dioxin and furan teq determination in contaminated soil using chemical, micro-erod, and immunoassay analysis., Chemosphere 2002, 48, 833–842

    Article  CAS  Google Scholar 

  38. Shimomura, M.; Nomura, Y.; Lee, K. H.; Ikebukuro, K.; Karube, I., Dioxin detection based on immunoassay using a polyclonal antibody against octa-chlorinated dibenzo-p-dioxin (ocdd). Analyst 2001, 126, 1207–1209

    Article  CAS  Google Scholar 

  39. Kobayashi, S.; Kitadai, M.; Sameshima, K.; Ishii, Y.; Tanaka, A., A theoretical investigation of the conformation changing of dioxins in binding site of dioxin receptor model; role of absolute hardness-electronegativity diagrams for biological activity. J. Mol. Struct. 1999, 475, 203–217

    Article  CAS  Google Scholar 

  40. Procopio, M.; Lahm, A.; Tramontano, A.; Bonati, L.; Pitea, D., A model for recognition of polychlorinated dibenzo-p-dioxins by the aryl hydrocarbon receptor. Eur. J. Biochem. 2002, 269, 13–18

    Article  CAS  Google Scholar 

  41. Recinos, A., III; Silvey, K. J.; Ow, D. J.; Jensen, R. H.; Stanker, L. H., Sequences of cDNAs encoding immunoglobulin heavy- and light-chain variable regions from two anti-dioxin monoclonal antibodies. Gene 1994, 149, 385–386

    Article  CAS  Google Scholar 

  42. Takahashi, M.; Nokihara, K.; Mihara, H., Construction of a protein-detection system using a loop peptide library with a fluorescence label. Chem. Biol. 2003, 10, 53–60

    Article  CAS  Google Scholar 

  43. Wenschuh, H.; Volkmer-Engert, R.; Schmidt, M.; Schulz, M.; Schneider-Mergener, J.; Reineke, U., Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides. Biopolym. (Peptide Sci.) 2000, 55, 188–206

    Article  CAS  Google Scholar 

  44. Tseng, M. C.; Chu, Y. H., Using surface plasmon resonance to directly identify molecules in a tripeptide library that bind tightly to a vancomycin chip. Anal. Biochem. 2005, 336, 172–177

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Chikashi Nakamura .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science + Business Media, LLC

About this chapter

Cite this chapter

Nakamura, C., Miyake, J. (2009). Combinatorially Developed Peptide Receptors for Biosensors. In: Potyrailo, R.A., Mirsky, V.M. (eds) Combinatorial Methods for Chemical and Biological Sensors. Integrated Analytical Systems. Springer, New York, NY. https://doi.org/10.1007/978-0-387-73713-3_8

Download citation

Publish with us

Policies and ethics