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Protein Engineering and Electrochemical Biosensors

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Part of the Advances in Biochemical Engineering/Biotechnology book series (ABE, volume 109)

Abstract

Protein engineered biosensors provide the next best step in the advancement of protein-based sensors that can specifically identify chemical substrates. The use of native proteins for this purpose cannot adequately embrace the limits of detection and level of stability required for a usable sensor, due to globular structure restraints. This review chapter attempts to give an accurate representation of the three main strategies employed in the engineering of more suitable biological components for use in biosensor construction.

The three main strategies in protein engineering for electrochemical biosensor implementation are: rational protein design, directed evolution and de novo protein design. Each design strategy has limitations to its use in a biosensor format and has advantages and disadvantages with respect to each. The three design techniques are used to modify aspects of stability, sensitivity, selectivity, surface tethering, and signal transduction within the biological environment.

Furthermore with the advent of new nanomaterials the implementation of these design strategies, with the attomolar promise of nanostructures, imparts important generational leaps in research for biosensor construction, based on highly specific, very robust, and electrically wired protein engineered biosensors.

Keywords

Gold Electrode Direct Evolution Protein Engineering Direct Electron Transfer Maltose Binding Protein 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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References

  1. 1.
    Marvin JS, Hellinga HW (1998) Engineering Biosensors by Introducing Fluorescent Allosteric Signal Transducers: Construction of a Novel Glucose Sensor. J Am Chem Soc 120(1):7–11 CrossRefGoogle Scholar
  2. 2.
    O'Fagain C (2003) Enzyme stabilization – recent experimental progress. Enzyme Microb Technol 33(2–3):137–149 CrossRefGoogle Scholar
  3. 3.
    Mezzasalma TM et al (2007) Enhancing Recombinant Protein Quality and Yield by Protein Stability Profiling. J Biomol Screen 12(3):418–428 CrossRefGoogle Scholar
  4. 4.
    Matthews BW, Nicholson H, Becktel WJ (1987) Enhanced Protein Thermostability from Site-Directed Mutations that Decrease the Entropy of Unfolding. PNAS 84(19):6663–6667 CrossRefGoogle Scholar
  5. 5.
    Sode K et al (2000) Increasing the thermal stability of the water-soluble pyrroloquinoline quinone glucose dehydrogenase by single amino acid replacement. Enzyme Microb Technol 26(7):491–496 CrossRefGoogle Scholar
  6. 6.
    Minagawa H, Shimada J, Kaneko H (2003) Effect of mutations at Glu160 and Val198 on the thermostability of lactate oxidase. Eur J Biochem 270(17):3628–3633 CrossRefGoogle Scholar
  7. 7.
    Wise KJ et al (2002) Optimization of bacteriorhodopsin for bioelectronic devices. Trends Biotechnol 20(9):387–394 CrossRefGoogle Scholar
  8. 8.
    Bryan PN (2000) Protein engineering of subtilisin. BBA Protein Struct M 1543(2):203–222 CrossRefGoogle Scholar
  9. 9.
    Gilardi G, Fantuzzi A, Sadeghi SJ (2001) Engineering and design in the bioelectrochemistry of metalloproteins. Curr Opin Struct Biol 11(4):491–499 CrossRefGoogle Scholar
  10. 10.
    Hock B, Seifert M, Kramer K (2002) Engineering receptors and antibodies for biosensors. Biosensor Bioelectron 17(3):239–249 CrossRefGoogle Scholar
  11. 11.
    Sotiropoulou S, Fournier D, Chaniotakis NA (2005) Genetically engineered acetylcholinesterase-based biosensor for attomolar detection of dichlorvos. Biosensor Bioelectron 20(11):2347–2352 CrossRefGoogle Scholar
  12. 12.
    Maly J et al (2002) Immobilisation of engineered molecules on electrodes and optical surfaces. Mater Sci Eng C 22(2):257–261 CrossRefGoogle Scholar
  13. 13.
    Kroger D et al (1999) Immobilization of histidine-tagged proteins on gold surfaces using chelator thioalkanes. Biosensor Bioelectron 14(2):155–161 CrossRefGoogle Scholar
  14. 14.
    Wei J et al. (2002) Direct Wiring of Cytochrome c's Heme Unit to an Electrode: Electrochemical Studies. J Am Chem Soc 124(32):9591–9599 CrossRefGoogle Scholar
  15. 15.
    Gorton L et al (1999) Direct electron transfer between heme-containing enzymes and electrodes as basis for third generation biosensors. Anal Chim Acta 400:91–108 CrossRefGoogle Scholar
  16. 16.
    Davis JJ, Halliwell CM, Hill HAO, Canters GW (1998) Protein adsorption at a gold electrode studied by insitu scanning tunnelling microscopy. New J Chem 22(1119–1123) Google Scholar
  17. 17.
    Klis M et al (2006) Electroreduction of laccase covalently bound to organothiol monolayers on gold electrodes. Surface Imaging/Spectroscopy at Solid/Liquid Interface (ISSIS). In: Selection of papers from the International Symposium on Surface Imaging/Spectroscopy at Solid/Liquid Interface (ISSIS), 28 May–1 June 2006, Krakow, Poland. Electrochim Acta 52(18):5591–5598 CrossRefGoogle Scholar
  18. 18.
    Torrance L et al (2006) Oriented immobilisation of engineered single-chain antibodies to develop biosensors for virus detection. J Virol Meth 134(1–2):164–170 CrossRefGoogle Scholar
  19. 19.
    Trammell SA et al (2001) Synthesis and Characterization of a Ruthenium(II)-Based Redox Conjugate for Reagentless Biosensing. Bioconjugate Chem 12(4):643–647 CrossRefGoogle Scholar
  20. 20.
    Trammell SA et al (2004) Orientated binding of photosynthetic reaction centers on gold using Ni–NTA self-assembled monolayers. Biosensor Bioelectron 19(12):1649–1655 CrossRefGoogle Scholar
  21. 21.
    Medintz IL et al (2004) A fluorescence resonance energy transfer-derived structure of a quantum dot-protein bioconjugate nanoassembly. PNAS 101(26):9612–9617 CrossRefGoogle Scholar
  22. 22.
    Medintz IL et al (2005) Self-Assembled TNT Biosensor Based on Modular Multifunctional Surface-Tethered Components. Anal Chem 77(2):365–372 CrossRefGoogle Scholar
  23. 23.
    Marvin JS, Hellinga HW (2001) Manipulation of ligand binding affinity by exploitation of conformational coupling. Nat Struct Mol Biol 8(9):795–798 CrossRefGoogle Scholar
  24. 24.
    Maly J et al (2004) Reversible immobilization of engineered molecules by Ni-NTA chelators. Proceedings of the XVIIth International Symposium on Bioelectrochemistry and Bioenergetics. Bioelectrochemistry 63(1–2):271–275 CrossRefGoogle Scholar
  25. 25.
    Brewster JD, Lightfield AR, Bermel PL (1995) Storage and Immobilization of Photosystem II. Reaction Centers Used in an Assay for Herbicides. Anal Chem 67(7):1296–1299 CrossRefGoogle Scholar
  26. 26.
    Nakamura C et al (2003) Rapid and specific detection of herbicides using a self-assembled photosynthetic reaction center from purple bacterium on an SPR chip. Selected papers from the 7th World Congress on Biosensors Kyoto, Japan 15–17 May 2002. Biosensor Bioelectron 18(5–6):599–603 CrossRefGoogle Scholar
  27. 27.
    Beissenhirtz MK, Scheller FW, Viezzoli MS, Lisdat F (2006) Engineered Superoxide Dismutase Monomers for Superoxide Biosensor Applications. Anal Chem 78(3):928–935 CrossRefGoogle Scholar
  28. 28.
    Marcus RA, Sutin N (1985) Electron transfers in chemistry and biology. BBA Rev Bioenerget 811(3):265–322 Google Scholar
  29. 29.
    Mayo S et al (1986) Long-range electron transfer in heme proteins. Science 233(4767):948–952 CrossRefGoogle Scholar
  30. 30.
    Van de Meere GC, Chen SYS (1994) Resonance Energy Transfer: Theory and Data. Wiley, New York Google Scholar
  31. 31.
    Benson DE et al (2001) Design of Bioelectronic Interfaces by Exploiting Hinge-Bending Motions in Proteins. Science 293(5535):1641–1644 CrossRefGoogle Scholar
  32. 32.
    Fehr M, Frommer WB, Lalonde S (2002) From the Cover: visualization of maltose uptake in living yeast cells by fluorescent nanosensors. PNAS 99(15):9846–9851 CrossRefGoogle Scholar
  33. 33.
    Fehr M et al (2003) In Vivo Imaging of the Dynamics of Glucose Uptake in the Cytosol of COS-7 Cells by Fluorescent Nanosensors. J Biol Chem 278(21):19127–19133 CrossRefGoogle Scholar
  34. 34.
    Lager I et al (2003) Development of a fluorescent nanosensor for ribose. FEBS Lett 553(1–2):85–89 CrossRefGoogle Scholar
  35. 35.
    Willner I, Willner B, Katz E (2002) Functional biosensor systems via surface-nanoengineering of electronic elements. Rev Mol Biotechnol 82(4):325–355 CrossRefGoogle Scholar
  36. 36.
    Cass AE et al (1984) Ferrocene-Mediated Enzyme Electrode for Amperometric Determination of Glucose. Anal Chem 56:667–671 CrossRefGoogle Scholar
  37. 37.
    Hui Yao NL, Wei Y-L, Zhu J-J (2005) A H2O2 Biosensor Based on Immobilization of Horseradish Peroxidase in a Gelatine Network Matrix. Sensors 5:277–283 CrossRefGoogle Scholar
  38. 38.
    Chen L-Q et al (2002) Genetic modification of glucose oxidase for improving performance of an amperometric glucose biosensor. Biosensor Bioelectron 17(10):851–857 CrossRefGoogle Scholar
  39. 39.
    Hecht HJ, et al (1993) Crystal Structure of Glucose Oxidase from Aspergillus niger Refined at 2⋅3 A Reslution. J Mol Biol 229(1):153–172 CrossRefGoogle Scholar
  40. 40.
    Heller A (1990) Electrical wiring of redox enzymes. Accounts Chem Res 23:128 CrossRefGoogle Scholar
  41. 41.
    Loechel C, Jaswir Basran AB, Scrutton NS, Hall EAH (2003) Using trimethylamine dehydrogenase in an enzyme linked amperometric electrode, Part 1. Wild-type enzyme redox mediation. Analyst 128:166–172 CrossRefGoogle Scholar
  42. 42.
    Loechel C, Jaswir Basran AB, Scrutton NS, Hall EAH (2003) Using trimethylamine dehydrogenase in an enzyme linked amperometric electrode, Part 2. Rational design engineering of a wired mutant. Analyst 128:889–898 CrossRefGoogle Scholar
  43. 43.
    Willner I, Riklin A (1994) Electrical Communication between Electrodes and NAD(P)+-Dependent Enzymes Using Pyrroloquinolinequinone-Enzyme Electrodes in a Self-Assembled Monolayer Configuration: Design of a New Class of Amperometric Biosensors. Anal Chem 66:1535–1539 CrossRefGoogle Scholar
  44. 44.
    Habermüller K, Mosbach M, Schumann W (2000) Electron-transfer mechanisms in amperometric biosensors. Fresen J Anal Chem 366:560–568 CrossRefGoogle Scholar
  45. 45.
    Badia A et al (1993) Intramolecular electron-transfer rates in ferrocene-derivatized glucose oxidase. J Am Chem Soc 115:7053–7060 CrossRefGoogle Scholar
  46. 46.
    Padeste C et al (2003) Redox labelled avidin for enzyme sensor architectures. Biosensor Bioelectron 19(3):239–247 CrossRefGoogle Scholar
  47. 47.
    Anicet N et al (1998) Electron Transfer in Organized Assemblies of Biomolecules. Construction and Dynamics of Avidin/Biotin Co-immobilized Glucose Oxidase/Ferrocene Monolayer Carbon Electrodes. J Am Chem Soc 120:7115–7116 CrossRefGoogle Scholar
  48. 48.
    Trojanowicz M, Miernik A (2001) Bilayer lipid membrane glucose biosensors with improved stability and sensitivity. Electrochim Acta 46(7):1053–1061 CrossRefGoogle Scholar
  49. 49.
    Wilson JR, Caruana DJ, Gilardi G (2003) Engineering redox functions in a nucleic acid binding protein. Chem Commun 356–357 Google Scholar
  50. 50.
    Astuti Y et al (2004) Proton-Coupled Electron Transfer of Flavodoxin Immobilized on Nanostructured Tin Dioxide Electrodes: Thermodynamics versus Kinetics Control of Protein Redox Function. J Am Chem Soc 126:8001–8009 CrossRefGoogle Scholar
  51. 51.
    Fromant M, Blanquet S, Plateau P (1995) Direct Random Mutagenesis of Gene-Sized DNA Fragments Using Polymerase Chain Reaction. Anal Biochem 224(1):347–353 CrossRefGoogle Scholar
  52. 52.
    Armold FH et al (1999) Directed Evolution of Mesophilic Enzymes into Their Thermophilic Counterparts. Ann NY Acad Sci 870(1):400–403 CrossRefGoogle Scholar
  53. 53.
    Stemmer W (1994) DNA Shuffling by Random Fragmentation and Reassembly: In vitro Recombination for Molecular Evolution. PNAS 91(22):10747–10751 CrossRefGoogle Scholar
  54. 54.
    Stemmer WP (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389–391 CrossRefGoogle Scholar
  55. 55.
    Vincent GH, Eijsink SG, Borchert TV, van den Burg B (2005) Directed evolution of enzyme stability. Biomol Eng 22:21–30 CrossRefGoogle Scholar
  56. 56.
    Tamakoshi M et al (1997) A new Thermus – Escherichia coli shuttle integration vector system. J Bacteriol 179:4811–4814 Google Scholar
  57. 57.
    Kaur J, Sharma R (2006) Directed Evolution: An Approach to Engineer Enzymes. Crit Rev Biotechnol 26(3):165–199 CrossRefGoogle Scholar
  58. 58.
    Hamamatsu N et al (2006) Directed evolution by accumulating tailored mutations: Thermostabilization of lactate oxidase with less trade-off with catalytic activity. Prot Eng Design Sel 19(11):483–489 CrossRefGoogle Scholar
  59. 59.
    Minagawa H et al (2007) Improving the thermal stability of lactate oxidase by directed evolution. Cell Mol Life Sci 64(1):77–81 CrossRefGoogle Scholar
  60. 60.
    Crameri A et al (1998) DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391(6664):288–291 CrossRefGoogle Scholar
  61. 61.
    Lorimer IAJ, Pastan I (1995) Nucleic Acids Res 23:3067–3068 CrossRefGoogle Scholar
  62. 62.
    Miyazaki K (2002) Random DNA fragmentation with endonuclease V: application to DNA shuffling. Nucl Acids Res 30(24):e139 CrossRefGoogle Scholar
  63. 63.
    Coco WM et al (2001) DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat Biotech 19(4):354–359 CrossRefGoogle Scholar
  64. 64.
    Ostermeier M, Shim JH, Benkovic SJ (1999) A combinatorial approach to hybrid enzymes independent of DNA homology. Nat Biotech 17(12):1205–1209 CrossRefGoogle Scholar
  65. 65.
    Lutz S et al (2001) Creating multiple-crossover DNA libraries independent of sequence identity. PNAS 98(20):11248–11253 CrossRefGoogle Scholar
  66. 66.
    Kolkman JA, Stemmer WPC (2001) Directed evolution of proteins by exon shuffling. Nat Biotech 19(5):423–428 CrossRefGoogle Scholar
  67. 67.
    Abecassis V, Pompon D, Truan G (2000) High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2. Nucl Acids Res 28(20):e88 CrossRefGoogle Scholar
  68. 68.
    Ness JE et al (2002) Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat Biotech 20(12):1251–1255 CrossRefGoogle Scholar
  69. 69.
    Shen Y et al (1993) Stabilization of the membrane protein bacteriorhodopsin to 140 °C in two-dimensional films. Nature 366(6450):48–50 CrossRefGoogle Scholar
  70. 70.
    Hillebrecht JR et al (2004) Directed Evolution of Bacteriorhodopsin for Device Applications. Method Enzymol 388:333–347 CrossRefGoogle Scholar
  71. 71.
    Gibney BR et al (1996) Ferredoxin and ferredoxin-heme maquettes. PNAS 93(26):15041–15046 CrossRefGoogle Scholar
  72. 72.
    Gibney BR, Rabanal F, Dutton PL (1997) Synthesis of novel proteins. Curr Opin Chem Biol 1(4):537–542 CrossRefGoogle Scholar
  73. 73.
    Rabanal F, DeGrado WF, Dutton PL (1996) Toward the Synthesis of a Photosynthetic Reaction Center Maquette: A Cofacial Porphyrin Pair Assembled between Two Subunits of a Synthetic Four-Helix Bundle Multiheme Protein. J Am Chem Soc 118(2):473–474 CrossRefGoogle Scholar
  74. 74.
    DeGrado WF et al (1999) De novo design and structural characterization of proteins and metalloproteins. Ann Rev Biochem 68(1):779–819 CrossRefGoogle Scholar
  75. 75.
    Kornilova AY et al (2000) Design and Characterization of A Synthetic Electron-Transfer Protein. J Am Chem Soc 122:7999–8006 CrossRefGoogle Scholar
  76. 76.
    McNeil SE (2005) Nanotechnology for the biologist. J Leukocyte Biol 78:585–594 CrossRefGoogle Scholar
  77. 77.
    Cui Y et al (2001) Nanowire Nanosensors for Highly Sensitive and Selective Detection of Biological and Chemical Species. Science 293:1289–1292 CrossRefGoogle Scholar
  78. 78.
    Yin YPW, Lü Y, Du P, Shi Y, Cai C (2007) Immobilization and direct electrochemistry of cytochrome c at a single-walled carbon nanotube-modified electrode. J Solid State Electrochem 11(3):390–397 CrossRefGoogle Scholar
  79. 79.
    Lombardi A et al (2000) Inaugural Article: Retrostructural analysis of metalloproteins: Application to the design of a minimal model for diiron proteins. PNAS 97(12):6298–6305 CrossRefGoogle Scholar
  80. 80.
    Dwyer MA, Looger LL, Hellinga HW (2004) Computational Design of a Biologically Active Enzyme. Science 304:1967–1971 CrossRefGoogle Scholar
  81. 81.
    Case MA, Ghadiri MR, Mutz MW, Mc Lendon GL (1998) Stereoselection in designed three-helix bundle metalloproteins. Chirality 10(1–2):35–40 Google Scholar
  82. 82.
    Willner I et al (1999) Integration of a Reconstituted de Novo Synthesized Hemoprotein and Native Metalloproteins with Electrode Supports for Bioelectronic and Bioelectrocatalytic Applications. J Am Chem Soc 121:6455–6468 CrossRefGoogle Scholar
  83. 83.
    Gouaux J et al (1994) Subunit Stoichiometry of Staphylococcal α-Hemolysin in Crystals and on Membranes: A Heptameric Transmembrane Pore. PNAS 91(26):12828–12831 CrossRefGoogle Scholar
  84. 84.
    Song L et al (1996) Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore. Science 274(5294):1859–1865 CrossRefGoogle Scholar
  85. 85.
    Braha O et al (1997) Designed protein pores as components for biosensors. Chem Biol 4(7):497–505 CrossRefGoogle Scholar
  86. 86.
    Walker B et al (1995) An intermediate in the assembly of a pore-forming protein trapped with a genetically-engineered switch. Chem Biol 2(2):99–105 CrossRefGoogle Scholar
  87. 87.
    Kasianowicz JJ et al (1999) Genetically Engineered Metal Ion Binding Sites on the Outside of a Channel's Transmembrane β-Barrel. Biophys J 76(2):837–845 CrossRefGoogle Scholar
  88. 88.
    Kasianowicz JJ, Bezrukov SM (1995) Protonation dynamics of the α-toxin ion channel from spectral analysis of pH-dependent current fluctuations. Biophys J 69(1):94–105 CrossRefGoogle Scholar
  89. 89.
    Kasianowicz JJ et al (1994) Genetically engineered pores as metal ion biosensors. MRS Symp 330:217–223 Google Scholar
  90. 90.
    Howorka S, Cheley S, Bayley H (2001) Sequence-specific detection of individual DNA strands using engineered nanopores. Nat Biotech 19(7):636–639 CrossRefGoogle Scholar
  91. 91.
    Ferapontova E et al (2002) Effect of cysteine mutations on direct electron transfer of horseradish peroxidase on gold. Biosensor Bioelectron 17(11–12):953–963 CrossRefGoogle Scholar
  92. 92.
    Aharoni A et al (2006) High-throughput screening methodology for the directed evolution of glycosyltransferases. Nat Meth 3(8):609–614 CrossRefGoogle Scholar
  93. 93.
    Valentini F et al (2007) Coupling of single-wall carbon nanotube and l-histidine on Ag microwires: New architectures for the assembling of NAD+ sensors. Sens Actuator B Chem 123(1):5–9 CrossRefGoogle Scholar

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© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  1. 1.Institute of BiotechnologyUniversity of CambridgeCambridgeUK

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