Advertisement

Creation of Hybrid Nanorods From Sequences of Natural Trimeric Fibrous Proteins Using the Fibritin Trimerization Motif

  • Katerina Papanikolopoulou
  • Mark J. van Raaij
  • Anna Mitraki
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 474)

Summary

Stable, artificial fibrous proteins that can be functionalized open new avenues in fields such as bionanomaterials design and fiber engineering. An important source of inspiration for the creation of such proteins are natural fibrous proteins such as collagen, elastin, insect silks, and fibers from phages and viruses. The fibrous parts of this last class of proteins usually adopt trimeric, β-stranded structural folds and are appended to globular, receptor-binding domains. It has been recently shown that the globular domains are essential for correct folding and trimerization and can be successfully substituted by a very small (27-amino acid) trimerization motif from phage T4 fibritin. The hybrid proteins are correctly folded nanorods that can withstand extreme conditions. When the fibrous part derives from the adenovirus fiber shaft, different tissue-targeting specificities can be engineered into the hybrid proteins, which therefore can be used as gene therapy vectors. The integration of such stable nanorods in devices is also a big challenge in the field of biomechanical design. The fibritin foldon domain is a versatile trimerization motif and can be combined with a variety of fibrous motifs, such as coiled-coil, collagenous, and triple β-stranded motifs, provided the appropriate linkers are used. The combination of different motifs within the same fibrous molecule to create stable rods with multiple functions can even be envisioned. We provide a comprehensive overview of the experimental procedures used for designing, creating, and characterizing hybrid fibrous nanorods using the fibritin trimerization motif.

Key Words:

Fibritin fibrous proteins fusion proteins nanorods trimerization 

References

  1. 1.
    Beck K, Brodsky B. (1998) Supercoiled protein motifs: the collagen triple-helix and the alpha-helical coiled coil. J. Struct. Biol. 122, 17–29.CrossRefGoogle Scholar
  2. 2.
    Geddes AJ, Parker KD, Atkins ED, Beighton E. (1968) “Cross-beta” conformation in proteins. J. Mol. Biol. 32, 343–358.CrossRefGoogle Scholar
  3. 3.
    Mitraki A, Miller S, van Raaij MJ. (2002) Review: conformation and folding of novel beta-structural elements in viral fiber proteins: the triple beta-spiral and triple beta-helix. J. Struct. Biol. 137, 236–247.CrossRefGoogle Scholar
  4. 4.
    Pauling L, Corey RB. (1951) The pleated sheet, a new layer configuration of polypeptide chains. Proc. Natl. Acad. Sci. U. S. A. 37, 251–256.CrossRefGoogle Scholar
  5. 5.
    Steinbacher S, Seckler R, Miller S, Steipe B, Huber R, Reinemer P. (1994) Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer. Science 265, 383–386.CrossRefGoogle Scholar
  6. 6.
    Gazit E. (2007) Use of biomolecular templates for the fabrication of metal nanowires. FEBS J. 274, 317–322.CrossRefGoogle Scholar
  7. 7.
    Rajagopal K, Schneider JP. (2004) Self-assembling peptides and proteins for nanotechnological applications. Curr. Opin. Struct. Biol. 14, 480–486.CrossRefGoogle Scholar
  8. 8.
    Woolfson DN, Ryadnov MG. (2006). Peptide-based fibrous biomaterials: some things old, new and borrowed. Curr. Opin. Chem. Biol. 10, 559–567.CrossRefGoogle Scholar
  9. 9.
    Mitraki A, Papanikolopoulou K, Van Raaij MJ. (2006) Natural triple beta-stranded fibrous folds. Adv. Protein Chem. 73, 97–124.CrossRefGoogle Scholar
  10. 10.
    Hong JS, Engler JA. (1996) Domains required for assembly of adenovirus type 2 fiber trimers. J. Virol. 70, 7071–7078.Google Scholar
  11. 11.
    Novelli A, Boulanger PA. (1991) Deletion analysis of functional domains in baculovirus-expressed adenovirus type 2 fiber. Virology 185, 365–376.CrossRefGoogle Scholar
  12. 12.
    Mitraki A, Barge A, Chroboczek J, Andrieu JP, Gagnon J, Ruigrok RW. (1999) Unfolding studies of human adenovirus type 2 fibre trimers. Evidence for a stable domain. Eur. J. Biochem. 264, 599–606.CrossRefGoogle Scholar
  13. 13.
    Papanikolopoulou K, Schoehn G, Forge V, et al. (2005) Amyloid fibril formation from sequences of a natural beta-structured fibrous protein, the adenovirus fiber. J. Biol. Chem. 280, 2481–2490.CrossRefGoogle Scholar
  14. 14.
    Reches M, Gazit E. (2003) Casting metal nanowires within discrete self-assembled peptide nanotubes. Science 300, 625–627.CrossRefGoogle Scholar
  15. 15.
    van Raaij MJ, Mitraki A. (2004) Beta-structured viral fibres: assembly, structure and implications for materials design. Curr. Opin. Solid State Mater. Sci. 8, 151–156.CrossRefGoogle Scholar
  16. 16.
    Yemini M, Reches M, Rishpon J, Gazit E. (2005) Novel electrochemical biosens-ing platform using self-assembled peptide nanotubes. Nano. Lett. 5, 183–186.CrossRefGoogle Scholar
  17. 17.
    Bewley MC, Springer K, Zhang YB, Freimuth P, Flanagan JM. (1999) Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR. Science 286, 1579–1583.CrossRefGoogle Scholar
  18. 18.
    Burmeister WP, Guilligay D, Cusack S, Wadell G, Arnberg N. (2004) Crystal structure of species D adenovirus fiber knobs and their sialic acid binding sites. J. Virol. 78, 7727–7736.CrossRefGoogle Scholar
  19. 19.
    Krasnykh V, Belousova N, Korokhov N, Mikheeva G, Curiel DT. (2001) Genetic targeting of an adenovirus vector via replacement of the fiber protein with the phage T4 fibritin. J. Virol. 75, 4176–4183.CrossRefGoogle Scholar
  20. 20.
    Glasgow JN, Everts M, Curiel DT. (2006) Transductional targeting of adenovirus vectors for gene therapy. Cancer Gene Ther. 13, 830–844.CrossRefGoogle Scholar
  21. 21.
    Nicklin SA, Wu E, Nemerow GR, Baker AH. (2005) The influence of adenovirus fiber structure and function on vector development for gene therapy. Mol. Ther. 12, 384–393.CrossRefGoogle Scholar
  22. 22.
    Noureddini SC, Curiel DT. (2005) Genetic targeting strategies for adenovirus. Mol. Pharm. 2, 341–347.CrossRefGoogle Scholar
  23. 23.
    Tao Y, Strelkov SV, Mesyanzhinov VV, Rossmann MG. (1997) Structure of bacteriophage T4 fibritin: a segmented coiled coil and the role of the C-terminal domain. Structure 5, 789–798.CrossRefGoogle Scholar
  24. 24.
    Frank S, Kammerer RA, Mechling D, et al. (2001) Stabilization of short collagenlike triple helices by protein engineering. J. Mol. Biol. 308, 1081–1089.CrossRefGoogle Scholar
  25. 25.
    Letarov AV, Londer YY, Boudko SP, Mesyanzhinov VV. (1999) The carboxy-terminal domain initiates trimerization of bacteriophage T4 fibritin. Biochemistry (Mosc.) 64, 817–823.Google Scholar
  26. 26.
    Miroshnikov KA, Marusich EI, Cerritelli ME, et al. (1998) Engineering trimeric fibrous proteins based on bacteriophage T4 adhesins. Protein Eng. 11, 329–332.CrossRefGoogle Scholar
  27. 27.
    Stetefeld J, Frank S, Jenny M, et al. (2003) Collagen stabilization at atomic level. Crystal structure of designed (GlyProPro)(10)foldon. Structure (Camb.) 11, 339–346.CrossRefGoogle Scholar
  28. 28.
    Yang X, Lee J, Mahony EM, Kwong PD, Wyatt R, Sodroski J. (2002) Highly stable trimers formed by human immunodeficiency virus type 1 envelope glycoproteins fused with the trimeric motif of T4 bacteriophage fibritin. J. Virol. 76, 4634–4642.CrossRefGoogle Scholar
  29. 29.
    van Raaij MJ, Mitraki A, Lavigne G, Cusack S. (1999) A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein. Nature 401, 935–938.CrossRefGoogle Scholar
  30. 30.
    Papanikolopoulou K, Forge V, Goeltz P, Mitraki A. (2004) Formation of highly stable chimeric trimers by fusion of an adenovirus fiber shaft fragment with the foldon domain of bacteriophage t4 fibritin. J. Biol. Chem. 279, 8991–8998.CrossRefGoogle Scholar
  31. 31.
    Papanikolopoulou K, Teixeira S, Belrhali H, Forsyth VT, Mitraki A, van Raaij MJ. (2004) Adenovirus fibre shaft sequences fold into the native triple beta-spiral fold when N-terminally fused to the bacteriophage T4 fibritin foldon trimerisa-tion motif. J. Mol. Biol. 342, 219–227.CrossRefGoogle Scholar
  32. 32.
    Tabor S. (1990) Expression using the T7 RNA polymerase/promoter system. In: Ausubel FA, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, and Struhl K, eds. Current Protocols in Molecular Biology. New York: Greene and Wiley-Interscience.Google Scholar
  33. 33.
    King J, Laemmli UK. (1971) Polypeptides of the tail fibres of bacteriophage T4. J. Mol. Biol. 62, 465–477.CrossRefGoogle Scholar
  34. 34.
    Schwarzer D, Stummeyer K, Gerardy-Schahn R, Muhlenhoff M. (2007) Characterization of a novel intramolecular chaperone domain conserved in endo-sialidases and other bacteriophage tail spike and fiber proteins. J. Biol. Chem. 282, 2821–2831.CrossRefGoogle Scholar
  35. 35.
    Jancarik J, Kim SH. (1991) Sparse matrix sampling: a screening method for crystallization of proteins. J. Appl. Cryst. 24, 409–411.CrossRefGoogle Scholar
  36. 36.
    Bergfors T. (1999)Protein Crystallization Techniques. International University Line, La Jolla, CA.Google Scholar
  37. 37.
    McPherson A. (1989)Preparation and Analysis of Protein. Crystals. Krieger, Malabar, FL.Google Scholar
  38. 38.
    McPherson A. (2004) Introduction to protein crystallization. Methods 34, 254–265.CrossRefGoogle Scholar
  39. 39.
    McPherson A. (2003) Macromolecular crystallization in the structural genomics era. J. Struct. Biol. 142, 1–2.CrossRefGoogle Scholar
  40. 40.
    Foster MP, McElroy CA, Amero CD. (2007) Solution NMR of large molecules and assemblies. Biochemistry 46, 331–340.CrossRefGoogle Scholar
  41. 41.
    Hope H. (1990) Crystallography of biological macromolecules at ultra-low temperature. Annu. Rev. Biophys. Biophys. Chem. 19, 107–126.CrossRefGoogle Scholar
  42. 42.
    Massover WH. (2007) Radiation damage to protein specimens from electron beam imaging and diffraction: a mini-review of anti-damage approaches, with special reference to synchrotron X-ray crystallography. J. Synchrotron Radiat. 14, 116–127.CrossRefGoogle Scholar
  43. 43.
    Rossmann MG. (2001) Molecular replacement—historical background. Acta Crystallogr. 57, 1360–1366.CrossRefGoogle Scholar
  44. 44.
    Ealick SE. (200) Advances in multiple wavelength anomalous diffraction crystallography. Curr. Opin. Chem. Biol. 4, 495–499.CrossRefGoogle Scholar
  45. 45.
    Dodson E. (2003) Is it jolly SAD? Acta Crystallogr. 59, 1958–1965.CrossRefGoogle Scholar
  46. 46.
    Hendrickson W. (1999) Maturation of MAD phasing for the determination of macromolecular structures. J. Synchrotron Radiat. 6, 845–851.CrossRefGoogle Scholar
  47. 47.
    Garman E, Murray JW. (2003) Heavy-atom derivatization. Acta Crystallogr. 59, 1903–1913.CrossRefGoogle Scholar
  48. 48.
    Hendrickson WA, Horton JR, LeMaster DM. (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665–1672.Google Scholar
  49. 49.
    Doublie S, Carter C. (1992) Preparation of Selenomethionyl Protein Crystals. Oxford University Press, New York.Google Scholar
  50. 50.
    Taylor G. (2003) The phase problem. Acta Crystallogr. 59, 1881–1890.CrossRefGoogle Scholar
  51. 51.
    Blow D. (2002) Outline of Crystallography for Biologists. Oxford University Press, New York.Google Scholar
  52. 52.
    Carter C. (2003) Methods in Enzymology Parts C and D. Elsevier, New York.Google Scholar
  53. 53.
    Drenth J. (1999) Principles of Protein X-ray Crystallography. Springer-Verlag, New York.Google Scholar
  54. 54.
    McPherson A. (2002) Introduction to Macromolecular Crystallography. Wiley, New York.Google Scholar
  55. 55.
    McRee D. (1999) Practical Protein Crystallography. Academic Press, New York.Google Scholar
  56. 56.
    Rhodes G. (1993) Crystallography Made Crystal Clear. Academic Press, New York.Google Scholar
  57. 57.
    Morris RJ, Perrakis A, Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol. 374, 229–244.CrossRefGoogle Scholar
  58. 58.
    Murshudov GN, Vagin AA, Dodson EJ. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. 53, 240–255.CrossRefGoogle Scholar
  59. 59.
    Lovell SC, Davis IW, Arendall WB 3rd, et al. (2003) Structure validation by C-alpha geometry: phi,psi and Cbeta deviation. Proteins 50, 437–450.CrossRefGoogle Scholar
  60. 60.
    Holm L, Sander C. (1999) Protein folds and families: sequence and structure alignments. Nucleic Acids Res. 27, 244–247.CrossRefGoogle Scholar
  61. 61.
    Boudko SP, Strelkov S V, Engel J, Stetefeld J. (2004) Design and crystal structure of bacteriophage T4 fibritin NCCF. J. Mol. Biol. 339, 927–935.CrossRefGoogle Scholar
  62. 62.
    DeLano WL. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA. Available at: http://www.pymol.org.Google Scholar

Copyright information

© Humana Press, a part of Springer Science + Business Media, LLC 2008

Authors and Affiliations

  • Katerina Papanikolopoulou
    • 1
  • Mark J. van Raaij
    • 2
  • Anna Mitraki
    • 3
  1. 1.Institute of Molecular Biology and GeneticsGreece
  2. 2.Institute of Molecular Biology of Barcelona (IBMBCSIC)Parc Cientific de BarcelonaSpain
  3. 3.Department of Materials Science and Technology, c/o Biology DepartmentUniversity of CreteVassilika VoutonGreece

Personalised recommendations