Cell free expression and APA for NAPPA and protein nanocrystallography

Functional Proteomics and Nanotechnology-Based Microarrays

Volumn , Issue , 2010, Pages 121-147

  Pechkova, Eugenia ^a   Chong, Shaorong ^b   Tripathi, Shailesh ^a   Nicolini, Claudio ^a  

^a UNIVERSITY OF GENOA   (Italy)

^b NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77954945761     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4032/9789814267779     Document Type: Chapter

References (54)

1. Asherie, N. (2004). Protein crystallization and phase diagrams. Methods, 34, pp. 266-272.
2. Chayen, N. E., Saridakis, E., El-Bahar, R. and Nemirovsky, Y. (2001). Porous silicon: an effective nucleation-inducing material for protein crystallization. Journal of Molecular Biology 312, pp. 591-595.
3. Czokan, P. (1980). Advances in Corrosion Science and Technology, Vol. 7 (Ed: M. G. Fontana, R. W. Staehle) Plenum New York p. 239.
4. Fermani, S., Falini, G., Minnucci, M. and Ripamonti, A. (2001). Protein crystallization on polymeric film surfaces. Journal of Crystal Growth, 224, pp. 327-334.
5. Foresi, J. S., Villeneuve, P. R., Ferrera, J., Thoen, E. R., Steinmeyer, G., Fan, S., Joannopoulos, J. D., Kimerling, L. C., Smith, H. I. and Ippen, E. P. (1997). Photonic-bandgap microcavities in optical waveguides. Nature, 390, pp. 143-145.
6. Gaponenko, N. V., Davidson, J.A., Hamilton, B., Skeldon, P., Thompson, G. E., Zhou, X. and Pivin, J. C. (2000). Strongly enhanced Tb luminescence from titania xerogel solids mesoscopically confined in porous anodic alumina. Applied Physics Letters, 76, pp. 1006-1008.
7. Gautier, A., Juillerat, A., Heinis, C., Correa, I. R., Jr., Kindermann, M., Beaufils, F. and Johnsson, K. (2008). An engineered protein tag for multiprotein labeling in living cells. Chemistry & Biology, 15, pp. 128-136.
8. Graslund, S., Nordlund, P., Weigelt, J., Bray, J., Gileadi, O., Knapp, S., Oppermann, U., Arrowsmith, C., Hui, R., Ming, J. et al. (2008). Protein production and purification. Nature Methods, 5, pp. 135-146.
9. Grasso V., Lambertini V., Ghisellini P., Valerio F., Stura E. Perlo P. and Nicolini, C. (2006). Nanostructuring of a porous alumina matrix for a biomolecular microarray. Nanotechnology, 17, pp. 795-798.
10. Hanes, J. and Pluckthun, A. (1997). In vitro selection and evolution of functional proteins by using ribosome display. Proceedings of the National Academy of Sciences USA, 94, pp. 4937-4942.
11. Hartman, M. C., Josephson, K., Lin, C. W. and Szostak, J. W. (2007). An expanded set of amino Acid analogs for the ribosomal translation of unnatural peptides. PLoS ONE, 2, pp. e972.
12. Hillebrecht, J. R. and Chong, S. R. (2008) A comparative study of protein synthesis in in vitro systems: from the prokaryotic reconstituted to the eukaryotic extract-based. BMC Biotechnology, 8, 58.
13. Jessensky, O., Müller, F. and Gösele, U. (1998). Self-organized formation of hexagonal pore arrays in anodic alumina. Applied Physics Letters, 72, pp. 1173-1175.
14. Johnsson, K. (2009). Visualizing biochemical activities in living cells. Nature Chemical Biology, 5, pp. 63-65.
15. Johnsson, N. and Johnsson, K. (2007). Chemical tools for biomolecular imaging. ACS Chemical Biology, 2, pp. 31-38.
16. Kaiser, C. M., Chang, H. C., Agashe, V. R., Lakshmipathy, S. K., Etchells, S. A., Hayer-Hartl, M., Hartl, F. U. and Barral, J. M. (2006). Real-time observation of trigger factor function on translating ribosomes. Nature, 444, pp. 455-460.
17. Katzen, F., Chang, G. and Kudlicki, W. (2005). The past, present and future of cell-free protein synthesis. Trends in Biotechnology, 23, pp. 150-156.
18. Li A. P., Müller, F., Birner, A., Nielsch, K. and Gösele, U. (1999). Fabrication and microstructuring of hexagonally ordered two-dimensional nanopore arrays in anodic alumina. Advanced Materials, 6, pp. 483+.
19. Li, A. P., Müller, F., Birner, A., Nielsch, K. and Gösele U. (1998). Hexagonal pore arrays with a 50-420 nm interpore distance formed by self-organization in anodic alumina. Journal of Applied Physics, 84, pp. 6023-6026.
20. MacDonald, G. M., Steenhuis, J. J. and Barry, B. A. (1995). A difference Fouriertransform infrared spectroscopy study of chlorophyll oxidation in hydroxylaminetreated photosystem-II. Journal of Biological Chemistry, 270, pp. 8420-8428.
21. Maki, K., Uno, K., Morita, T. and Aiba, H. (2008). RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA. Proceedings of the National Academy of Sciences USA, 105, pp. 10332-10337.
22. Masuda, H. and Fukuda, K. (1995). Ordered metal nanohole arrays made by a two-step replication of honeycomb structures of anodic alumina. Science, 268, pp. 1466-1470.
23. Masuda, H. and Satoh, M. (1996). Fabrication of gold nanodot array using anodic porous alumina as an evaporation mask. Japanese Journal of Applied Physics, 35, pp. L126-L129.
24. Masuda, H., Hasegawa, F. and Ono, S. (1997). Self-ordering of cell arrangement of anodic porous alumina formed in sulfuric acid solution. Journal of Electrochemistry Society, 144, pp. L127-L130.
25. McPherson, A. and Schlichta, P. (1988). Heterogeneous and epitaxial nucleation of protein crystals on mineral surfaces. Science, 239, pp. 385-387.
26. McPherson, A., (1999) CSHL Press, Cold Spring Harbor.
27. Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S. and Dodson, E. J. (1999). Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallographica D, 55, pp. 247-255.
28. Nanev, C. and Tsekova, D. (2000). Heterogeneous nucleation of hen-egg-white lysozyme - Molecular approach. Crystal Research and Technology, 35, pp. 189-195.
29. Nicolini, C. and Pechkova, E. (2006). Nanostructured biofilms and biocrystal. Journal of Nanoscience and Nanotechnology, 6, pp. 2209-2236.
30. Nirenberg, M. W. and Matthaei, J. H. (1961). The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proceedings of the National Academy of Sciences USA, 47, pp. 1588-1602.
31. Noren, C. J., Anthony-Cahill, S. J., Griffith, M. C. and Schultz, P. G. (1989). A general method for site-specific incorporation of unnatural amino acids into proteins. Science, 244, pp. 182-188.
32. Pechkova, E. and Nicolini, C. (2001). Accelerated protein crystal growth onto the protein thin film. Journal of Crystal Growth, 231, 599-602.
33. Pechkova, E. and Nicolini, C. (2003). Proteomics and Nanocrystallography, Kluwer Academic Publishers, pp. 1-212.
34. Pechkova, E. and Nicolini, C. (2004). Protein nanocrystallography: a new approach to structural proteomics. Trends in Biotechnology, 22, pp. 117-122.
35. Pechkova, E. and Nicolini, C. (2009). APA induced crystal growth and design. Crystal Growth and Design, submitted.
36. Pechkova, E., Sivozhelezov, V., Tropiano, G., Fiordoro S. and Nicolini, C. (2005). Comparison of lysozyme structures derived from thin-film-based and classical crystals. Acta Crystallographica D 61, pp. 803-808.
37. Pechkova, E., Tropiano, G., Riekel, C. and Nicolini, C. (2004). Radiation stability of protein crystal grown by nanostructured templates synchrotron. Spectrochimica Acta B, 59, pp. 1687-1693.
38. Ramachandran, N., Raphael, J. V., Hainsworth, E., Demirkan, G., Fuentes, M. G., Rolfs, A., Hu, Y. and LaBaer, J. (2008). Next-generation high-density self-assembling functional protein arrays. Nature Methods, 5, pp. 535-538.
39. Roberts, R. W. and Szostak, J. W. (1997). RNA-peptide fusions for the in vitro selection of peptides and proteins. Proceedings of the National Academy of Sciences USA, 94, pp. 12297-12302.
40. Rong, L., Komatsu, H., Yoshizaki, I., Kadowaki, A. and Yoda, S. (2004). Protein crystallization by using porous glass substrate. Journal of Synchrotron Radiation, 11, pp. 27-29.
41. See, E. G., Joannopoulos, J. D., Meade, R. D. and Winn, J. N. (1995). Photonic crystals: molding the flow of light, Princeton University Press, Princeton, NJ.
42. See, E. G., Keller, F., Hunter, M. S. and Robinson, D. L. (1953) Journal of the Electrochemical Society, 100, pp. 411.
43. Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K. and Ueda, T. (2001). Cell-free translation reconstituted with purified components. Nature Biotechnology, 19, pp. 751-755.
44. Stura E., Bruzzese D., Valerio F., Grasso F., Perlo P. and Nicolini C. (2007). Anodic porous alumina as mechanical stability enhancer for LDL-cholesterol sensitive electrodes, Biosensors & Bioelectronics, 23, pp. 655-660.
45. Suzuki, Y., Saito, J., Horii, Y. and Kasagi, N. (2003). The International Symposium on Micro-Mechanical Engineering.
46. Tang, L., Huang, Y. B., Liu, D. Q., Li, J. L., Mao, K., Liu, L., Cheng, Z. J, Gong, W. M., Hu, J. and He, J. H. (2005). Effects of the silanized mica surface on protein crystallization. Acta Crystallographica D 61, pp. 53-59.
47. Tawfik, D. S. and Griffiths, A. D. (1998). Man-made cell-like compartments for molecular evolution. Nature Biotechnology, 16, pp. 652-656.
48. Templin, M. F, Stoll, D., Schrenk, M., Traub, P. C., Vohringer C. F. and Joos, T. O. (2002). Protein microarray technology. Trends in Biotechnology, 20, pp. 160-166.
49. Thompson, G. E., and Wood, G. C. (1983) Treatise on Materials Science and Technology, Vol. 23 (Ed: J. C. Scully) Academic New York p. 205.
50. Troitsky, V., Ghisellini, P., Pechkova, E. and Nicolini, C. (2002). DNASER II. Novel surface patterning for biomolecular microarray. IEEE Transactions on Nanobiosciences, 1, pp. 73-77.
51. Tsekova, D. S. (2009). Formation and growth of tetragonal lysozyme crystal at some boundary conditions. Crystal Growth & Design, 9, pp. 1312-1317.
52. Villemagne, D., Jackson, R. and Douthwaite, J. A. (2006). Highly efficient ribosome display selection by use of purified components for in vitro translation. Journal of Immunological Methods, 313, pp. 140-148.
53. Yablonovitch, E. (1987). Inhibited spontaneous emission in solid-state physics and electronics. Physics Review Letters, 58, pp. 2059-2062.
54. Zheng, Y. and Roberts, R. J. (2007). Selection of restriction endonucleases using artificial cells. Nucleic Acids Research, 35, pp. e83.